diff --git a/.gitignore b/.gitignore index b0c0f37..a0430d0 100644 --- a/.gitignore +++ b/.gitignore @@ -131,3 +131,5 @@ dmypy.json # Mac *.DS_Store +.conda/ +.vscode/ diff --git a/physical_properties/microstates/all_microstates.csv b/physical_properties/microstates/all_microstates.csv new file mode 100644 index 0000000..83de4db --- /dev/null +++ b/physical_properties/microstates/all_microstates.csv @@ -0,0 +1,291 @@ +microstate ID,canonical isomeric SMILES,Estimated Formal Charge +SAMPL8-16_micro000,CC(C)(C)OC(=O)NCc1[nH]c2ccccc2n1,0 +SAMPL8-16_micro001,CC(C)(C)OC(=NCC1=Nc2ccccc2[NH2+]1)O,1 +SAMPL8-16_micro002,CC(C)(C)OC(=NC=C1Nc2ccccc2N1)O,0 +SAMPL8-16_micro003,CC(C)(C)OC(=O)NC=C1[NH2+]c2ccccc2N1,1 +SAMPL8-16_micro004,CC(C)(C)OC(=O)NCc1[nH]c2ccccc2[nH+]1,1 +SAMPL8-16_micro005,CC(C)(C)OC(=O)N=CC1Nc2ccccc2N1,0 +SAMPL8-16_micro006,CC(C)(C)OC(=O)N=CC1[NH2+]c2ccccc2N1,1 +SAMPL8-16_micro007,CC(C)(C)OC(=O)NC=C1Nc2ccccc2N1,0 +SAMPL8-16_micro008,CC(C)(C)OC(=NCc1[nH]c2ccccc2[nH+]1)O,1 +SAMPL8-16_micro009,CC(C)(C)OC(=NC=C1[NH2+]c2ccccc2N1)O,1 +SAMPL8-16_micro010,CC(C)(C)OC(=O)NCC1=Nc2ccccc2[NH2+]1,1 +SAMPL8-16_micro011,CC(C)(C)OC(=NCc1[nH]c2ccccc2n1)O,0 +SAMPL8-7_micro000,c1cc2c(cc1Br)n(c(n2)N)CC3(CCOCC3)O,0 +SAMPL8-7_micro001,c1cc2c(cc1Br)n(c(=N)[n-]2)CC3(CCOCC3)O,-1 +SAMPL8-7_micro002,c1cc2c(cc1Br)[n+](c([nH]2)N)CC3(CCOCC3)O,1 +SAMPL8-7_micro003,c1cc2c(cc1Br)n(c(n2)[NH3+])CC3(CCOCC3)O,1 +SAMPL8-7_micro004,c1cc2c(cc1Br)n(c(=N)[nH]2)CC3(CCOCC3)O,0 +SAMPL8-8_micro000,COC(=O)c1cn2cccc(c2n1)C(F)(F)F,0 +SAMPL8-8_micro001,COC(=C1C=[n+]2cccc(c2=[NH+]1)C(F)(F)F)[O-],1 +SAMPL8-8_micro002,COC(=C1C=[n+]2cccc(c2=N1)C(F)(F)F)O,1 +SAMPL8-19_micro000,CN1c2ccccc2NC1=CSc3[nH]c(=O)c(cn3)Cc4cnc(nc4)OC,0 +SAMPL8-19_micro001,CN1c2ccccc2[NH2+]C1=CSc3[nH]cc(c(=O)n3)Cc4cnc(nc4)OC,1 +SAMPL8-19_micro002,C[n+]1c2ccccc2[nH]c1CSc3[nH]cc(c(=O)[nH+]3)Cc4cnc(nc4)OC,2 +SAMPL8-19_micro003,Cn1c2ccccc2[nH+]c1CSc3[nH+]c(c(cn3)Cc4cnc(nc4)OC)O,2 +SAMPL8-19_micro004,CN1c2ccccc2NC1=CSc3[nH+]cc(c(n3)O)Cc4cnc(nc4)OC,1 +SAMPL8-19_micro005,C[n+]1c2ccccc2[nH]c1CSc3[nH]c(=O)c(cn3)Cc4cnc(nc4)OC,1 +SAMPL8-19_micro006,Cn1c2ccccc2nc1CSc3[nH]cc(c(=O)[nH+]3)Cc4cnc(nc4)OC,1 +SAMPL8-19_micro007,Cn1c2ccccc2nc1CSc3[nH]c(=O)c(cn3)Cc4cnc(nc4)OC,0 +SAMPL8-19_micro008,C[n+]1c2ccccc2[nH]c1CSc3ncc(c(n3)O)Cc4cnc(nc4)OC,1 +SAMPL8-19_micro009,Cn1c2ccccc2[nH+]c1CSc3[nH]cc(c(=O)n3)Cc4cnc(nc4)OC,1 +SAMPL8-19_micro010,CN1c2ccccc2NC1=CSc3[n-]c(=O)c(cn3)Cc4cnc(nc4)OC,-1 +SAMPL8-19_micro011,Cn1c2ccccc2nc1CSc3[n-]c(=O)c(cn3)Cc4cnc(nc4)OC,-1 +SAMPL8-19_micro012,CN1c2ccccc2[NH2+]C1=CSc3[nH]c(=O)c(c[nH+]3)Cc4cnc(nc4)OC,2 +SAMPL8-19_micro013,Cn1c2ccccc2nc1CSc3[nH]cc(c(=O)n3)Cc4cnc(nc4)OC,0 +SAMPL8-19_micro014,CN1c2ccccc2[NH2+]C1=CSc3[n-]c(=O)c(cn3)Cc4cnc(nc4)OC,0 +SAMPL8-19_micro015,Cn1c2ccccc2nc1CSc3ncc(c(n3)O)Cc4cnc(nc4)OC,0 +SAMPL8-19_micro016,CN1c2ccccc2[NH2+]C1=CSc3[nH]c(=O)c(cn3)Cc4cnc(nc4)OC,1 +SAMPL8-19_micro017,Cn1c2ccccc2[nH+]c1CSc3[nH+]cc(c(n3)O)Cc4cnc(nc4)OC,2 +SAMPL8-19_micro018,Cn1c2ccccc2nc1CSc3[nH+]c(c(cn3)Cc4cnc(nc4)OC)O,1 +SAMPL8-19_micro019,Cn1c2ccccc2nc1CSc3[nH+]cc(c(n3)O)Cc4cnc(nc4)OC,1 +SAMPL8-19_micro020,CN1c2ccccc2NC1=CSc3ncc(c(n3)O)Cc4cnc(nc4)OC,0 +SAMPL8-19_micro021,CN1c2ccccc2[NH2+]C1=CSc3[nH+]cc(c(n3)O)Cc4cnc(nc4)OC,2 +SAMPL8-19_micro022,CN1c2ccccc2NC1=CSc3[nH]c(=O)c(c[nH+]3)Cc4cnc(nc4)OC,1 +SAMPL8-19_micro023,CN1c2ccccc2[NH2+]C1=CSc3ncc(c(n3)O)Cc4cnc(nc4)OC,1 +SAMPL8-19_micro024,Cn1c2ccccc2[nH+]c1CSc3ncc(c(n3)[O-])Cc4cnc(nc4)OC,0 +SAMPL8-19_micro025,CN1c2ccccc2NC1=CSc3[nH]cc(c(=O)n3)Cc4cnc(nc4)OC,0 +SAMPL8-23_micro000,C=C1Nc2cc(ccc2S1)O,0 +SAMPL8-23_micro001,C=C1[NH2+]c2cc(ccc2S1)O,1 +SAMPL8-23_micro002,C=C1Nc2cc(ccc2S1)[O-],-1 +SAMPL8-23_micro003,Cc1[nH+]c2cc(ccc2s1)[O-],0 +SAMPL8-23_micro004,C=C1[NH2+]c2cc(ccc2S1)[O-],0 +SAMPL8-23_micro005,Cc1nc2cc(ccc2s1)[O-],-1 +SAMPL8-23_micro006,Cc1[nH+]c2cc(ccc2s1)O,1 +SAMPL8-23_micro007,Cc1nc2cc(ccc2s1)O,0 +SAMPL8-11_micro000,Cn1c2c(c(cnc2ccc1=O)F)OC[C@H]3CC[C@@H](CC3)N,0 +SAMPL8-11_micro001,Cn1c2c(c(cnc2ccc1=O)F)OC[C@H]3CC[C@@H](CC3)[NH3+],1 +SAMPL8-11_micro002,C[n+]1c2c(c(c[nH+]c2ccc1[O-])F)OC[C@H]3CC[C@@H](CC3)N,1 +SAMPL8-11_micro003,Cn1c2c(c(c[nH+]c2ccc1=O)F)OC[C@H]3CC[C@@H](CC3)[NH3+],2 +SAMPL8-11_micro004,C[n+]1c2c(c(cnc2ccc1O)F)OC[C@H]3CC[C@@H](CC3)N,1 +SAMPL8-11_micro005,C[n+]1c2c(c(cnc2ccc1O)F)OC[C@H]3CC[C@@H](CC3)[NH3+],2 +SAMPL8-22_micro000,COc1cc2c(cc1OC)nc([nH]c2=N)Cl,0 +SAMPL8-22_micro001,COc1cc2c(cc1OC)[n-]c(nc2=N)Cl,-1 +SAMPL8-22_micro002,COc1cc2c(cc1OC)nc(nc2N)Cl,0 +SAMPL8-22_micro003,COc1cc2c(cc1OC)[nH]c(nc2=N)Cl,0 +SAMPL8-22_dortmund002,COc1cc2[nH+]c(Cl)nc(N)c2cc1OC,1 +SAMPL8-22_dortmund004,COc1cc2nc(Cl)[nH]c(=[NH2+])c2cc1OC,1 +SAMPL8-22_dortmund005,COc1cc2[nH]c(Cl)nc(=[NH2+])c2cc1OC,1 +SAMPL8-22_dortmund001,COc1cc2[nH+]c(Cl)[nH]c(=[NH2+])c2cc1OC,2 +SAMPL8-22_dortmund003,COc1cc2[nH+]c(Cl)[nH]c(=[NH2+])c2cc1OC,2 +SAMPL8-1_micro000,c1ccc(c(c1)C(=O)O)Nc2cccc(c2)C(F)(F)F,0 +SAMPL8-1_micro001,c1cc(cc(c1)N=C2C=CC=CC2C(=O)[O-])C(F)(F)F,-1 +SAMPL8-1_micro002,c1cc(cc(c1)N=C2C=CC=CC2=C(O)[O-])C(F)(F)F,-1 +SAMPL8-1_micro003,c1cc(cc(c1)N=C2CC=CC=C2C(=O)[O-])C(F)(F)F,-1 +SAMPL8-1_micro004,c1ccc(c(c1)C(=O)[O-])Nc2cccc(c2)C(F)(F)F,-1 +SAMPL8-1_micro005,c1cc(cc(c1)[NH+]=C2C=CC=CC2=C([O-])[O-])C(F)(F)F,-1 +SAMPL8-1_micro006,c1cc(cc(c1)N=C2C=CC=CC2=C(O)O)C(F)(F)F,0 +SAMPL8-1_micro007,c1cc(cc(c1)N=C2CC=CC=C2C(=O)O)C(F)(F)F,0 +SAMPL8-1_micro008,c1cc(cc(c1)N=C2C=CCC=C2C(=O)[O-])C(F)(F)F,-1 +SAMPL8-1_micro009,c1cc(cc(c1)N=C2C=CC=CC2C(=O)O)C(F)(F)F,0 +SAMPL8-1_micro010,c1cc(cc(c1)N=C2C=CCC=C2C(=O)O)C(F)(F)F,0 +SAMPL8-1_dortmund001,O=C(O)c1ccccc1[NH2+]c1cccc(C(F)(F)F)c1,1 +SAMPL8-10_micro000,CS(=O)(=O)c1cccc(c1)c2ccc(cc2)CNCc3c(cccc3Cl)F,0 +SAMPL8-10_micro001,CS(=O)(=O)c1cccc(c1)c2ccc(cc2)C[NH2+]Cc3c(cccc3Cl)F,1 +SAMPL8-17_micro000,c1cc2c(cc1Br)n(c(n2)N)CC3(CCOCC3)CO,0 +SAMPL8-17_micro001,c1cc2c(cc1Br)n(c(n2)[NH-])CC3(CCOCC3)CO,-1 +SAMPL8-17_micro002,c1cc2c(cc1Br)n(c([nH+]2)N)CC3(CCOCC3)CO,1 +SAMPL8-17_micro003,c1cc2c(cc1Br)n(c(n2)[NH3+])CC3(CCOCC3)CO,1 +SAMPL8-17_micro004,c1cc2c(cc1Br)n(c(=N)[nH]2)CC3(CCOCC3)CO,0 +SAMPL8-17_micro005,c1cc2c(cc1Br)n(c(n2)N)CC3(CCOCC3)C[O-],-1 +SAMPL8-6_micro000,Cc1ccc(cc1NCc2ccc(s2)C(=O)O)Cl,0 +SAMPL8-6_micro001,Cc1ccc(cc1NCc2ccc(s2)C(=O)[O-])Cl,-1 +SAMPL8-6_micro002,Cc1ccc(cc1[NH2+]C=c2ccc(=C(O)O)s2)Cl,1 +SAMPL8-6_micro003,Cc1ccc(cc1[NH2+]Cc2ccc(s2)C(=O)O)Cl,1 +SAMPL8-6_micro004,Cc1ccc(cc1[NH2+]C=c2ccc(=C(O)[O-])s2)Cl,0 +SAMPL8-6_micro005,Cc1ccc(cc1NC=c2ccc(=C(O)O)s2)Cl,0 +SAMPL8-6_micro006,Cc1ccc(cc1N=Cc2ccc(s2)C(O)[O-])Cl,-1 +SAMPL8-6_micro007,Cc1ccc(cc1[NH2+]Cc2ccc(s2)C(=O)[O-])Cl,0 +SAMPL8-6_micro008,Cc1ccc(cc1N=Cc2ccc(s2)C(O)O)Cl,0 +SAMPL8-6_micro009,Cc1ccc(cc1NC=c2ccc(=C(O)[O-])s2)Cl,-1 +SAMPL8-9_micro000,c1cc2c(cc1Br)n(c(n2)N)CC3(CCCCC3)O,0 +SAMPL8-9_micro001,c1cc2c(cc1Br)n(c(=N)[n-]2)CC3(CCCCC3)O,-1 +SAMPL8-9_micro002,c1cc2c(cc1Br)[n+](c([nH]2)N)CC3(CCCCC3)O,1 +SAMPL8-9_micro003,c1cc2c(cc1Br)n(c(=N)[nH]2)CC3(CCCCC3)O,0 +SAMPL8-9_micro004,c1cc2c(cc1Br)n(c(n2)[NH3+])CC3(CCCCC3)O,1 +SAMPL8-18_micro000,COc1ccc(cc1OC)N=c2c3ccccc3nc([nH]2)Cl,0 +SAMPL8-18_micro001,COc1ccc(cc1OC)N=c2c3ccccc3[nH]c(n2)Cl,0 +SAMPL8-18_micro002,COc1ccc(cc1OC)Nc2c3ccccc3nc(n2)Cl,0 +SAMPL8-18_micro003,COc1ccc(cc1OC)Nc2c3ccccc3nc([nH+]2)Cl,1 +SAMPL8-18_micro004,COc1ccc(cc1OC)Nc2c3ccccc3[nH+]c(n2)Cl,1 +SAMPL8-18_micro005,COc1ccc(cc1OC)[N-]c2c3ccccc3nc(n2)Cl,-1 +SAMPL8-20_micro000,c1ccc(cc1)c2c(cc3c(=N)[nH][nH]c3n2)Cl,0 +SAMPL8-20_micro001,c1ccc(cc1)c2c(cc-3c(=N)[nH]nc3[nH]2)Cl,0 +SAMPL8-20_micro002,c1ccc(cc1)c2c(cc-3c(n[nH+]c3[nH]2)N)Cl,1 +SAMPL8-20_micro003,c1ccc(cc1)c2c(cc3c([nH+][nH]c3n2)N)Cl,1 +SAMPL8-20_micro004,c1ccc(cc1)C2=NC3=NN=C(C3=CC2Cl)N,0 +SAMPL8-20_micro005,c1ccc(cc1)C2=C(CC3C(=[NH2+])N=NC3=N2)Cl,1 +SAMPL8-20_micro006,c1ccc(cc1)c2c(cc-3c([nH+]nc3[nH]2)N)Cl,1 +SAMPL8-20_micro007,c1ccc(cc1)C2=NC3=NNC(=[NH2+])C3C=C2Cl,1 +SAMPL8-20_micro008,c1ccc(cc1)C2C(C=C3C(=N)N=NC3=N2)Cl,0 +SAMPL8-20_micro009,c1ccc(cc1)C2=NC3=NNC(=N)C3=CC2Cl,0 +SAMPL8-20_micro010,c1ccc(cc1)C2=C(CC3=C(N=NC3=N2)N)Cl,0 +SAMPL8-20_micro011,c1ccc(cc1)c2c(cc3c([nH]nc3n2)[NH3+])Cl,1 +SAMPL8-20_micro012,c1ccc(cc1)C2=C(CC3=C(N2)N=NC3=N)Cl,0 +SAMPL8-20_micro013,c1ccc(cc1)C2=NC3=NNC(=N)C3C=C2Cl,0 +SAMPL8-20_micro014,c1ccc(cc1)C2=NC3=C(CC2Cl)C(=[NH2+])N=N3,1 +SAMPL8-20_micro015,c1ccc(cc1)c2c(cc-3c(nnc3[nH]2)[NH3+])Cl,1 +SAMPL8-20_micro016,c1ccc(cc1)c2c(cc-3c(=N)[nH][nH+]c3[nH]2)Cl,1 +SAMPL8-20_micro017,c1ccc(cc1)c2c(cc3c([nH]nc3n2)N)Cl,0 +SAMPL8-20_micro018,c1ccc(cc1)c2c(cc-3c(nnc3[nH]2)N)Cl,0 +SAMPL8-20_micro019,c1ccc(cc1)C2C(=CC3=C(N=NC3=N2)N)Cl,0 +SAMPL8-20_micro020,c1ccc(cc1)C2C(=CC3C(=N)N=NC3=N2)Cl,0 +SAMPL8-20_micro021,c1ccc(cc1)C2=NC3=NN=C(C3C=C2Cl)N,0 +SAMPL8-20_micro022,c1ccc(cc1)c2c(cc3c(n[nH]c3n2)N)Cl,0 +SAMPL8-20_micro023,c1ccc(cc1)C2C(=CC3=C(N2)N=NC3=N)Cl,0 +SAMPL8-20_micro024,c1ccc(cc1)C2=NC3=C(CC2Cl)C(=N)N=N3,0 +SAMPL8-20_micro025,c1ccc(cc1)C2=C(CC3=C(N2)N=NC3=[NH2+])Cl,1 +SAMPL8-20_micro026,c1ccc(cc1)c2c(cc3c(n[nH]c3n2)[NH3+])Cl,1 +SAMPL8-20_micro027,c1ccc(cc1)C2=C(CC3C(=N)N=NC3=N2)Cl,0 +SAMPL8-20_micro028,c1ccc(cc1)C2=C(CC3=C(N=NC3=N2)[NH3+])Cl,1 +SAMPL8-3_micro000,c1cc(oc1)CN=C2C=C(C(=CC2=C(O)O)S(=O)(=O)N)Cl,0 +SAMPL8-3_micro001,c1cc(oc1)CN=C2CC(=C(C=C2C(=O)[O-])S(=O)(=O)N)Cl,-1 +SAMPL8-3_micro002,c1cc(oc1)CN=C2CC(=C(C=C2C(=O)O)S(=O)(=O)N)Cl,0 +SAMPL8-3_micro003,c1cc(oc1)CN=C2CC(=C(C=C2C(=O)O)S(=O)(=O)[NH-])Cl,-1 +SAMPL8-3_micro004,c1cc(oc1)CN=C2C=C(C(C=C2C(=O)O)S(=O)(=O)N)Cl,0 +SAMPL8-3_micro005,c1cc(oc1)CN=C2C=C(C(=CC2=C(O)[O-])S(=O)(=O)N)Cl,-1 +SAMPL8-3_micro006,c1cc(oc1)CNc2cc(c(cc2C(=O)O)S(=O)(=O)N)Cl,0 +SAMPL8-3_micro007,c1cc(oc1)CN=C2C=C(C(C=C2C(=O)[O-])S(=O)(=O)[NH-])Cl,-2 +SAMPL8-3_micro008,c1cc(oc1)CN=C2C=C(C(=CC2C(=O)O)S(=O)(=O)N)Cl,0 +SAMPL8-3_micro009,c1cc(oc1)CN=C2C=C(C(=CC2C(=O)[O-])S(=O)(=O)N)Cl,-1 +SAMPL8-3_micro010,c1cc(oc1)CNc2cc(c(cc2C(=O)[O-])S(=O)(=O)N)Cl,-1 +SAMPL8-3_micro011,c1cc(oc1)CN=C2C=C(C(C=C2C(=O)O)S(=O)(=O)[NH-])Cl,-1 +SAMPL8-3_micro012,c1cc(oc1)CN=C2C=C(C(=CC2=C(O)[O-])S(=O)(=O)[NH-])Cl,-2 +SAMPL8-3_micro013,c1cc(oc1)C[NH+]=C2C=C(C(=CC2=C([O-])[O-])S(=O)(=O)[NH-])Cl,-2 +SAMPL8-3_micro014,c1cc(oc1)CNc2cc(c(cc2C(=O)[O-])S(=O)(=O)[NH-])Cl,-2 +SAMPL8-3_micro015,c1cc(oc1)CN=C2C=C(C(=CC2=C(O)O)S(=O)(=O)[NH-])Cl,-1 +SAMPL8-3_micro016,c1cc(oc1)CNc2cc(c(cc2C(=O)O)S(=O)(=O)[NH-])Cl,-1 +SAMPL8-3_micro017,c1cc(oc1)CN=C2C=C(C(=CC2C(=O)O)S(=O)(=O)[NH-])Cl,-1 +SAMPL8-3_micro018,c1cc(oc1)CN=C2C=C(C(C=C2C(=O)[O-])S(=O)(=O)N)Cl,-1 +SAMPL8-3_micro019,c1cc(oc1)CN=C2CC(=C(C=C2C(=O)[O-])S(=O)(=O)[NH-])Cl,-2 +SAMPL8-3_micro020,c1cc(oc1)C[NH+]=C2C=C(C(=CC2=C([O-])[O-])S(=O)(=O)N)Cl,-1 +SAMPL8-3_micro021,c1cc(oc1)CN=C2C=C(C(=CC2C(=O)[O-])S(=O)(=O)[NH-])Cl,-2 +SAMPL8-3_dortmund001,NS(=O)(=O)C1=CC(=C(O)O)/C(=[NH+]/Cc2ccco2)C=C1Cl,1 +SAMPL8-12_micro000,Cc1ccc(cc1)Cc2cnc(nc2N3CCOCC3)N,0 +SAMPL8-12_micro001,Cc1ccc(cc1)Cc2c[n-]c(nc2=[N+]3CCOCC3)[NH-],-1 +SAMPL8-12_micro002,Cc1ccc(cc1)Cc2cnc(=N)[nH]c2N3CCOCC3,0 +SAMPL8-12_micro003,Cc1ccc(cc1)Cc2c[nH]c(=N)nc2N3CCOCC3,0 +SAMPL8-12_dortmund002,Cc1ccc(Cc2c[nH+]c(N)nc2N2CCOCC2)cc1,1 +SAMPL8-12_dortmund004,Cc1ccc(Cc2c[nH]c(=[NH2+])nc2N2CCOCC2)cc1,1 +SAMPL8-12_dortmund006,Cc1ccc(Cc2cnc(=[NH2+])[nH]c2N2CCOCC2)cc1,1 +SAMPL8-12_dortmund001,Cc1ccc(Cc2c[nH+]c(N)[nH]c2=[N+]2CCOCC2)cc1,2 +SAMPL8-12_dortmund003,Cc1ccc(Cc2c[nH]c(=[NH2+])nc2[NH+]2CCOCC2)cc1,2 +SAMPL8-12_dortmund005,Cc1ccc(Cc2c[nH+]c(=[NH2+])[nH]c2N2CCOCC2)cc1,2 +SAMPL8-15_micro000,Cc1ccccc1N=c2c3ccccc3[nH]c(n2)Cl,0 +SAMPL8-15_micro001,Cc1ccccc1Nc2c3ccccc3nc(n2)Cl,0 +SAMPL8-15_micro002,Cc1ccccc1N=c2c3ccccc3nc([nH]2)Cl,0 +SAMPL8-15_micro003,CC1=CC=CC=C1NC2=C3C=CC=CC3=NC(=[NH+]2)Cl,1 +SAMPL8-15_micro004,CC1=CC=CC=C1NC1=C2C=CC=CC2=[NH+]C(Cl)=N1,1 +SAMPL8-4_micro000,Cc1c([nH]c(=Nc2ccc(c(c2)Cl)C#N)s1)C(=O)O,0 +SAMPL8-4_micro001,Cc1c([nH+]c(s1)Nc2ccc(c(c2)Cl)C#N)C(=O)[O-],0 +SAMPL8-4_micro002,Cc1c([nH+]c(s1)Nc2ccc(c(c2)Cl)C#N)C(=O)O,1 +SAMPL8-4_micro003,Cc1c([nH]c(=Nc2ccc(c(c2)Cl)C#N)s1)C(=O)[O-],-1 +SAMPL8-4_micro004,Cc1c([nH]c(=Nc2ccc(c(c2)Cl)C#N)s1)C(=O)O,0 +SAMPL8-4_micro005,Cc1c(nc(s1)Nc2ccc(c(c2)Cl)C#N)C(=O)[O-],-1 +SAMPL8-4_micro006,Cc1c(nc(s1)[NH+]=C2C=CC(=C=[N-])C(=C2)Cl)C(=O)[O-],-1 +SAMPL8-4_micro007,Cc1c([nH+]c(s1)[NH+]=C2C=CC(=C=[N-])C(=C2)Cl)C(=O)O,1 +SAMPL8-4_micro008,Cc1c(nc(s1)N=C2C=CC(=C=[N-])C(=C2)Cl)C(=O)O,-1 +SAMPL8-4_micro009,Cc1c([nH+]c(s1)N=C2C=CC(=C=[N-])C(=C2)Cl)C(=O)[O-],-1 +SAMPL8-4_micro010,Cc1c(nc(s1)Nc2ccc(c(c2)Cl)C#N)C(=O)O,0 +SAMPL8-14_micro000,Cc1cc(cc(c1O)C(C)(C)C)Cc2cnc(=N)[nH]c2N,0 +SAMPL8-14_micro001,Cc1cc(cc(c1[O-])C(C)(C)C)Cc2cnc(=N)[n-]c2N,-2 +SAMPL8-14_micro002,Cc1cc(cc(c1O)C(C)(C)C)Cc2cnc([nH]c2=N)N,0 +SAMPL8-14_micro003,Cc1cc(cc(c1[O-])C(C)(C)C)Cc2c[n-]c(nc2=N)N,-2 +SAMPL8-14_micro004,Cc1cc(cc(c1O)C(C)(C)C)Cc2c[nH+]c(nc2[NH-])[NH-],-1 +SAMPL8-14_micro005,Cc1cc(cc(c1O)C(C)(C)C)Cc2cnc(nc2N)[NH-],-1 +SAMPL8-14_micro006,Cc1cc(cc(c1O)C(C)(C)C)Cc2c[nH]c(=N)[nH]c2=N,0 +SAMPL8-14_micro007,Cc1cc(cc(c1[O-])C(C)(C)C)Cc2cnc([nH]c2=N)[NH-],-2 +SAMPL8-14_micro008,Cc1cc(cc(c1[O-])C(C)(C)C)Cc2cnc(nc2N)N,-1 +SAMPL8-14_micro09,Cc1cc(cc(c1O)C(C)(C)C)Cc2c[nH]c(=N)[n-]c2=N,-1 +SAMPL8-14_micro010,Cc1cc(cc(c1O)C(C)(C)C)Cc2c[n-]c(nc2=N)N,-1 +SAMPL8-14_micro011,Cc1cc(cc(c1[O-])C(C)(C)C)Cc2cnc(=[NH2+])[n-]c2[NH-],-2 +SAMPL8-14_micro012,Cc1cc(cc(c1O)C(C)(C)C)Cc2cnc([n-]c2=[NH2+])[NH-],-1 +SAMPL8-14_micro013,Cc1cc(cc(c1O)C(C)(C)C)Cc2c[nH]c(=N)nc2N,0 +SAMPL8-14_micro014,Cc1cc(cc(c1[O-])C(C)(C)C)Cc2cnc(=N)[n-]c2[NH-],-3 +SAMPL8-14_micro015,Cc1cc(cc(c1[O-])C(C)(C)C)Cc2c[n-]c([nH+]c2=N)[NH-],-2 +SAMPL8-14_micro016,Cc1cc(cc(c1O)C(C)(C)C)Cc2cnc(=N)[nH]c2N,0 +SAMPL8-14_micro017,Cc1cc(cc(c1O)C(C)(C)C)Cc2c[nH]c(nc2=N)N,0 +SAMPL8-14_micro018,Cc1cc(cc(c1O)C(C)(C)C)Cc2cnc([n-]c2=N)[NH-],-2 +SAMPL8-14_micro019,Cc1cc(cc(c1O)C(C)(C)C)Cc2cnc(=[NH2+])[n-]c2[NH-],-1 +SAMPL8-14_micro020,Cc1cc(cc(c1[O-])C(C)(C)C)Cc2c[nH]c(=N)[n-]c2=N,-2 +SAMPL8-14_micro021,Cc1cc(cc(c1O)C(C)(C)C)Cc2cnc([nH]c2=N)[NH-],-1 +SAMPL8-14_micro022,Cc1cc(cc(c1[O-])C(C)(C)C)Cc2c[nH]c(nc2=N)N,-1 +SAMPL8-14_micro023,Cc1cc(cc(c1O)C(C)(C)C)Cc2cnc([nH]c2=N)N,0 +SAMPL8-14_micro024,Cc1cc(cc(c1O)C(C)(C)C)Cc2cnc(nc2N)N,0 +SAMPL8-14_micro025,Cc1cc(cc(c1O)C(C)(C)C)Cc2c[n-]c([nH+]c2=N)[NH-],-1 +SAMPL8-14_micro026,Cc1cc(cc(c1[O-])C(C)(C)C)Cc2c[nH+]c(=N)[n-]c2[NH-],-2 +SAMPL8-14_micro027,Cc1cc(cc(c1[O-])C(C)(C)C)Cc2c[nH]c(=N)[nH]c2=N,-1 +SAMPL8-14_micro028,Cc1cc(cc(c1[O-])C(C)(C)C)Cc2c[nH]c(=N)nc2N,-1 +SAMPL8-14_micro029,Cc1cc(cc(c1[O-])C(C)(C)C)Cc2cnc(=N)[nH]c2N,-1 +SAMPL8-14_micro030,Cc1cc(cc(c1O)C(C)(C)C)Cc2c[nH]c(nc2=N)N,0 +SAMPL8-14_micro031,Cc1cc(cc(c1[O-])C(C)(C)C)Cc2cnc([n-]c2=[NH2+])[NH-],-2 +SAMPL8-14_micro032,Cc1cc(cc(c1[O-])C(C)(C)C)Cc2cnc([nH]c2=N)N,-1 +SAMPL8-14_micro033,Cc1cc(cc(c1O)C(C)(C)C)Cc2c[nH]c(=N)nc2N,0 +SAMPL8-14_micro034,Cc1cc(cc(c1O)C(C)(C)C)Cc2c[nH]c(=N)[nH]c2=N,0 +SAMPL8-14_dortmund002,Cc1cc(Cc2c[nH+]c(N)nc2N)cc(C(C)(C)C)c1O,1 +SAMPL8-14_dortmund004,Cc1cc(Cc2cnc(=[NH2+])[nH]c2N)cc(C(C)(C)C)c1O,1 +SAMPL8-14_dortmund006,Cc1cc(Cc2c[nH]c(=N)[nH]c2=[NH2+])cc(C(C)(C)C)c1O,1 +SAMPL8-14_dortmund007,Cc1cc(Cc2c[nH]c(=N)[nH]c2=[NH2+])cc(C(C)(C)C)c1O,1 +SAMPL8-14_dortmund009,Cc1cc(Cc2cnc(N)[nH]c2=[NH2+])cc(C(C)(C)C)c1O,1 +SAMPL8-14_dortmund011,Cc1cc(Cc2c[nH]c(=[NH2+])nc2N)cc(C(C)(C)C)c1O,1 +SAMPL8-14_dortmund012,Cc1cc(Cc2c[nH]c(N)nc2=[NH2+])cc(C(C)(C)C)c1O,1 +SAMPL8-14_dortmund001,Cc1cc(Cc2c[nH+]c(N)[nH]c2=[NH2+])cc(C(C)(C)C)c1O,2 +SAMPL8-14_dortmund003,Cc1cc(Cc2c[nH+]c(=[NH2+])[nH]c2N)cc(C(C)(C)C)c1O,2 +SAMPL8-14_dortmund005,Cc1cc(Cc2c[nH]c(=[NH2+])[nH]c2=[NH2+])cc(C(C)(C)C)c1O,2 +SAMPL8-14_dortmund008,Cc1cc(Cc2c[nH+]c(N)[nH]c2=[NH2+])cc(C(C)(C)C)c1O,2 +SAMPL8-14_dortmund010,Cc1cc(Cc2c[nH]c(=[NH2+])nc2[NH3+])cc(C(C)(C)C)c1O,2 +SAMPL8-5_micro000,c1ccc(c(c1)CC(=O)O)Nc2c(cccc2Cl)Cl,0 +SAMPL8-5_micro001,c1ccc(c(c1)CC(=O)[O-])[NH2+]c2c(cccc2Cl)Cl,0 +SAMPL8-5_micro002,c1ccc(c(c1)C=C(O)[O-])Nc2c(cccc2Cl)Cl,-1 +SAMPL8-5_micro003,c1ccc(c(c1)CC(=O)O)[NH2+]c2c(cccc2Cl)Cl,1 +SAMPL8-5_micro004,c1ccc(c(c1)C=C(O)[O-])[NH2+]c2c(cccc2Cl)Cl,0 +SAMPL8-5_micro005,c1ccc(c(c1)C=C(O)O)Nc2c(cccc2Cl)Cl,0 +SAMPL8-5_micro006,c1ccc(c(c1)C=C(O)O)[NH2+]c2c(cccc2Cl)Cl,1 +SAMPL8-5_micro007,c1ccc(c(c1)CC(=O)[O-])Nc2c(cccc2Cl)Cl,-1 +SAMPL8-21_micro000,COc1cc(cc(c1O)OC)Cc2c(=N)[nH]c(=N)[nH]c2OC,0 +SAMPL8-21_micro001,COc1cc(cc(c1[O-])OC)Cc2c(=N)[nH+]c([n-]c2OC)[NH-],-2 +SAMPL8-21_micro002,COc1cc(cc(c1[O-])OC)Cc2c(nc([nH+]c2OC)[NH-])[NH-],-2 +SAMPL8-21_micro003,COc1cc(cc(c1O)OC)Cc2c(nc(=[NH2+])[n-]c2OC)[NH-],-1 +SAMPL8-21_micro004,COc1cc(cc(c1[O-])OC)Cc2c(=N)nc([nH]c2OC)[NH-],-2 +SAMPL8-21_micro005,COc1cc(cc(c1[O-])OC)Cc2c(=N)[n-]c(=[NH2+])[n-]c2OC,-2 +SAMPL8-21_micro006,COc1cc(cc(c1O)OC)Cc2c(=N)[nH]c(=N)[n-]c2OC,-1 +SAMPL8-21_micro007,COc1cc(cc(c1O)OC)Cc2c(=N)[n-]c(=N)[nH]c2OC,-1 +SAMPL8-21_micro008,COc1cc(cc(c1O)OC)Cc2c(=N)nc([nH]c2OC)N,0 +SAMPL8-21_micro009,COc1cc(cc(c1O)OC)Cc2c(=[NH2+])nc([n-]c2OC)[NH-],-1 +SAMPL8-21_micro010,COc1cc(cc(c1[O-])OC)Cc2c(=N)[n-]c(nc2OC)[NH-],-3 +SAMPL8-21_micro011,COc1cc(cc(c1O)OC)Cc2c([nH+]c(=N)[n-]c2OC)[NH-],-1 +SAMPL8-21_micro012,COc1cc(cc(c1O)OC)Cc2c(=N)nc([n-]c2OC)[NH-],-2 +SAMPL8-21_micro013,COc1cc(cc(c1[O-])OC)Cc2c(=N)[nH]c(nc2OC)[NH-],-2 +SAMPL8-21_micro014,COc1cc(cc(c1O)OC)Cc2c([n-]c(=N)nc2OC)N,-1 +SAMPL8-21_micro015,COc1cc(cc(c1[O-])OC)Cc2c(=[NH2+])nc([n-]c2OC)[NH-],-2 +SAMPL8-21_micro016,COc1cc(cc(c1O)OC)Cc2c(nc(nc2OC)N)[NH-],-1 +SAMPL8-21_micro017,COc1cc(cc(c1[O-])OC)Cc2c(nc(=N)[n-]c2OC)N,-2 +SAMPL8-21_micro018,COc1cc(cc(c1[O-])OC)Cc2c(=N)[nH]c(nc2OC)N,-1 +SAMPL8-21_micro019,COc1cc(cc(c1O)OC)Cc2c([n-]c(=N)[nH+]c2OC)[NH-],-1 +SAMPL8-21_micro020,COc1cc(cc(c1[O-])OC)Cc2c(nc(=N)[nH]c2OC)N,-1 +SAMPL8-21_micro021,COc1cc(cc(c1[O-])OC)Cc2c(=N)[n-]c(nc2OC)N,-2 +SAMPL8-21_micro022,COc1cc(cc(c1[O-])OC)Cc2c(nc(nc2OC)N)N,-1 +SAMPL8-21_micro023,COc1cc(cc(c1O)OC)Cc2c(=N)[nH]c(nc2OC)N,0 +SAMPL8-21_micro024,COc1cc(cc(c1[O-])OC)Cc2c([nH]c(=N)nc2OC)N,-1 +SAMPL8-21_micro025,COc1cc(cc(c1O)OC)Cc2c([nH]c(=N)nc2OC)N,0 +SAMPL8-21_micro026,COc1cc(cc(c1[O-])OC)Cc2c(=N)nc([nH]c2OC)N,-1 +SAMPL8-21_micro027,COc1cc(cc(c1[O-])OC)Cc2c(=N)[nH]c(=N)[nH]c2OC,-1 +SAMPL8-21_micro028,COc1cc(cc(c1O)OC)Cc2c(nc(nc2OC)N)N,0 +SAMPL8-21_micro029,COc1cc(cc(c1O)OC)Cc2c(nc(=N)[nH]c2OC)N,0 +SAMPL8-21_dortmund002,COc1cc(Cc2c(OC)nc(N)[nH+]c2N)cc(OC)c1O,1 +SAMPL8-21_dortmund004,COc1cc(Cc2c(OC)[nH]c(=N)[nH]c2=[NH2+])cc(OC)c1O,1 +SAMPL8-21_dortmund006,COc1cc(Cc2c(OC)nc(=[NH2+])[nH]c2N)cc(OC)c1O,1 +SAMPL8-21_dortmund008,COc1cc(Cc2c(N)nc(=[NH2+])[nH]c2OC)cc(OC)c1O,1 +SAMPL8-21_dortmund009,COc1cc(Cc2c(OC)[nH]c(N)nc2=[NH2+])cc(OC)c1O,1 +SAMPL8-21_dortmund011,COc1cc(Cc2c(OC)nc(N)[nH]c2=[NH2+])cc(OC)c1O,1 +SAMPL8-21_dortmund001,COc1cc(Cc2c(N)[nH+]c(N)[nH+]c2OC)cc(OC)c1O,2 +SAMPL8-21_dortmund003,COc1cc(Cc2c(OC)[nH]c(=[NH2+])[nH]c2=[NH2+])cc(OC)c1O,2 +SAMPL8-21_dortmund007,COc1cc(Cc2c([NH3+])nc(=[NH2+])[nH]c2OC)cc(OC)c1O,2 +SAMPL8-21_dortmund010,COc1cc(Cc2c(OC)[nH+]c(N)[nH]c2=[NH2+])cc(OC)c1O,2 +SAMPL8-2_micro000,CS(=O)(=O)c1ccc(cc1)CCC(=O)O,0 +SAMPL8-2_micro001,CS(=O)(=O)c1ccc(cc1)CCC(=O)[O-],-1 +SAMPL8-2_micro002,CS(=O)(=O)c1ccc(cc1)CC=C(O)O,0 +SAMPL8-2_micro003,CS(=O)(=O)c1ccc(cc1)CC=C(O)[O-],-1 +SAMPL8-13_micro000,C[C@H](c1ccccc1Cl)Oc2cc(sc2C(=O)N)n3cnc4c3cc(cc4)S(=O)(=O)C,0 +SAMPL8-13_micro001,C[C@H](c1ccccc1Cl)Oc2cc(sc2C(=O)N)n3c[nH+]c4c3cc(cc4)S(=O)(=O)C,1 +SAMPL8-13_micro002,C[C@@H](Oc1cc(sc1C([NH-])=O)-n1cnc2ccc(cc12)S(C)(=O)=O)c1ccccc1Cl,-1 diff --git a/physical_properties/microstates/microstate_issues/SAMPL8_12/COSMO_RS_extra003_c0.mol2 b/physical_properties/microstates/microstate_issues/SAMPL8_12/COSMO_RS_extra003_c0.mol2 new file mode 100755 index 0000000..7897fdd --- /dev/null +++ b/physical_properties/microstates/microstate_issues/SAMPL8_12/COSMO_RS_extra003_c0.mol2 @@ -0,0 +1,105 @@ +# Created by COSMOvis on Mon Aug 09 22:24:20 CEST 2021 +# +# + +# +# + +@MOLECULE +SAMPL8-12_extra003_c0 +42 44 +SMALL +USER_CHARGES + +@ATOM +1 C 0.039800 4.229800 -0.094300 C 0 XO 0.000000 +2 C 0.859400 3.026400 -2.010400 C 1 XO 0.000000 +3 C -0.464600 3.037400 0.438300 C 2 XO 0.000000 +4 C 0.357800 1.835600 -1.480500 C 3 XO 0.000000 +5 C 1.377500 0.170200 1.385400 C 4 XO 0.000000 +6 C 0.708900 4.247800 -1.328300 C 5 XO 0.000000 +7 C -0.312900 1.822400 -0.245500 C 6 XO 0.000000 +8 C 0.198600 -0.374200 0.954600 C 7 XO 0.000000 +9 C 0.125200 -1.826600 1.024600 C 8 XO 0.000000 +10 C 2.355900 -1.963600 1.674100 C 9 XO 0.000000 +11 C -0.950600 -3.991900 0.511700 C 10 XO 0.000000 +12 C -2.378400 -2.067600 0.956900 C 11 XO 0.000000 +13 C -1.654700 -4.749200 1.635000 C 12 XO 0.000000 +14 C -3.034600 -2.893300 2.071000 C 13 XO 0.000000 +15 C 1.223200 5.537600 -1.920300 C 14 XO 0.000000 +16 C -0.859400 0.528800 0.328600 C 15 XO 0.000000 +17 N 2.424800 -0.600900 1.802300 N 16 XO 0.000000 +18 N 1.230800 -2.559300 1.303400 N 17 XO 0.000000 +19 N -0.998400 -2.536800 0.747700 N 18 XO 0.000000 +20 N 3.450100 -2.691100 1.947200 N 19 XO 1.000000 +21 O -3.013000 -4.298500 1.787400 O 20 XO 0.000000 +22 H -0.091000 5.162200 0.460500 H 21 XO 0.000000 +23 H 1.375900 3.009300 -2.973400 H 22 XO 0.000000 +24 H -0.984600 3.054200 1.399500 H 23 XO 0.000000 +25 H 0.488500 0.902600 -2.034600 H 24 XO 0.000000 +26 H 1.563100 1.242000 1.382200 H 25 XO 0.000000 +27 H 0.092000 -4.309700 0.425500 H 26 XO 0.000000 +28 H -1.471400 -4.180800 -0.440800 H 27 XO 0.000000 +29 H -2.943100 -2.181600 0.019000 H 28 XO 0.000000 +30 H -2.395500 -1.019100 1.258000 H 29 XO 0.000000 +31 H -1.702900 -5.819000 1.395500 H 30 XO 0.000000 +32 H -1.107600 -4.615900 2.586400 H 31 XO 0.000000 +33 H -2.519100 -2.695900 3.029700 H 32 XO 0.000000 +34 H -4.089300 -2.603900 2.165100 H 33 XO 0.000000 +35 H 0.482700 5.976200 -2.609100 H 34 XO 0.000000 +36 H 1.427200 6.283500 -1.139900 H 35 XO 0.000000 +37 H 2.145300 5.375200 -2.496300 H 36 XO 0.000000 +38 H -1.637100 0.779400 1.067200 H 37 XO 0.000000 +39 H -1.357600 -0.033800 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37 1 + 19 16 15 1 + 20 16 34 1 + 21 15 14 1 + 22 15 33 1 + 23 14 9 1 + 24 11 32 1 + 25 11 10 1 + 26 9 10 2 + 27 9 8 1 + 28 10 31 1 + 29 29 8 1 + 30 8 5 1 + 31 8 30 1 + 32 26 4 1 + 33 5 4 ar + 34 5 6 ar + 35 4 3 ar + 36 27 6 1 + 37 6 7 ar + 38 3 25 1 + 39 3 2 ar + 40 22 1 1 + 41 7 2 ar + 42 7 28 1 + 43 24 1 1 + 44 2 1 1 + 45 1 23 1 diff --git a/physical_properties/microstates/microstate_issues/SAMPL8_12/microstate_analysis.ipynb b/physical_properties/microstates/microstate_issues/SAMPL8_12/microstate_analysis.ipynb new file mode 100644 index 0000000..de89d23 --- /dev/null +++ b/physical_properties/microstates/microstate_issues/SAMPL8_12/microstate_analysis.ipynb @@ -0,0 +1,114 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "# Import required OpenEye modules\n", + "from openeye.oechem import * # For basic molecular operations and file I/O\n", + "from openeye.oedepict import * # For 2D depiction\n", + "from openeye.oeiupac import * # For IUPAC name generation\n", + "from openeye.oeomega import * # For 3D conformer generation\n", + "from openeye.oeshape import * # For shape analysis\n", + "from IPython.display import Image\n" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [], + "source": [ + "mol2_file_path = \"/Users/aakankschitnandkeolyar/Desktop/SAMPL8/physical_properties/microstates/SAMPL8-12_micro003.mol2\"" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [], + "source": [ + "mol_3d = OEMol()\n", + "ifs = oemolistream(mol2_file_path)\n", + "OEReadMolecule(ifs, mol_3d)\n", + "ifs.close()" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Total charge of the molecule: 0\n" + ] + } + ], + "source": [ + "# total_charge = sum(atom.GetFormalCharge() for atom in mol_3d.GetAtoms())\n", + "# total_charge = OENetCharge(mol_3d)\n", + "print(f\"Total charge of the molecule: {OENetCharge(mol_3d)}\")" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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", + "text/plain": [ + "" + ] + }, + "execution_count": 13, + "metadata": { + "image/png": { + "width": 200 + } + }, + "output_type": "execute_result" + } + ], + "source": [ + "OEPrepareDepiction(mol_3d)\n", + "OERenderMolecule(\"DepictMolSimple.png\", mol_3d)\n", + "Image('DepictMolSimple.png',width = 200)\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.11" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/physical_properties/microstates/microstate_issues/SAMPL8_12/molecule_visualization.png b/physical_properties/microstates/microstate_issues/SAMPL8_12/molecule_visualization.png new file mode 100644 index 0000000..eb25ee9 Binary files /dev/null and b/physical_properties/microstates/microstate_issues/SAMPL8_12/molecule_visualization.png differ diff --git a/physical_properties/microstates/microstate_issues/SAMPL8_14/COSMO_RS_extra001_c0.mol2 b/physical_properties/microstates/microstate_issues/SAMPL8_14/COSMO_RS_extra001_c0.mol2 new file mode 100755 index 0000000..2767b60 --- /dev/null +++ b/physical_properties/microstates/microstate_issues/SAMPL8_14/COSMO_RS_extra001_c0.mol2 @@ -0,0 +1,108 @@ +# Created by COSMOvis on Mon Aug 09 22:24:20 CEST 2021 +# +# + +# +# + +@MOLECULE +SAMPL8-14_extra001_c0 +44 45 +SMALL +USER_CHARGES + +@ATOM +1 C -2.115000 -2.982800 2.146300 C 0 XO 0.000000 +2 C -3.275300 -1.084400 1.228200 C 1 XO 0.000000 +3 C -3.120500 -3.621000 -1.193500 C 2 XO 0.000000 +4 C -3.229000 -2.463500 1.478000 C 3 XO 0.000000 +5 C -1.066000 -2.154100 2.559400 C 4 XO 0.000000 +6 C -2.256200 -0.199700 1.615800 C 5 XO 0.000000 +7 C -4.186200 -3.911700 -0.393400 C 6 XO 0.000000 +8 C -1.145900 -0.770800 2.286500 C 7 XO 0.000000 +9 C -5.177700 -4.788300 -0.975200 C 8 XO 0.000000 +10 C -3.998000 -4.962800 -2.952000 C 9 XO 0.000000 +11 C 0.132300 -2.713700 3.288000 C 10 XO 0.000000 +12 C -3.658400 1.675400 0.588200 C 11 XO 0.000000 +13 C -1.174700 1.752700 0.416600 C 12 XO 0.000000 +14 C -2.329000 2.115000 2.647900 C 13 XO 0.000000 +15 C -4.349100 -3.369300 1.012100 C 14 XO 0.000000 +16 C -2.351900 1.312700 1.322600 C 15 XO 0.000000 +17 N -3.022400 -4.137400 -2.457100 N 16 XO 0.000000 +18 N -5.065200 -5.288800 -2.224000 N 17 XO 0.000000 +19 N -6.266100 -5.141600 -0.278000 N 18 XO 0.000000 +20 N -3.861700 -5.444800 -4.195300 N 19 XO 1.000000 +21 O -0.120100 0.059400 2.687800 O 20 XO 0.000000 +22 H -2.056200 -4.053600 2.359300 H 21 XO 0.000000 +23 H -4.149600 -0.688500 0.711100 H 22 XO 0.000000 +24 H -2.301800 -2.975800 -0.883000 H 23 XO 0.000000 +25 H 0.033800 -3.798700 3.416900 H 24 XO 0.000000 +26 H 1.072100 -2.534400 2.738200 H 25 XO 0.000000 +27 H 0.248300 -2.273900 4.293400 H 26 XO 0.000000 +28 H -3.737500 1.172800 -0.387400 H 27 XO 0.000000 +29 H -4.550500 1.425800 1.182200 H 28 XO 0.000000 +30 H -3.674300 2.760000 0.405300 H 29 XO 0.000000 +31 H -1.204800 1.215600 -0.543500 H 30 XO 0.000000 +32 H -1.252500 2.830600 0.204800 H 31 XO 0.000000 +33 H -0.203900 1.563900 0.890300 H 32 XO 0.000000 +34 H -2.408100 3.191400 2.430100 H 33 XO 0.000000 +35 H -3.182500 1.834300 3.283800 H 34 XO 0.000000 +36 H -1.404600 1.943700 3.211800 H 35 XO 0.000000 +37 H -4.441500 -4.221800 1.707100 H 36 XO 0.000000 +38 H -5.307100 -2.823300 1.066600 H 37 XO 0.000000 +39 H -6.431000 -4.812600 0.667100 H 38 XO 0.000000 +40 H -6.956800 -5.758500 -0.697100 H 39 XO 0.000000 +41 H -4.584200 -6.051300 -4.569100 H 40 XO 0.000000 +42 H -3.066000 -5.217700 -4.782300 H 41 XO 0.000000 +43 H 0.565100 -0.473700 3.134900 H 42 XO 0.000000 +44 H -2.212700 -3.900400 -3.029100 H 43 XO 0.000000 + +@BOND +1 1 4 ar +2 1 5 ar +3 2 4 ar +4 2 6 ar +5 3 7 2 +6 3 17 1 +7 4 15 1 +8 5 8 ar +9 5 11 1 +10 6 8 ar +11 6 16 1 +12 7 9 1 +13 7 15 1 +14 8 21 1 +15 9 18 2 +16 9 19 1 +17 10 17 1 +18 10 18 1 +19 10 20 2 +20 12 16 1 +21 13 16 1 +22 14 16 1 +23 1 22 1 +24 2 23 1 +25 3 24 1 +26 11 25 1 +27 11 26 1 +28 11 27 1 +29 12 28 1 +30 12 29 1 +31 12 30 1 +32 13 31 1 +33 13 32 1 +34 13 33 1 +35 14 34 1 +36 14 35 1 +37 14 36 1 +38 15 37 1 +39 15 38 1 +40 17 44 1 +41 19 39 1 +42 19 40 1 +43 20 41 1 +44 20 42 1 +45 21 43 1 + +@TOTAL_CHARGE +1.0 diff --git a/physical_properties/microstates/microstate_issues/SAMPL8_14/EC_RISM_extra001.mol2 b/physical_properties/microstates/microstate_issues/SAMPL8_14/EC_RISM_extra001.mol2 new file mode 100644 index 0000000..bd7a1ac --- /dev/null +++ b/physical_properties/microstates/microstate_issues/SAMPL8_14/EC_RISM_extra001.mol2 @@ -0,0 +1,99 @@ +@MOLECULE +SAMPL8-14_extra001 + 45 46 0 0 0 +SMALL +GASTEIGER + +@ATOM + 1 C -3.1290 3.8045 -0.2162 C.3 1 LIG1 -0.0362 + 2 C -2.3209 2.5669 0.1674 C.ar 1 LIG1 -0.0085 + 3 C -1.0041 2.7370 0.5926 C.ar 1 LIG1 -0.0519 + 4 C -0.2310 1.6353 0.9492 C.ar 1 LIG1 -0.0423 + 5 C -0.7870 0.3563 0.8918 C.ar 1 LIG1 -0.0511 + 6 C -2.1119 0.1386 0.4681 C.ar 1 LIG1 -0.0001 + 7 C -2.8732 1.2762 0.1044 C.ar 1 LIG1 0.1234 + 8 O -4.1723 1.1690 -0.3207 O.3 1 LIG1 -0.5062 + 9 C -2.6963 -1.3093 0.4099 C.3 1 LIG1 -0.0092 + 10 C -1.6833 -2.4013 0.8525 C.3 1 LIG1 -0.0559 + 11 C -3.9119 -1.4460 1.3590 C.3 1 LIG1 -0.0559 + 12 C -3.1090 -1.6733 -1.0372 C.3 1 LIG1 -0.0559 + 13 C 1.2069 1.8242 1.4190 C.3 1 LIG1 0.0027 + 14 C 2.2434 1.1255 0.5363 C.2 1 LIG1 0.0374 + 15 C 3.1667 0.3185 1.1082 C.3 1 LIG1 0.0615 + 16 N 4.1187 -0.3079 0.3467 N.3 1 LIG1 -0.2497 + 17 C 4.1961 -0.1555 -0.9754 C.3 1 LIG1 0.2795 + 18 N 5.1297 -0.7626 -1.7018 N.3 1 LIG1 -0.2722 + 19 N 3.2855 0.6395 -1.5342 N.pl3 1 LIG1 -0.2013 + 20 C 2.3169 1.2719 -0.8573 C.2 1 LIG1 0.2569 + 21 N 1.4721 2.0147 -1.5622 N.pl3 1 LIG1 -0.2515 + 22 H -3.4566 3.7453 -1.2551 H 1 LIG1 0.0279 + 23 H -4.0188 3.8934 0.4086 H 1 LIG1 0.0279 + 24 H -2.5566 4.7266 -0.1038 H 1 LIG1 0.0279 + 25 H -0.5822 3.7322 0.6486 H 1 LIG1 0.0624 + 26 H -0.1532 -0.4665 1.1849 H 1 LIG1 0.0624 + 27 H -4.5255 2.0444 -0.5186 H 1 LIG1 0.2922 + 28 H -1.3558 -2.2608 1.8837 H 1 LIG1 0.0238 + 29 H -2.1178 -3.4010 0.8011 H 1 LIG1 0.0238 + 30 H -0.7968 -2.4178 0.2167 H 1 LIG1 0.0238 + 31 H -4.7551 -0.8258 1.0594 H 1 LIG1 0.0238 + 32 H -4.2860 -2.4703 1.3904 H 1 LIG1 0.0238 + 33 H -3.6519 -1.1661 2.3808 H 1 LIG1 0.0238 + 34 H -2.2746 -1.5555 -1.7300 H 1 LIG1 0.0238 + 35 H -3.4469 -2.7079 -1.1123 H 1 LIG1 0.0238 + 36 H -3.9276 -1.0607 -1.4111 H 1 LIG1 0.0238 + 37 H 1.4579 2.8866 1.4443 H 1 LIG1 0.0361 + 38 H 1.2758 1.4905 2.4568 H 1 LIG1 0.0361 + 39 H 3.2294 0.1184 2.1708 H 1 LIG1 0.0530 + 40 H 4.8004 -0.9062 0.7894 H 1 LIG1 0.1281 + 41 H 5.1828 -0.6420 -2.7026 H 1 LIG1 0.1237 + 42 H 5.8234 -1.3662 -1.2851 H 1 LIG1 0.1237 + 43 H 3.3233 0.7664 -2.5325 H 1 LIG1 0.2945 + 44 H 0.6794 2.4256 -1.0918 H 1 LIG1 0.2881 + 45 H 1.5513 2.1390 -2.5593 H 1 LIG1 0.2881 +@BOND + 1 41 18 1 + 2 45 21 1 + 3 43 19 1 + 4 34 12 1 + 5 18 42 1 + 6 18 17 1 + 7 21 44 1 + 8 21 20 1 + 9 19 17 1 + 10 19 20 1 + 11 36 12 1 + 12 22 1 1 + 13 35 12 1 + 14 12 9 1 + 15 17 16 1 + 16 20 14 2 + 17 27 8 1 + 18 8 7 1 + 19 1 24 1 + 20 1 2 1 + 21 1 23 1 + 22 7 2 ar + 23 7 6 ar + 24 2 3 ar + 25 30 10 1 + 26 16 40 1 + 27 16 15 1 + 28 9 6 1 + 29 9 10 1 + 30 9 11 1 + 31 6 5 ar + 32 14 15 1 + 33 14 13 1 + 34 3 25 1 + 35 3 4 ar + 36 29 10 1 + 37 10 28 1 + 38 5 4 ar + 39 5 26 1 + 40 4 13 1 + 41 31 11 1 + 42 15 39 1 + 43 11 32 1 + 44 11 33 1 + 45 13 37 1 + 46 13 38 1 diff --git a/physical_properties/microstates/microstate_issues/mymolecule.mol2 b/physical_properties/microstates/microstate_issues/mymolecule.mol2 new file mode 100644 index 0000000..4e05a6b --- /dev/null +++ b/physical_properties/microstates/microstate_issues/mymolecule.mol2 @@ -0,0 +1,51 @@ +@MOLECULE +***** + 21 22 0 0 0 +SMALL +NO_CHARGES + +@ATOM + 1 C1 -0.4966 -2.0341 0.4940 C.ar 1 <0> 0.0000 + 2 C2 -0.0479 -3.3542 0.5448 C.ar 1 <0> 0.0000 + 3 C3 3.4207 -2.9899 -0.7267 C.ar 1 <0> 0.0000 + 4 C4 3.8693 -4.3100 -0.6758 C.ar 1 <0> 0.0000 + 5 C5 0.3500 -1.0275 0.0392 C.ar 1 <0> 0.0000 + 6 C6 1.7243 -5.0072 0.1848 C.ar 1 <0> 0.0000 + 7 C7 1.2560 -3.6839 0.1403 C.ar 1 <0> 0.0000 + 8 C8 2.1168 -2.6602 -0.3222 C.ar 1 <0> 0.0000 + 9 C9 3.0228 -5.3167 -0.2210 C.ar 1 <0> 0.0000 + 10 C10 1.6484 -1.3369 -0.3665 C.ar 1 <0> 0.0000 + 11 C11 3.5042 -6.7273 -0.1668 C.3 1 <0> 0.0000 + 12 Cl1 2.6181 -0.0066 -0.9155 Cl 1 <0> 0.0000 + 13 H1 -1.5075 -1.7929 0.8097 H 1 <0> 0.0000 + 14 H2 -0.7273 -4.1251 0.9026 H 1 <0> 0.0000 + 15 H3 4.1207 -2.2422 -1.0895 H 1 <0> 0.0000 + 16 H4 4.8822 -4.5432 -0.9933 H 1 <0> 0.0000 + 17 H5 -0.0191 -0.0052 0.0084 H 1 <0> 0.0000 + 18 H6 1.0718 -5.8045 0.5367 H 1 <0> 0.0000 + 19 H7 3.9631 -6.9370 0.8071 H 1 <0> 0.0000 + 20 H8 2.6803 -7.4357 -0.3230 H 1 <0> 0.0000 + 21 H9 4.2463 -6.9253 -0.9512 H 1 <0> 0.0000 +@BOND + 1 1 2 ar + 2 1 5 ar + 3 2 7 ar + 4 3 4 ar + 5 3 8 ar + 6 4 9 ar + 7 5 10 ar + 8 6 7 ar + 9 6 9 ar + 10 7 8 ar + 11 8 10 ar + 12 9 11 1 + 13 10 12 1 + 14 1 13 1 + 15 2 14 1 + 16 3 15 1 + 17 4 16 1 + 18 5 17 1 + 19 6 18 1 + 20 11 19 1 + 21 11 20 1 + 22 11 21 1 diff --git a/physical_properties/pKa/README.md b/physical_properties/pKa/README.md index f4dc671..26093fe 100644 --- a/physical_properties/pKa/README.md +++ b/physical_properties/pKa/README.md @@ -9,4 +9,4 @@ - [`relative_microstate_free_energy_predictions`](relative_microstate_free_energy_predictions)-A folder that contains the microstate predictions submitted by the participants. - [`SAMPL8-pKa-user-map.csv`](SAMPL8-pKa-user-map.csv)-A .csv file that contains a list of participants Experimental data collection is described in this [paper](https://link.springer.com/article/10.1007/s10822-021-00427-0) in JCAMD or the pre-print which is available [here](https://chemrxiv.org/engage/chemrxiv/article-details/61547c46b19c7e6aade3c2b1) -- [`experimental_pKas.csv`](experimental_pKas.csv)- A .csv file that contains all of the experimental pKa values provided by GSK. +- [`experimental_pKas.csv`](experimental_pKas.csv)- A .csv file that contains all of the experimental pKa values provided by GSK. This file has been modified to remove the second pKa value (11.44 associated with formal charge of -1) since this formal charge state was not account for in the provided list of microstates. diff --git a/physical_properties/pKa/experimental_pKas.csv b/physical_properties/pKa/experimental_pKas.csv index 1861e00..217c22b 100644 --- a/physical_properties/pKa/experimental_pKas.csv +++ b/physical_properties/pKa/experimental_pKas.csv @@ -17,9 +17,8 @@ SAMPL8-16, 5.10, 0.10 SAMPL8-17, 6.58, 0.05 SAMPL8-18, 2.72, 0.09 SAMPL8-19, 4.93, 0.24 -SAMPL8-19,6.99,0.22 +SAMPL8-19, 6.99, 0.22 SAMPL8-20, 2.44, 0.10 -SAMPL8-20, 11.44, 0.16 SAMPL8-21, 5.38, 0.24 SAMPL8-22, 3.36, 0.09 SAMPL8-23, 2.65, 0.05 diff --git a/physical_properties/pKa/macrostate_analysis/README.md b/physical_properties/pKa/macrostate_analysis/README.md index e4ac15e..499ea48 100644 --- a/physical_properties/pKa/macrostate_analysis/README.md +++ b/physical_properties/pKa/macrostate_analysis/README.md @@ -42,5 +42,5 @@ The [selected transitions](selected_transitions.csv) were compiled based on the - [`pKa_macrostate_analysis_selected_transitions.py`](pKa_macrostate_analysis_popular_transitions.py)- Script used to generate performance statistics for macro-pKa analysis using selected transition states. - [`functions_pKa_macrostate_analysis.py`](functions_pKa_macrostate_analysis.py)- Script that contains functions used in the estimation of performance statistics for macrostate analysis. - [`popular_transitions_analysis/`](popular_transitions_analysis/)- This directory contains plots associated with analysis of all and ranked methods using popular transition states. -- [`selected_transitions_analysis/`](selected_transitions_analysis/)- This directory contains plots associated with analysis of all and ranked methods using selected transition states. +- [`selected_transitions_analysis/`](selected_transitions_analysis/)- This directory contains plots associated with analysis of all and ranked methods using selected transition states. Note that this file has been modified to a pKa value of SAMPL8-20 (Specifically 11.44 associated with a formal charge of -1) since this formal charge state was not account for in the provided list of microstates. diff --git a/physical_properties/pKa/macrostate_analysis/check_microstate_charges.ipynb b/physical_properties/pKa/macrostate_analysis/check_microstate_charges.ipynb new file mode 100644 index 0000000..43abecb --- /dev/null +++ b/physical_properties/pKa/macrostate_analysis/check_microstate_charges.ipynb @@ -0,0 +1,737 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [], + "source": [ + "from functions_pKa_macrostate_analysis import getdataset\n", + "from pKa_macrostate_analysis_selected_transitions import load_submissions" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [], + "source": [ + "# Load Experimental Data \n", + "with open(EXPERIMENTAL_DATA_FILE_PATH, 'r') as f:\n", + " # experimental_data = pd.read_json(f, orient='index')\n", + " names = ('Molecule ID', 'pKa mean', 'pKa SEM')\n", + " experimental_data = pd.read_csv(f, names=names, skiprows=1)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "file_name: \n", + " pKa-3DS-1\n", + "\n", + "file_name: \n", + " pKa-RobertRaddi_AdaBoost\n", + "\n", + "file_name: \n", + " pKa-3DS-2\n", + "\n", + "file_name: \n", + " pKa-3DS-3\n", + "\n", + "file_name: \n", + " pKa_SabatinoRodriguezPaluch_uESE\n", + "\n", + "file_name: \n", + " pKa-RobertRaddi_DeepGP\n", + "\n", + "file_name: \n", + " pKa-ZhiyiWu-1\n", + "\n", + "file_name: \n", + " pKa-RobertRaddi_RF\n", + "\n", + "file_name: \n", + " PKA_ECRISM\n", + "\n", + "file_name: \n", + " pKa-RobertRaddi_XGBoost\n", + "\n", + "file_name: \n", + " pKa_Chemaxon\n", + "\n", + "file_name: \n", + " pKa_SabatinoRodriguezPaluch_uESE_extra\n", + "\n" + ] + } + ], + "source": [ + "# Load the data from the microstate pKa submissions\n", + "microstates_df = load_submissions(pKa_SUBMISSIONS_DIR_PATH,USER_MAP_FILE_PATH)" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [], + "source": [ + "# Compile into a Dataset of pKa values\n", + "test_microstates_df = microstates_df[0:1]\n", + "pKa_dt = getdataset(test_microstates_df, experimental_data, output_PATH_DIR)" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "data": { + "application/vnd.microsoft.datawrangler.viewer.v0+json": { + "columns": [ + { + "name": "Molecule ID", + "rawType": "object", + "type": "string" + }, + { + "name": "ID tag", + "rawType": "object", + "type": "string" + }, + { + "name": "total charge", + "rawType": "int64", + "type": "integer" + }, + { + "name": "pKa mean", + "rawType": "float64", + "type": "float" + }, + { + "name": "pKa SEM", + "rawType": "float64", + "type": "float" + }, + { + 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ID tagtotal chargepKa meanpKa SEMpKa model uncertainty
Molecule ID
SAMPL8-1_micro000SAMPL8-1_extra00111.100.11.4
SAMPL8-1_micro000SAMPL8-1_extra00211.120.11.4
SAMPL8-1_micro000SAMPL8-1_micro00000.000.11.4
SAMPL8-1_micro000SAMPL8-1_micro007015.420.11.4
SAMPL8-1_micro000SAMPL8-1_micro010014.070.11.4
..................
SAMPL8-9_micro002SAMPL8-9_micro0021-10.600.11.4
SAMPL8-9_micro002SAMPL8-9_micro0041-0.110.11.4
SAMPL8-9_micro002SAMPL8-9_micro00000.000.11.4
SAMPL8-9_micro002SAMPL8-9_micro00302.200.11.4
SAMPL8-9_micro002SAMPL8-9_micro001-116.750.11.4
\n", + "

203 rows × 5 columns

\n", + "
" + ], + "text/plain": [ + " ID tag total charge pKa mean pKa SEM \\\n", + "Molecule ID \n", + "SAMPL8-1_micro000 SAMPL8-1_extra001 1 1.10 0.1 \n", + "SAMPL8-1_micro000 SAMPL8-1_extra002 1 1.12 0.1 \n", + "SAMPL8-1_micro000 SAMPL8-1_micro000 0 0.00 0.1 \n", + "SAMPL8-1_micro000 SAMPL8-1_micro007 0 15.42 0.1 \n", + "SAMPL8-1_micro000 SAMPL8-1_micro010 0 14.07 0.1 \n", + "... ... ... ... ... \n", + "SAMPL8-9_micro002 SAMPL8-9_micro002 1 -10.60 0.1 \n", + "SAMPL8-9_micro002 SAMPL8-9_micro004 1 -0.11 0.1 \n", + "SAMPL8-9_micro002 SAMPL8-9_micro000 0 0.00 0.1 \n", + "SAMPL8-9_micro002 SAMPL8-9_micro003 0 2.20 0.1 \n", + "SAMPL8-9_micro002 SAMPL8-9_micro001 -1 16.75 0.1 \n", + "\n", + " pKa model uncertainty \n", + "Molecule ID \n", + "SAMPL8-1_micro000 1.4 \n", + "SAMPL8-1_micro000 1.4 \n", + "SAMPL8-1_micro000 1.4 \n", + "SAMPL8-1_micro000 1.4 \n", + "SAMPL8-1_micro000 1.4 \n", + "... ... \n", + "SAMPL8-9_micro002 1.4 \n", + "SAMPL8-9_micro002 1.4 \n", + "SAMPL8-9_micro002 1.4 \n", + "SAMPL8-9_micro002 1.4 \n", + "SAMPL8-9_micro002 1.4 \n", + "\n", + "[203 rows x 5 columns]" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "microstates_df[0].data" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "sampl8_old", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.11.11" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/physical_properties/pKa/macrostate_analysis/functions_pKa_macrostate_analysis.py b/physical_properties/pKa/macrostate_analysis/functions_pKa_macrostate_analysis.py index 0a9c306..d05b48d 100644 --- a/physical_properties/pKa/macrostate_analysis/functions_pKa_macrostate_analysis.py +++ b/physical_properties/pKa/macrostate_analysis/functions_pKa_macrostate_analysis.py @@ -137,7 +137,7 @@ def getdataset(submission_collection,experimental_data,output_directory): temp_df = pd.DataFrame({"pH":pH_microstates, "pop_charge":n_frac, "formal_charge":microstates}) - charge_dist_df = charge_dist_df.append({"pH":pH,"pop_charge":pop_charge(pH,charges,mol_details),"formal_charge":charges},ignore_index = True) + charge_dist_df = pd.concat([charge_dist_df, pd.DataFrame([{"pH":pH,"pop_charge":pop_charge(pH,charges,mol_details),"formal_charge":charges}])], ignore_index=True) # Experimental Macro pKas exp_pKas = experimental_data.loc[experimental_data.index==names.split('_')[0],'pKa mean'].values # Macrostate Calculation and Absolute Error Computation @@ -214,7 +214,12 @@ def getpopulartransitions(data, experimental_data): return popular_transitions -def getpopulartransitionsdata(popular_transitions, data, experimental_data, output_directory): +def getpopulartransitionsdata(popular_transitions, data, experimental_data, output_directory, file_name): + """ + This function is used to get the data for the popular transition states for each submission. + It takes in the popular transitions, the data, the experimental data, the output directory, and the file name. + It returns the pKa data for the popular transition states. + """ pKa_dt_pop_transition_states = pd.DataFrame(columns=['Submission','Method Name','Method Type','Molecule ID','Formal Charge','Predicted pKa','Experimental pKa','Absolute Error']) for submission in data.loc[:,'Submission'].unique(): submission_data = data.loc[data.loc[:,'Submission']==submission,] #Slice off data for that particular submission @@ -222,46 +227,34 @@ def getpopulartransitionsdata(popular_transitions, data, experimental_data, outp if idx in popular_transitions.loc[:,"Molecule ID"].tolist(): popular_transitions_mol = popular_transitions.loc[(popular_transitions.loc[:,'Experimental pKa']==row['pKa mean']) & (popular_transitions.loc[:,"Molecule ID"]==idx),] if row['pKa mean'] in submission_data.loc[:,"Experimental pKa"].tolist() and idx in submission_data.loc[:,"Molecule ID"].tolist(): - df_temp1 = submission_data.loc[(submission_data.loc[:,'Experimental pKa']==row['pKa mean']) & (submission_data.loc[:,"Molecule ID"]==idx),] - # df_temp2 = df_temp1.loc[df_temp1.loc[:,'Formal Charge']==popular_transitions_mol.loc[:,"Formal Charge"].values.item(),] - if popular_transitions_mol.loc[:,"Formal Charge"].values.item() in df_temp1.loc[:,'Formal Charge'].tolist(): + df_temp1 = submission_data.loc[(submission_data.loc[:,'Experimental pKa']==row['pKa mean']) & (submission_data.loc[:,"Molecule ID"]==idx),] # Slide off data for the same pKa and molecule + if popular_transitions_mol.loc[:,"Formal Charge"].values.item() in df_temp1.loc[:,'Formal Charge'].tolist(): # Only those molecules in a submission with matching formal charge will be used for analysis and computing statistics df_temp2 = df_temp1.loc[df_temp1.loc[:,'Formal Charge']==popular_transitions_mol.loc[:,"Formal Charge"].values.item(),] - else: - df_temp1 = df_temp1.reset_index() - df_temp1 = df_temp1.drop(['index'],axis=1) - df_temp2 = df_temp1.loc[0,].to_frame().T - df_temp2.loc[:,'Formal Charge'] = popular_transitions_mol.loc[:,"Formal Charge"].values.item() - if abs(df_temp2.loc[:,'Experimental pKa'].values-14) > abs(df_temp2.loc[:,'Experimental pKa'].values-0): - df_temp2.loc[:,'Predicted pKa'] = 14 - df_temp2.loc[:,'Absolute Error'] = abs(df_temp2.loc[:,'Experimental pKa']-14) - else: - df_temp2.loc[:,'Predicted pKa']=0 - df_temp2.loc[:,'Absolute Error'] = abs(df_temp2.loc[:,'Experimental pKa']-0) - - pKa_dt_pop_transition_states = pd.concat([pKa_dt_pop_transition_states,df_temp2],ignore_index=True) - + pKa_dt_pop_transition_states = pd.concat([pKa_dt_pop_transition_states,df_temp2],ignore_index=True) if not os.path.exists(output_directory): os.makedirs(output_directory) - pKa_dt_pop_transition_states.to_csv(output_directory+"popular_transitions_pKa_data.csv") - plt.figure(figsize=(15,10)) + pKa_dt_pop_transition_states.to_csv(output_directory+file_name) + plt.figure(figsize=(17,5)) with sns.axes_style("darkgrid"): sns.barplot(x='Method Name',y='Absolute Error',hue="Method Type",palette="Set1",data=pKa_dt_pop_transition_states,dodge=False) - plt.xlabel("Method", fontsize=14) - plt.ylabel("Absolute Error", fontsize=14) - plt.title("Absolute Error based on method",fontsize=16) + plt.xlabel("Method", fontsize=18) + plt.ylabel("Absolute Error", fontsize=18) + plt.title("Absolute error based on method",fontsize=18) plt.gcf().subplots_adjust(bottom=0.25) - plt.xticks(rotation=90) + plt.yticks(fontsize=12) + plt.xticks(rotation=60, fontsize=18) plt.savefig(output_directory+"abs_error_bymethod_plot"+".pdf", bbox_inches="tight") - plt.figure(figsize=(15,10)) + plt.figure(figsize=(17,5)) sns.barplot(x='Molecule ID',y='Absolute Error',data=pKa_dt_pop_transition_states,dodge=False) - plt.xlabel("Method", fontsize=14) - plt.ylabel("Absolute Error", fontsize=14) - plt.title("Absolute Error for each Molecule",fontsize=16) + plt.xlabel("Method", fontsize=18) + plt.ylabel("Absolute Error", fontsize=18) + plt.title("Absolute error for each molecule",fontsize=18) plt.gcf().subplots_adjust(bottom=0.25) - plt.xticks(rotation=90) + plt.yticks(fontsize=12) + plt.xticks(rotation=60, fontsize=18) plt.savefig(output_directory+"abs_error_bymol_plot"+".pdf", bbox_inches="tight") return pKa_dt_pop_transition_states @@ -335,7 +328,7 @@ def getpKaErrorstats(data,output_directory): error = mol_dt.loc[:,'Predicted pKa'].astype(float)-mol_dt.loc[:,'Experimental pKa'].astype(float) me = error.mean() mae = np.array(mol_dt.loc[:,"Absolute Error"]).mean() - rmse = np.sqrt(error**2).mean() + rmse = np.sqrt(np.mean(error**2)) df_temp = pd.DataFrame({"Molecule ID": mol_names,"Mean Error":[me],"Mean Absolute Error":[mae],"Root Mean Squared Error":[rmse]}) perform_stats_mols = pd.concat([perform_stats_mols,df_temp],ignore_index=True) @@ -348,7 +341,7 @@ def getpKaErrorstats(data,output_directory): sns.barplot(x="Molecule ID",y="Root Mean Squared Error",data=perform_stats_mols) plt.xlabel("Molecule ID",fontsize=14) plt.ylabel("RMSE",fontsize=14) - plt.title("RMSE across all Molecules",fontsize=16) + plt.title("RMSE across all molecules",fontsize=16) plt.xticks(rotation=90) plt.subplots_adjust(bottom=0.15) plt.savefig(output_directory+"rmse_plot"+".pdf", bbox_inches="tight") @@ -357,7 +350,7 @@ def getpKaErrorstats(data,output_directory): sns.barplot(x="Molecule ID",y="Mean Error",data=perform_stats_mols) plt.xlabel("Molecule ID",fontsize=14) plt.ylabel("Mean Error",fontsize=14) - plt.title("Mean Error across all Molecules",fontsize=16) + plt.title("Mean error across all molecules",fontsize=16) plt.xticks(rotation=90) plt.subplots_adjust(bottom=0.15) plt.savefig(output_directory+"mean_error_plot"+".pdf", bbox_inches="tight") @@ -366,7 +359,7 @@ def getpKaErrorstats(data,output_directory): sns.barplot(x="Molecule ID",y="Mean Absolute Error",data=perform_stats_mols) plt.xlabel("Molecule ID",fontsize=14) plt.ylabel("Mean Absolute Error",fontsize=14) - plt.title("Mean Absolute Error across all Molecules",fontsize=16) + plt.title("Mean absolute error across all molecules",fontsize=16) plt.xticks(rotation=90) plt.subplots_adjust(bottom=0.15) plt.savefig(output_directory+"mean_abs_error_plot"+".pdf", bbox_inches="tight") diff --git a/physical_properties/pKa/macrostate_analysis/pKa_macrostate_analysis_popular_transitions.py b/physical_properties/pKa/macrostate_analysis/pKa_macrostate_analysis_popular_transitions.py index 601bba0..d3e1ec2 100644 --- a/physical_properties/pKa/macrostate_analysis/pKa_macrostate_analysis_popular_transitions.py +++ b/physical_properties/pKa/macrostate_analysis/pKa_macrostate_analysis_popular_transitions.py @@ -25,13 +25,13 @@ # ============================================================================= # CONSTANTS # ============================================================================= -pKa_SUBMISSIONS_DIR_PATH = '../submissions' -EXPERIMENTAL_DATA_FILE_PATH = '../experimental_pKas.csv' +pKa_SUBMISSIONS_DIR_PATH = '/Users/aakankschitnandkeolyar/Desktop/SAMPL8/physical_properties/pKa/submissions' +EXPERIMENTAL_DATA_FILE_PATH = '/Users/aakankschitnandkeolyar/Desktop/SAMPL8/physical_properties/pKa/experimental_pKas.csv' USER_MAP_FILE_PATH = '../SAMPL8-pKa-user-map.csv' -output_PATH_DIR = "popular_transitions_analysis/analysis_outputs_all/" +output_PATH_DIR = "/Users/aakankschitnandkeolyar/Desktop/SAMPL8/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/" if not os.path.exists(output_PATH_DIR): os.makedirs(output_PATH_DIR) -output_PATH_DIR_ranked = "popular_transitions_analysis/analysis_outputs_ranked/" +output_PATH_DIR_ranked = "/Users/aakankschitnandkeolyar/Desktop/SAMPL8/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/" if not os.path.exists(output_PATH_DIR_ranked): os.makedirs(output_PATH_DIR_ranked) @@ -263,8 +263,10 @@ def load_ranked_submissions(directory_path, user_map): ## Compute Popular Transition States across all submission in pKaCollection- popular_transitions = getpopulartransitions(pKa_dt,experimental_data) + + pKa_data_file_name = "popular_transitions_pKa_data.csv" - popular_transitions_pKa_dt = getpopulartransitionsdata(popular_transitions,pKa_dt,experimental_data,output_PATH_DIR) + popular_transitions_pKa_dt = getpopulartransitionsdata(popular_transitions,pKa_dt,experimental_data,output_PATH_DIR, pKa_data_file_name) ## Correlation Statistics Corr_stats = getpKaCorrelationstats(popular_transitions_pKa_dt,output_PATH_DIR) @@ -279,7 +281,7 @@ def load_ranked_submissions(directory_path, user_map): ## Compute Popular Transition States across all ranked submissions popular_transitions_ranked = getpopulartransitions(pKa_dt_ranked,experimental_data) - popular_transitions_pKa_dt_ranked = getpopulartransitionsdata(popular_transitions_ranked,pKa_dt_ranked,experimental_data,output_PATH_DIR_ranked) + popular_transitions_pKa_dt_ranked = getpopulartransitionsdata(popular_transitions_ranked,pKa_dt_ranked,experimental_data,output_PATH_DIR_ranked, pKa_data_file_name) ## Correlation Statistics for each submission Corr_stats_ranked = getpKaCorrelationstats(popular_transitions_pKa_dt_ranked,output_PATH_DIR_ranked) diff --git a/physical_properties/pKa/macrostate_analysis/pKa_macrostate_analysis_selected_transitions.py b/physical_properties/pKa/macrostate_analysis/pKa_macrostate_analysis_selected_transitions.py index fcdeaa6..745e524 100644 --- a/physical_properties/pKa/macrostate_analysis/pKa_macrostate_analysis_selected_transitions.py +++ b/physical_properties/pKa/macrostate_analysis/pKa_macrostate_analysis_selected_transitions.py @@ -25,14 +25,14 @@ # ============================================================================= # CONSTANTS # ============================================================================= -pKa_SUBMISSIONS_DIR_PATH = '../submissions' -EXPERIMENTAL_DATA_FILE_PATH = '../experimental_pKas.csv' +pKa_SUBMISSIONS_DIR_PATH = '/Users/aakankschitnandkeolyar/Desktop/SAMPL8/physical_properties/pKa/submissions' +EXPERIMENTAL_DATA_FILE_PATH = '/Users/aakankschitnandkeolyar/Desktop/SAMPL8/physical_properties/pKa/experimental_pKas.csv' USER_MAP_FILE_PATH = '../SAMPL8-pKa-user-map.csv' -SELECTED_TRANSITIONS_DATA_FILE = './selected_transitions.csv' -output_PATH_DIR = "selected_transitions_analysis/analysis_outputs_all/" +SELECTED_TRANSITIONS_DATA_FILE = '/Users/aakankschitnandkeolyar/Desktop/SAMPL8/physical_properties/pKa/macrostate_analysis/selected_transitions.csv' +output_PATH_DIR = "/Users/aakankschitnandkeolyar/Desktop/SAMPL8/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/" if not os.path.exists(output_PATH_DIR): os.makedirs(output_PATH_DIR) -output_PATH_DIR_ranked = "selected_transitions_analysis/analysis_outputs_ranked/" +output_PATH_DIR_ranked = "/Users/aakankschitnandkeolyar/Desktop/SAMPL8/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/" if not os.path.exists(output_PATH_DIR_ranked): os.makedirs(output_PATH_DIR_ranked) @@ -268,8 +268,10 @@ def load_ranked_submissions(directory_path, user_map): ## Compute Selected Transition States across all submission in pKaCollection- # Note that while I am using the getpopulartransitionsdata function I am using the selected transitions .csv file as an input hence the analysis is performed using the selected transitions + + pKa_data_file_name = "selected_transitions_pKa_data.csv" - selected_transitions_pKa_dt = getpopulartransitionsdata(selected_transitions, pKa_dt, experimental_data, output_PATH_DIR) + selected_transitions_pKa_dt = getpopulartransitionsdata(selected_transitions, pKa_dt, experimental_data, output_PATH_DIR, pKa_data_file_name) ## Correlation Statistics Corr_stats = getpKaCorrelationstats(selected_transitions_pKa_dt,output_PATH_DIR) @@ -283,7 +285,7 @@ def load_ranked_submissions(directory_path, user_map): ## Compute Selected Transition States across all ranked submissions # Similar to the above Note regarding the function - selected_transitions_pKa_dt_ranked = getpopulartransitionsdata(selected_transitions,pKa_dt_ranked,experimental_data,output_PATH_DIR_ranked) + selected_transitions_pKa_dt_ranked = getpopulartransitionsdata(selected_transitions,pKa_dt_ranked,experimental_data,output_PATH_DIR_ranked, pKa_data_file_name) ## Correlation Statistics for each submission Corr_stats_ranked = getpKaCorrelationstats(selected_transitions_pKa_dt_ranked,output_PATH_DIR_ranked) diff --git a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/Correlation_Plots/Correlation_statistics.csv b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/Correlation_Plots/Correlation_statistics.csv index 9d5e6bf..16056fb 100644 --- a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/Correlation_Plots/Correlation_statistics.csv +++ b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/Correlation_Plots/Correlation_statistics.csv @@ -1,13 +1,13 @@ ,Submission,R-squared,Slope,Kendall Tau -0,pKa-3DS-1,0.5245860054478703,0.9207053521258916,0.40536070267724306 -1,pKa-RobertRaddi_AdaBoost,-0.08533162521237111,-0.12980000635577701,0.08754407248840759 -2,pKa-3DS-2,0.5059034081864056,1.0550304661576377,0.375841042307218 -3,pKa-3DS-3,0.5089782608344262,0.8591364921378156,0.3785599950622187 -4,pKa_SabatinoRodriguezPaluch_uESE,0.13251748438257538,0.3389750424841242,0.2094702182271488 -5,pKa-RobertRaddi_DeepGP,-0.09848107595233223,-0.14454850544782252,0.02352971085197877 -6,pKa-ZhiyiWu-1,0.1437306658667328,0.3364382103959766,0.210350877437666 -7,pKa-RobertRaddi_RF,-0.12254975074382217,-0.18347474509688025,-0.0033500884518780413 -8,PKA_ECRISM,0.3190251409344672,0.769303435736348,0.36120401337792646 -9,pKa-RobertRaddi_XGBoost,-0.05778409936421786,-0.09050537653053457,0.08695652173913043 -10,pKa_Chemaxon,0.26281123110470545,0.5193753572304938,0.32545364836392554 -11,pKa_SabatinoRodriguezPaluch_uESE_extra,0.28483349687259574,0.8803416494971519,0.30588624107572404 +0,pKa-RobertRaddi_AdaBoost_modified,0.3498585065537494,0.5425145377722311,0.27147060556360336 +1,pKa_SabatinoRodriguezPaluch_uESE_modified,0.4583391862444568,1.3693137448072297,0.3770893794462222 +2,pKa-ZhiyiWu-1_modified,0.5114112317885932,1.3965268554265962,0.3992094861660079 +3,pKa-3DS-1_modified,0.5318524369412801,1.1208114543371857,0.3970862689350704 +4,PKA_ECRISM_modified,0.5872854620820575,1.665426102465623,0.46545454545454534 +5,pKa-RobertRaddi_XGBoost_modified,0.3649503280932059,0.589025668366932,0.2613866510869666 +6,pKa_SabatinoRodriguezPaluch_uESE_extra_modified,0.489094276263061,1.8071870371515906,0.43062200956937796 +7,pKa_Chemaxon_modified,0.7270883000876077,1.2417536967452814,0.6207093079955922 +8,pKa-3DS-3_modified,0.5135221256370863,1.0410442705333236,0.36794232259121196 +9,pKa-3DS-2_modified,0.5105299890758485,1.2789669751264348,0.36496593430090596 +10,pKa-RobertRaddi_DeepGP_modified,0.3726977022917608,0.5497191866348876,0.19522532113522006 +11,pKa-RobertRaddi_RF_modified,0.2832078393928553,0.4235913679909584,0.16269969372271226 diff --git a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/Correlation_Plots/PKA_ECRISMCorr_plot.pdf 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Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/Correlation_Plots/pKa_SabatinoRodriguezPaluch_uESE_modifiedCorr_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/Error_statistics.csv b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/Error_statistics.csv index f1b9579..8307d15 100644 --- a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/Error_statistics.csv +++ b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/Error_statistics.csv @@ -1,22 +1,22 @@ ,Molecule ID,Mean Error,Mean Absolute Error,Root Mean Squared Error -0,SAMPL8-1,1.9208333333332905,5.195833333333364,5.195833333333364 -1,SAMPL8-2,1.2316666666665932,2.188333333333303,2.1883333333333024 -2,SAMPL8-3,0.7249999999999299,1.391666666666639,1.391666666666639 -3,SAMPL8-4,-0.9116666666667368,2.8100000000000267,2.8100000000000267 -4,SAMPL8-5,-0.45333333333339887,2.053333333333337,2.053333333333337 -5,SAMPL8-6,-1.1783333333333972,1.8150000000000162,1.8150000000000162 -6,SAMPL8-7,4.578333333333258,4.849999999999936,4.849999999999936 -7,SAMPL8-8,0.7283333333332679,1.7316666666666396,1.7316666666666396 -8,SAMPL8-9,5.078333333333258,5.4416666666666025,5.4416666666666025 -9,SAMPL8-10,-0.5850000000000786,1.326666666666675,1.326666666666675 -10,SAMPL8-12,7.9866666666665855,7.9866666666665855,7.9866666666665855 -11,SAMPL8-14,2.396666666666579,3.153333333333269,3.15333333333327 -12,SAMPL8-15,1.4183333333332657,2.3283333333333043,2.3283333333333043 -13,SAMPL8-16,0.5999999999999268,1.5999999999999825,1.5999999999999825 -14,SAMPL8-17,4.069999999999909,5.239999999999955,5.239999999999956 -15,SAMPL8-18,7.321666666666586,7.321666666666586,7.321666666666586 -16,SAMPL8-19,0.439999999999924,1.6641666666666544,1.6641666666666548 -17,SAMPL8-20,-3.206666666666715,5.350000000000005,5.350000000000005 -18,SAMPL8-21,3.2699999999999165,4.543333333333281,4.543333333333281 -19,SAMPL8-22,8.63166666666658,8.63166666666658,8.63166666666658 -20,SAMPL8-23,0.16083333333325903,1.4541666666666613,1.4541666666666615 +0,SAMPL8-1,-2.007058823529473,2.6164705882353365,4.116789154326051 +1,SAMPL8-2,1.2316666666665932,2.188333333333303,2.86637401606974 +2,SAMPL8-3,0.7249999999999299,1.391666666666639,1.7066048165875665 +3,SAMPL8-4,-0.9116666666667368,2.8100000000000267,3.146993274010405 +4,SAMPL8-5,-0.45333333333339887,2.0533333333333377,2.512846990964634 +5,SAMPL8-6,-1.1783333333333972,1.8150000000000162,2.4040036050999283 +6,SAMPL8-7,4.019999999999909,4.345999999999924,5.270948681214719 +7,SAMPL8-8,0.7283333333332679,1.7316666666666396,1.8707128765971943 +8,SAMPL8-9,4.509999999999908,4.9459999999999225,5.630719314616837 +9,SAMPL8-10,-0.5850000000000786,1.3266666666666753,1.5239531926320478 +10,SAMPL8-12,8.179999999999902,8.179999999999902,8.364018173103066 +11,SAMPL8-14,2.3966666666665795,3.15333333333327,3.991394910721419 +12,SAMPL8-15,1.4183333333332657,2.3283333333333043,2.588583911459399 +13,SAMPL8-16,0.5999999999999268,1.5999999999999825,1.7781076082921863 +14,SAMPL8-17,4.069999999999909,5.239999999999955,6.2071786398222635 +15,SAMPL8-18,6.961818181818092,6.961818181818092,8.307129468113438 +16,SAMPL8-19,0.439999999999924,1.6641666666666548,2.2484068433744877 +17,SAMPL8-20,1.6433333333332658,2.6433333333333136,3.148322304550959 +18,SAMPL8-21,3.2699999999999165,4.5433333333332815,5.856654335027745 +19,SAMPL8-22,8.449090909090813,8.449090909090813,9.355832405510387 +20,SAMPL8-23,0.16083333333325903,1.4541666666666615,1.9661595391354398 diff --git a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/abs_error_bymethod_plot.pdf b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/abs_error_bymethod_plot.pdf index 0abaae8..404b1c3 100644 Binary files a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/abs_error_bymethod_plot.pdf and b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/abs_error_bymethod_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/abs_error_bymol_plot.pdf b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/abs_error_bymol_plot.pdf index b9ff077..88bad58 100644 Binary files a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/abs_error_bymol_plot.pdf and b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/abs_error_bymol_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/macrostate_pKa_data.csv b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/macrostate_pKa_data.csv index 383ddac..abb5fd4 100644 --- a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/macrostate_pKa_data.csv +++ b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/macrostate_pKa_data.csv @@ -1,529 +1,510 @@ ,Submission,Method Name,Method Type,Molecule ID,Formal Charge,Predicted pKa,Experimental pKa,Absolute Error -0,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 -1,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,-1,14.499999999999895,6.98,7.519999999999895 -2,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,0,8.499999999999917,6.98,1.519999999999916 -3,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,1,2.699999999999937,6.98,4.280000000000063 -4,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,-2,13.599999999999898,7.27,6.329999999999899 -5,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,-1,9.699999999999912,7.27,2.4299999999999127 -6,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,0,8.599999999999916,7.27,1.3299999999999166 -7,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,1,3.3999999999999346,7.27,3.870000000000065 -8,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 -9,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,-2,12.099999999999904,5.1,6.999999999999904 -10,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,-1,10.699999999999909,5.1,5.599999999999909 -11,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,0,6.699999999999923,5.1,1.5999999999999233 -12,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-17,-1,11.499999999999906,6.58,4.919999999999906 -13,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-17,0,7.299999999999921,6.58,0.7199999999999207 -14,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-18,-1,11.199999999999907,2.72,8.479999999999906 -15,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-18,0,5.199999999999928,2.72,2.479999999999928 -16,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,-1,6.699999999999923,4.93,1.7699999999999232 -17,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,-1,6.699999999999923,6.99,0.2900000000000773 -18,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,0,5.999999999999925,4.93,1.0699999999999257 -19,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,0,5.999999999999925,6.99,0.9900000000000748 -20,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,1,3.3999999999999346,4.93,1.530000000000065 -21,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,1,3.3999999999999346,6.99,3.5900000000000656 -22,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,-1,3.599999999999934,2.54,1.0599999999999339 -23,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,-1,3.599999999999934,5.01,1.4100000000000659 -24,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,0,-0.6000000000000512,2.54,3.140000000000051 -25,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,0,-0.6000000000000512,5.01,5.610000000000051 -26,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,-1,10.09999999999991,2.44,7.659999999999911 -27,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,-1,10.09999999999991,11.44,1.3400000000000887 -28,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,0,4.69999999999993,2.44,2.25999999999993 -29,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,0,4.69999999999993,11.44,6.7400000000000695 -30,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,1,0.199999999999946,2.44,2.240000000000054 -31,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,1,0.199999999999946,11.44,11.240000000000054 -32,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,-2,12.9999999999999,5.38,7.619999999999901 -33,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,-1,8.599999999999916,5.38,3.2199999999999163 -34,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,0,7.799999999999919,5.38,2.419999999999919 -35,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,1,2.8999999999999364,5.38,2.4800000000000635 -36,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,-1,12.499999999999902,3.36,9.139999999999903 -37,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,0,5.499999999999927,3.36,2.1399999999999273 -38,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,1,-0.9000000000000501,3.36,4.2600000000000495 -39,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,-1,8.899999999999915,2.65,6.249999999999915 -40,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,-1,8.899999999999915,9.02,0.12000000000008448 -41,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,0,4.399999999999931,2.65,1.7499999999999312 -42,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,0,4.399999999999931,9.02,4.6200000000000685 -43,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 -44,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-3,-2,7.299999999999921,4.0,3.2999999999999208 -45,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-3,-1,3.299999999999935,4.0,0.700000000000065 -46,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-3,0,-1.1000000000000494,4.0,5.100000000000049 -47,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 -48,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-4,0,2.399999999999938,5.77,3.3700000000000614 -49,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-5,-1,3.1999999999999353,3.92,0.7200000000000646 -50,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-5,0,-1.6000000000000476,3.92,5.5200000000000475 -51,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-6,-1,3.3999999999999346,4.17,0.7700000000000653 -52,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-6,0,3.3999999999999346,4.17,0.7700000000000653 -53,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-7,-1,11.899999999999904,6.63,5.2699999999999045 -54,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-7,0,7.899999999999919,6.63,1.2699999999999187 -55,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-8,0,1.7999999999999403,2.78,0.9800000000000595 -56,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-9,-1,12.199999999999903,6.08,6.119999999999903 -57,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-9,0,7.699999999999919,6.08,1.6199999999999193 -58,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-10,0,5.299999999999928,7.71,2.410000000000072 -59,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-12,-1,13.799999999999898,6.98,6.819999999999897 -60,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-14,-2,3.9999999999999325,7.27,3.270000000000067 -61,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-14,-1,8.099999999999918,7.27,0.8299999999999184 -62,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-15,0,6.299999999999924,2.54,3.7599999999999243 -63,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-16,0,7.199999999999921,5.1,2.0999999999999215 -64,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-17,-1,5.199999999999928,6.58,1.3800000000000718 -65,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-18,-1,3.899999999999933,2.72,1.1799999999999327 -66,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-19,-1,5.199999999999928,4.93,0.2699999999999285 -67,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-19,-1,5.199999999999928,6.99,1.790000000000072 -68,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-19,0,7.799999999999919,4.93,2.8699999999999193 -69,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-19,0,7.799999999999919,6.99,0.8099999999999188 -70,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-19,1,-2.600000000000044,4.93,7.530000000000044 -71,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-19,1,-2.600000000000044,6.99,9.590000000000044 -72,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-1,-1,4.999999999999929,2.54,2.459999999999929 -73,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-1,-1,4.999999999999929,5.01,0.010000000000070841 -74,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-20,0,7.59999999999992,2.44,5.15999999999992 -75,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-20,0,7.59999999999992,11.44,3.84000000000008 -76,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-21,-2,9.499999999999913,5.38,4.119999999999913 -77,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-21,-1,2.8999999999999364,5.38,2.4800000000000635 -78,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-22,-1,7.0999999999999215,3.36,3.7399999999999216 -79,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-23,-1,7.999999999999918,2.65,5.349999999999918 -80,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-23,-1,7.999999999999918,9.02,1.0200000000000813 -81,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-23,0,3.599999999999934,2.65,0.949999999999934 -82,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-23,0,3.599999999999934,9.02,5.420000000000066 -83,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-2,-1,7.199999999999921,4.41,2.789999999999921 -84,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-3,-1,4.999999999999929,4.0,0.999999999999929 -85,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 -86,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-5,-1,0.29999999999994564,3.92,3.6200000000000543 -87,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-5,0,13.999999999999897,3.92,10.079999999999897 -88,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-6,-1,-0.10000000000005294,4.17,4.270000000000053 -89,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-6,0,13.999999999999897,4.17,9.829999999999897 -90,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-7,-1,8.099999999999918,6.63,1.469999999999918 -91,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-8,0,5.6999999999999265,2.78,2.9199999999999267 -92,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-9,-1,7.999999999999918,6.08,1.9199999999999182 -93,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 -94,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-12,-1,15.299999999999892,6.98,8.319999999999892 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-167,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-19,-1,7.299999999999921,4.93,2.369999999999921 -168,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-19,-1,7.299999999999921,6.99,0.30999999999992056 -169,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-19,0,6.699999999999923,4.93,1.7699999999999232 -170,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-19,0,6.699999999999923,6.99,0.2900000000000773 -171,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-19,1,4.099999999999932,4.93,0.8300000000000676 -172,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-19,1,4.099999999999932,6.99,2.890000000000068 -173,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-1,-1,4.299999999999931,2.54,1.7599999999999314 -174,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-1,-1,4.299999999999931,5.01,0.7100000000000684 -175,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-1,0,0.199999999999946,2.54,2.340000000000054 -176,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-1,0,0.199999999999946,5.01,4.810000000000054 -177,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-20,-1,10.699999999999909,2.44,8.25999999999991 -178,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-20,-1,10.699999999999909,11.44,0.7400000000000908 -179,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-20,0,5.3999999999999275,2.44,2.9599999999999276 -180,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-20,0,5.3999999999999275,11.44,6.040000000000072 -181,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-20,1,0.9999999999999432,2.44,1.4400000000000568 -182,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-20,1,0.9999999999999432,11.44,10.440000000000056 -183,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-21,-2,13.499999999999899,5.38,8.119999999999898 -184,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-21,-1,9.199999999999914,5.38,3.819999999999914 -185,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-21,0,8.399999999999917,5.38,3.019999999999917 -186,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-21,1,3.599999999999934,5.38,1.780000000000066 -187,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-22,-1,12.9999999999999,3.36,9.639999999999901 -188,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-22,0,6.099999999999925,3.36,2.739999999999925 -189,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-22,1,-0.10000000000005294,3.36,3.460000000000053 -190,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-23,-1,9.499999999999913,2.65,6.849999999999913 -191,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-23,-1,9.499999999999913,9.02,0.4799999999999134 -192,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-23,0,5.099999999999929,2.65,2.4499999999999287 -193,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-23,0,5.099999999999929,9.02,3.920000000000071 -194,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 -195,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-3,-2,7.999999999999918,4.0,3.9999999999999183 -196,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-3,-1,3.9999999999999325,4.0,6.750155989720952e-14 -197,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-3,0,-0.3000000000000522,4.0,4.300000000000052 -198,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-4,-1,4.199999999999932,5.77,1.5700000000000678 -199,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-4,0,3.1999999999999353,5.77,2.5700000000000642 -200,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-5,-1,3.899999999999933,3.92,0.020000000000067075 -201,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-5,0,-0.8000000000000504,3.92,4.72000000000005 -202,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-6,-1,4.199999999999932,4.17,0.02999999999993186 -203,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-6,0,4.099999999999932,4.17,0.07000000000006779 -204,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-7,-1,12.499999999999902,6.63,5.869999999999902 -205,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-7,0,8.499999999999917,6.63,1.8699999999999166 -206,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-8,0,4.099999999999932,2.78,1.3199999999999323 -207,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-9,-1,12.699999999999902,6.08,6.6199999999999015 -208,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-9,0,8.299999999999917,6.08,2.219999999999917 -209,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-10,0,6.499999999999924,7.71,1.2100000000000763 -210,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-12,-1,14,6.98,7.02 -211,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-14,-3,-9.20000000000002,7.27,16.47000000000002 -212,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-14,-1,15.099999999999893,7.27,7.8299999999998935 -213,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-15,0,1.0999999999999428,2.54,1.4400000000000572 -214,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-16,0,3.599999999999934,5.1,1.5000000000000657 -215,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-17,-1,17.999999999999883,6.58,11.419999999999883 -216,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-17,0,5.199999999999928,6.58,1.3800000000000718 -217,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-18,-1,16.799999999999887,2.72,14.079999999999886 -218,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-18,0,1.599999999999941,2.72,1.1200000000000592 -219,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,-1,11.999999999999904,4.93,7.069999999999904 -220,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,-1,11.999999999999904,6.99,5.009999999999904 -221,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,0,3.0999999999999357,4.93,1.830000000000064 -222,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,0,3.0999999999999357,6.99,3.8900000000000645 -223,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-1,-1,7.59999999999992,2.54,5.05999999999992 -224,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-1,-1,7.59999999999992,5.01,2.58999999999992 -225,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-20,0,1.1999999999999424,2.44,1.2400000000000575 -226,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-20,0,1.1999999999999424,11.44,10.240000000000057 -227,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-21,-1,17.199999999999886,5.38,11.819999999999887 -228,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-22,-1,17.499999999999886,3.36,14.139999999999887 -229,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,-1,13.499999999999899,2.65,10.849999999999898 -230,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,-1,13.499999999999899,9.02,4.479999999999899 -231,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,0,2.0999999999999392,2.65,0.5500000000000607 -232,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,0,2.0999999999999392,9.02,6.92000000000006 -233,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-2,-1,8.099999999999918,4.41,3.689999999999918 -234,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-3,-1,6.299999999999924,4.0,2.2999999999999243 -235,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-4,-1,11.099999999999907,5.77,5.329999999999908 -236,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-4,0,-8.000000000000025,5.77,13.770000000000024 -237,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-5,-1,7.59999999999992,3.92,3.67999999999992 -238,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-5,0,-10.100000000000017,3.92,14.020000000000017 -239,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-6,-1,5.799999999999926,4.17,1.6299999999999262 -240,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-6,0,-5.3000000000000345,4.17,9.470000000000034 -241,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-7,0,8.799999999999915,6.63,2.1699999999999156 -242,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-8,0,4.59999999999993,2.78,1.8199999999999306 -243,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-9,0,5.899999999999926,6.08,0.18000000000007432 -244,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999914,7.71,1.489999999999914 -245,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-12,-1,14.299999999999896,6.98,7.3199999999998955 -246,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-2,5.099999999999929,7.27,2.170000000000071 -247,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-1,7.299999999999921,7.27,0.0299999999999212 -248,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,6.999999999999922,2.54,4.459999999999922 -249,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 -250,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-17,-1,4.199999999999932,6.58,2.3800000000000683 -251,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-18,-1,4.999999999999929,2.72,2.2799999999999288 -252,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,4.93,4.269999999999914 -253,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 -254,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 -255,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,6.99,0.5900000000000762 -256,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,4.93,6.130000000000049 -257,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,6.99,8.19000000000005 -258,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,2.54,2.0599999999999303 -259,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 -260,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 -261,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,11.44,4.640000000000077 -262,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-2,19.399999999999878,5.38,14.019999999999879 -263,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-1,6.299999999999924,5.38,0.9199999999999244 -264,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-22,-1,5.199999999999928,3.36,1.8399999999999284 -265,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,2.65,6.549999999999914 -266,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 -267,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 -268,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,9.02,4.920000000000067 -269,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 -270,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 -271,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 -272,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 -273,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,0,14.599999999999895,3.92,10.679999999999895 -274,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 -275,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,0,13.1999999999999,4.17,9.0299999999999 -276,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-7,-1,4.999999999999929,6.63,1.630000000000071 -277,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 -278,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-9,-1,3.899999999999933,6.08,2.180000000000067 -279,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-10,0,5.599999999999927,7.71,2.110000000000073 -280,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-12,-1,19.09999999999988,6.98,12.11999999999988 -281,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-2,11.599999999999905,7.27,4.329999999999906 -282,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-1,11.499999999999906,7.27,4.229999999999906 -283,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-15,0,4.299999999999931,2.54,1.7599999999999314 -284,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-16,0,4.69999999999993,5.1,0.40000000000006963 -285,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,-1,12.299999999999903,6.58,5.719999999999903 -286,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,0,4.499999999999931,6.58,2.0800000000000693 -287,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,-1,9.599999999999913,2.72,6.879999999999912 -288,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,0,4.199999999999932,2.72,1.4799999999999316 -289,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,4.93,6.169999999999908 -290,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,6.99,4.109999999999907 -291,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,4.93,4.2300000000000555 -292,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,6.99,6.290000000000056 -293,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,1,-0.9000000000000501,4.93,5.83000000000005 -294,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,1,-0.9000000000000501,6.99,7.89000000000005 -295,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,2.54,1.559999999999932 -296,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,5.01,0.9100000000000676 -297,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,0,1.3999999999999417,2.44,1.0400000000000582 -298,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,0,1.3999999999999417,11.44,10.040000000000058 -299,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-3,19.899999999999878,5.38,14.519999999999879 -300,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-2,16.29999999999989,5.38,10.919999999999892 -301,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-1,13.699999999999898,5.38,8.319999999999897 -302,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-22,-1,13.899999999999897,3.36,10.539999999999898 -303,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,9.999999999999911,2.65,7.349999999999911 -304,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,9.999999999999911,9.02,0.9799999999999116 -305,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.299999999999935,2.65,0.6499999999999351 -306,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.299999999999935,9.02,5.720000000000065 -307,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-2,-1,6.099999999999925,4.41,1.689999999999925 -308,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-2,8.799999999999915,4.0,4.7999999999999154 -309,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-1,6.699999999999923,4.0,2.699999999999923 -310,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,-1,6.499999999999924,5.77,0.729999999999924 -311,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,0,-5.3290705182007514e-14,5.77,5.770000000000053 -312,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,-1,4.499999999999931,3.92,0.5799999999999308 -313,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,0,-1.200000000000049,3.92,5.120000000000049 -314,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 -315,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,0,1.9999999999999396,4.17,2.1700000000000603 -316,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,-1,16.39999999999989,6.63,9.76999999999989 -317,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,0,11.299999999999907,6.63,4.669999999999907 -318,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-8,0,4.399999999999931,2.78,1.6199999999999313 -319,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,-1,15.699999999999891,6.08,9.61999999999989 -320,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,0,4.499999999999931,6.08,1.5800000000000693 -321,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-10,0,6.399999999999924,7.71,1.310000000000076 -322,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-12,-1,13.1999999999999,6.98,6.219999999999899 -323,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-14,-2,3.9999999999999325,7.27,3.270000000000067 -324,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-14,-1,4.099999999999932,7.27,3.1700000000000674 -325,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-15,0,5.499999999999927,2.54,2.959999999999927 -326,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-16,0,6.199999999999925,5.1,1.099999999999925 -327,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-17,-1,4.499999999999931,6.58,2.0800000000000693 -328,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-18,-1,4.499999999999931,2.72,1.7799999999999305 -329,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,-1,5.299999999999928,4.93,0.36999999999992816 -330,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,-1,5.299999999999928,6.99,1.6900000000000723 -331,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,0,5.899999999999926,4.93,0.969999999999926 -332,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,0,5.899999999999926,6.99,1.0900000000000745 -333,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,1,-1.3000000000000487,4.93,6.230000000000048 -334,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,1,-1.3000000000000487,6.99,8.290000000000049 -335,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-1,-1,4.59999999999993,2.54,2.0599999999999303 -336,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 -337,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-20,0,7.699999999999919,2.44,5.25999999999992 -338,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-20,0,7.699999999999919,11.44,3.74000000000008 -339,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-21,-2,9.999999999999911,5.38,4.619999999999911 -340,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-21,-1,2.399999999999938,5.38,2.9800000000000617 -341,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-22,-1,7.799999999999919,3.36,4.43999999999992 -342,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-23,-1,5.499999999999927,2.65,2.8499999999999273 -343,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-23,-1,5.499999999999927,9.02,3.5200000000000724 -344,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-23,0,1.6999999999999407,2.65,0.9500000000000592 -345,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-23,0,1.6999999999999407,9.02,7.320000000000059 -346,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-2,-1,4.899999999999929,4.41,0.48999999999992916 -347,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-3,-1,4.69999999999993,4.0,0.69999999999993 -348,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-4,-1,3.299999999999935,5.77,2.4700000000000646 -349,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-5,-1,0.29999999999994564,3.92,3.6200000000000543 -350,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-5,0,9.499999999999913,3.92,5.579999999999913 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fitting,QM,SAMPL8-7,0,11.299999999999907,6.63,4.669999999999907 +106,pKa-ZhiyiWu-1_modified,QM with linear fitting,QM,SAMPL8-8,0,4.399999999999931,2.78,1.6199999999999313 +107,pKa-ZhiyiWu-1_modified,QM with linear fitting,QM,SAMPL8-9,-1,15.699999999999891,6.08,9.61999999999989 +108,pKa-ZhiyiWu-1_modified,QM with linear fitting,QM,SAMPL8-9,0,4.499999999999931,6.08,1.5800000000000693 +109,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 +110,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-12,-1,14.499999999999895,6.98,7.519999999999895 +111,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-12,0,8.499999999999917,6.98,1.519999999999916 +112,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-12,1,2.699999999999937,6.98,4.280000000000063 +113,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,-2,13.599999999999898,7.27,6.329999999999899 +114,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,-1,9.699999999999912,7.27,2.4299999999999127 +115,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,0,8.599999999999916,7.27,1.3299999999999166 +116,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,1,3.3999999999999346,7.27,3.870000000000065 +117,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 +118,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-16,-2,12.099999999999904,5.1,6.999999999999904 +119,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-16,-1,10.699999999999909,5.1,5.599999999999909 +120,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-16,0,6.699999999999923,5.1,1.5999999999999233 +121,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-17,-1,11.499999999999906,6.58,4.919999999999906 +122,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-17,0,7.299999999999921,6.58,0.7199999999999207 +123,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-18,-1,11.199999999999907,2.72,8.479999999999906 +124,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-18,0,5.199999999999928,2.72,2.479999999999928 +125,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,-1,6.699999999999923,4.93,1.7699999999999232 +126,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,-1,6.699999999999923,6.99,0.2900000000000773 +127,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,0,5.999999999999925,4.93,1.0699999999999257 +128,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,0,5.999999999999925,6.99,0.9900000000000748 +129,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,1,3.3999999999999346,4.93,1.530000000000065 +130,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,1,3.3999999999999346,6.99,3.5900000000000656 +131,pKa-3DS-1_modified,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,-1,3.599999999999934,2.54,1.0599999999999339 +132,pKa-3DS-1_modified,COSMO-RS one pKa 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fit,QM+LEC,SAMPL8-23,0,3.0999999999999357,9.02,5.920000000000064 +426,pKa-3DS-2_modified,COSMO-RS base pKa fit,QM+LEC,SAMPL8-2,-1,1.599999999999941,4.41,2.810000000000059 +427,pKa-3DS-2_modified,COSMO-RS base pKa fit,QM+LEC,SAMPL8-3,-2,6.599999999999923,4.0,2.5999999999999233 +428,pKa-3DS-2_modified,COSMO-RS base pKa fit,QM+LEC,SAMPL8-3,-1,1.6999999999999407,4.0,2.3000000000000593 +429,pKa-3DS-2_modified,COSMO-RS base pKa fit,QM+LEC,SAMPL8-3,0,-3.6000000000000405,4.0,7.6000000000000405 +430,pKa-3DS-2_modified,COSMO-RS base pKa fit,QM+LEC,SAMPL8-4,-1,1.7999999999999403,5.77,3.9700000000000593 +431,pKa-3DS-2_modified,COSMO-RS base pKa fit,QM+LEC,SAMPL8-4,0,0.6999999999999442,5.77,5.070000000000055 +432,pKa-3DS-2_modified,COSMO-RS base pKa fit,QM+LEC,SAMPL8-5,-1,1.4999999999999414,3.92,2.4200000000000585 +433,pKa-3DS-2_modified,COSMO-RS base pKa fit,QM+LEC,SAMPL8-5,0,-4.300000000000038,3.92,8.220000000000038 +434,pKa-3DS-2_modified,COSMO-RS base pKa fit,QM+LEC,SAMPL8-6,-1,1.7999999999999403,4.17,2.3700000000000596 +435,pKa-3DS-2_modified,COSMO-RS base pKa fit,QM+LEC,SAMPL8-6,0,1.89999999999994,4.17,2.27000000000006 +436,pKa-3DS-2_modified,COSMO-RS base pKa fit,QM+LEC,SAMPL8-7,-1,12.099999999999904,6.63,5.469999999999904 +437,pKa-3DS-2_modified,COSMO-RS base pKa fit,QM+LEC,SAMPL8-7,0,7.299999999999921,6.63,0.6699999999999209 +438,pKa-3DS-2_modified,COSMO-RS base pKa fit,QM+LEC,SAMPL8-8,0,1.7999999999999403,2.78,0.9800000000000595 +439,pKa-3DS-2_modified,COSMO-RS base pKa fit,QM+LEC,SAMPL8-9,-1,12.399999999999903,6.08,6.319999999999903 +440,pKa-3DS-2_modified,COSMO-RS base pKa fit,QM+LEC,SAMPL8-9,0,6.999999999999922,6.08,0.9199999999999218 +441,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999914,7.71,1.489999999999914 +442,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-12,-1,14.299999999999896,6.98,7.3199999999998955 +443,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-2,5.099999999999929,7.27,2.170000000000071 +444,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-1,7.299999999999921,7.27,0.0299999999999212 +445,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,6.999999999999922,2.54,4.459999999999922 +446,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 +447,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-17,-1,4.199999999999932,6.58,2.3800000000000683 +448,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-18,-1,4.999999999999929,2.72,2.2799999999999288 +449,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,4.93,4.269999999999914 +450,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 +451,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 +452,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,6.99,0.5900000000000762 +453,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,4.93,6.130000000000049 +454,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,6.99,8.19000000000005 +455,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,2.54,2.0599999999999303 +456,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 +457,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 +458,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-2,19.399999999999878,5.38,14.019999999999879 +459,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-1,6.299999999999924,5.38,0.9199999999999244 +460,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-22,-1,5.199999999999928,3.36,1.8399999999999284 +461,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,2.65,6.549999999999914 +462,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 +463,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 +464,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,9.02,4.920000000000067 +465,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 +466,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 +467,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 +468,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 +469,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-5,0,14.599999999999895,3.92,10.679999999999895 +470,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 +471,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-6,0,13.1999999999999,4.17,9.0299999999999 +472,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-7,-1,4.999999999999929,6.63,1.630000000000071 +473,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 +474,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-9,-1,3.899999999999933,6.08,2.180000000000067 +475,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-10,0,6.399999999999924,7.71,1.310000000000076 +476,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-12,-1,13.1999999999999,6.98,6.219999999999899 +477,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-14,-2,3.9999999999999325,7.27,3.270000000000067 +478,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-14,-1,4.099999999999932,7.27,3.1700000000000674 +479,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-15,0,5.499999999999927,2.54,2.959999999999927 +480,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-16,0,6.199999999999925,5.1,1.099999999999925 +481,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-17,-1,4.499999999999931,6.58,2.0800000000000693 +482,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-18,-1,4.499999999999931,2.72,1.7799999999999305 +483,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-19,-1,5.299999999999928,4.93,0.36999999999992816 +484,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-19,-1,5.299999999999928,6.99,1.6900000000000723 +485,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-19,0,5.899999999999926,4.93,0.969999999999926 +486,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-19,0,5.899999999999926,6.99,1.0900000000000745 +487,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-19,1,-1.3000000000000487,4.93,6.230000000000048 +488,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-19,1,-1.3000000000000487,6.99,8.290000000000049 +489,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-1,-1,4.59999999999993,2.54,2.0599999999999303 +490,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 +491,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-20,0,7.699999999999919,2.44,5.25999999999992 +492,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-21,-2,9.999999999999911,5.38,4.619999999999911 +493,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-21,-1,2.399999999999938,5.38,2.9800000000000617 +494,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-22,-1,7.799999999999919,3.36,4.43999999999992 +495,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-23,-1,5.499999999999927,2.65,2.8499999999999273 +496,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-23,-1,5.499999999999927,9.02,3.5200000000000724 +497,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-23,0,1.6999999999999407,2.65,0.9500000000000592 +498,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-23,0,1.6999999999999407,9.02,7.320000000000059 +499,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-2,-1,4.899999999999929,4.41,0.48999999999992916 +500,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-3,-1,4.69999999999993,4.0,0.69999999999993 +501,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-4,-1,3.299999999999935,5.77,2.4700000000000646 +502,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-5,-1,0.29999999999994564,3.92,3.6200000000000543 +503,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-5,0,9.499999999999913,3.92,5.579999999999913 +504,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-6,-1,-0.10000000000005294,4.17,4.270000000000053 +505,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-6,0,13.899999999999897,4.17,9.729999999999897 +506,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-7,-1,7.59999999999992,6.63,0.9699999999999198 +507,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-8,0,3.9999999999999325,2.78,1.2199999999999327 +508,pKa-RobertRaddi_RF_modified,Random Forest,QSPR/ML,SAMPL8-9,-1,7.999999999999918,6.08,1.9199999999999182 diff --git a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/mean_abs_error_plot.pdf b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/mean_abs_error_plot.pdf index 89f1042..3678344 100644 Binary files a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/mean_abs_error_plot.pdf and b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/mean_abs_error_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/mean_error_plot.pdf b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/mean_error_plot.pdf index e4d476d..d88d7f8 100644 Binary files a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/mean_error_plot.pdf and b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/mean_error_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/popular_transitions_pKa_data.csv b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/popular_transitions_pKa_data.csv index d51f601..d6488eb 100644 --- a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/popular_transitions_pKa_data.csv +++ b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_all/popular_transitions_pKa_data.csv @@ -1,301 +1,274 @@ ,Submission,Method Name,Method Type,Molecule ID,Formal Charge,Predicted pKa,Experimental pKa,Absolute Error -0,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,0,-0.6000000000000512,2.54,3.140000000000051 -1,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,-1,3.599999999999934,5.01,1.4100000000000659 -2,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 -3,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-3,-1,3.299999999999935,4.0,0.700000000000065 -4,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 -5,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-5,-1,3.1999999999999353,3.92,0.7200000000000646 -6,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-6,-1,3.3999999999999346,4.17,0.7700000000000653 -7,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-7,-1,11.899999999999904,6.63,5.2699999999999045 -8,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-8,0,1.7999999999999403,2.78,0.9800000000000595 -9,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-9,-1,12.199999999999903,6.08,6.119999999999903 -10,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 -11,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,-1,14.499999999999895,6.98,7.519999999999895 -12,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,-1,9.699999999999912,7.27,2.4299999999999127 -13,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 -14,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,0,6.699999999999923,5.1,1.5999999999999233 -15,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-17,-1,11.499999999999906,6.58,4.919999999999906 -16,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-18,-1,11.199999999999907,2.72,8.479999999999906 -17,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,0,5.999999999999925,4.93,1.0699999999999257 -18,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,-1,6.699999999999923,6.99,0.2900000000000773 -19,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,0,4.69999999999993,2.44,2.25999999999993 -20,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,-1,10.09999999999991,11.44,1.3400000000000887 -21,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,-1,8.599999999999916,5.38,3.2199999999999163 -22,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,-1,12.499999999999902,3.36,9.139999999999903 -23,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,0,4.399999999999931,2.65,1.7499999999999312 -24,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,-1,8.899999999999915,9.02,0.12000000000008448 -25,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-1,0,14,2.54,11.46 -26,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-1,-1,4.999999999999929,5.01,0.010000000000070841 -27,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-2,-1,7.199999999999921,4.41,2.789999999999921 -28,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-3,-1,4.999999999999929,4.0,0.999999999999929 -29,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 -30,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-5,-1,0.29999999999994564,3.92,3.6200000000000543 -31,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-6,-1,-0.10000000000005294,4.17,4.270000000000053 -32,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-7,-1,8.099999999999918,6.63,1.469999999999918 -33,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-8,0,5.6999999999999265,2.78,2.9199999999999267 -34,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-9,-1,7.999999999999918,6.08,1.9199999999999182 -35,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-10,0,5.299999999999928,7.71,2.410000000000072 -36,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-12,-1,13.799999999999898,6.98,6.819999999999897 -37,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-14,-1,8.099999999999918,7.27,0.8299999999999184 -38,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-15,0,6.299999999999924,2.54,3.7599999999999243 -39,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-16,0,7.199999999999921,5.1,2.0999999999999215 -40,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-17,-1,5.199999999999928,6.58,1.3800000000000718 -41,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-18,-1,3.899999999999933,2.72,1.1799999999999327 -42,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-19,0,7.799999999999919,4.93,2.8699999999999193 -43,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-19,-1,5.199999999999928,6.99,1.790000000000072 -44,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-20,0,7.59999999999992,2.44,5.15999999999992 -45,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-20,-1,0,11.44,11.44 -46,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-21,-1,2.8999999999999364,5.38,2.4800000000000635 -47,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-22,-1,7.0999999999999215,3.36,3.7399999999999216 -48,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-23,0,3.599999999999934,2.65,0.949999999999934 -49,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-23,-1,7.999999999999918,9.02,1.0200000000000813 -50,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-1,0,-3.0000000000000426,2.54,5.540000000000043 -51,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-1,-1,2.0999999999999392,5.01,2.9100000000000605 -52,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-2,-1,1.599999999999941,4.41,2.810000000000059 -53,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-3,-1,1.6999999999999407,4.0,2.3000000000000593 -54,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-4,-1,1.7999999999999403,5.77,3.9700000000000593 -55,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-5,-1,1.4999999999999414,3.92,2.4200000000000585 -56,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-6,-1,1.7999999999999403,4.17,2.3700000000000596 -57,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-7,-1,12.099999999999904,6.63,5.469999999999904 -58,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-8,0,1.7999999999999403,2.78,0.9800000000000595 -59,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-9,-1,12.399999999999903,6.08,6.319999999999903 -60,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 -61,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-12,-1,15.299999999999892,6.98,8.319999999999892 -62,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-14,-1,9.399999999999913,7.27,2.1299999999999137 -63,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 -64,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-16,0,5.799999999999926,5.1,0.6999999999999265 -65,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-17,-1,11.599999999999905,6.58,5.019999999999905 -66,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-18,-1,11.299999999999907,2.72,8.579999999999906 -67,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-19,0,4.999999999999929,4.93,0.06999999999992923 -68,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-19,-1,5.6999999999999265,6.99,1.2900000000000738 -69,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-20,0,3.299999999999935,2.44,0.859999999999935 -70,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-20,-1,9.899999999999912,11.44,1.540000000000088 -71,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-21,-1,8.099999999999918,5.38,2.719999999999918 -72,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-22,-1,12.799999999999901,3.36,9.439999999999902 -73,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-23,0,3.0999999999999357,2.65,0.4499999999999358 -74,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-23,-1,8.399999999999917,9.02,0.6200000000000827 -75,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-1,0,0.199999999999946,2.54,2.340000000000054 -76,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-1,-1,4.299999999999931,5.01,0.7100000000000684 -77,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 -78,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-3,-1,3.9999999999999325,4.0,6.750155989720952e-14 -79,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-4,-1,4.199999999999932,5.77,1.5700000000000678 -80,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-5,-1,3.899999999999933,3.92,0.020000000000067075 -81,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-6,-1,4.199999999999932,4.17,0.02999999999993186 -82,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-7,-1,12.499999999999902,6.63,5.869999999999902 -83,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-8,0,4.099999999999932,2.78,1.3199999999999323 -84,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-9,-1,12.699999999999902,6.08,6.6199999999999015 -85,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-10,0,9.399999999999913,7.71,1.6899999999999133 -86,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-12,-1,14.999999999999893,6.98,8.019999999999893 -87,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-14,-1,10.29999999999991,7.27,3.0299999999999105 -88,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-15,0,5.799999999999926,2.54,3.259999999999926 -89,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-16,0,7.39999999999992,5.1,2.2999999999999208 -90,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-17,-1,11.999999999999904,6.58,5.419999999999904 -91,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-18,-1,11.799999999999905,2.72,9.079999999999904 -92,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-19,0,6.699999999999923,4.93,1.7699999999999232 -93,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-19,-1,7.299999999999921,6.99,0.30999999999992056 -94,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-20,0,5.3999999999999275,2.44,2.9599999999999276 -95,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-20,-1,10.699999999999909,11.44,0.7400000000000908 -96,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-21,-1,9.199999999999914,5.38,3.819999999999914 -97,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-22,-1,12.9999999999999,3.36,9.639999999999901 -98,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-23,0,5.099999999999929,2.65,2.4499999999999287 -99,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-23,-1,9.499999999999913,9.02,0.4799999999999134 -100,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-1,0,14,2.54,11.46 -101,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-1,-1,7.59999999999992,5.01,2.58999999999992 -102,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-2,-1,8.099999999999918,4.41,3.689999999999918 -103,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-3,-1,6.299999999999924,4.0,2.2999999999999243 -104,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-4,-1,11.099999999999907,5.77,5.329999999999908 -105,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-5,-1,7.59999999999992,3.92,3.67999999999992 -106,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-6,-1,5.799999999999926,4.17,1.6299999999999262 -107,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-7,-1,14,6.63,7.37 -108,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-8,0,4.59999999999993,2.78,1.8199999999999306 -109,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-9,-1,14,6.08,7.92 -110,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-10,0,6.499999999999924,7.71,1.2100000000000763 -111,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-12,-1,14,6.98,7.02 -112,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-14,-1,15.099999999999893,7.27,7.8299999999998935 -113,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-15,0,1.0999999999999428,2.54,1.4400000000000572 -114,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-16,0,3.599999999999934,5.1,1.5000000000000657 -115,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-17,-1,17.999999999999883,6.58,11.419999999999883 -116,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-18,-1,16.799999999999887,2.72,14.079999999999886 -117,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,0,3.0999999999999357,4.93,1.830000000000064 -118,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,-1,11.999999999999904,6.99,5.009999999999904 -119,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-20,0,1.1999999999999424,2.44,1.2400000000000575 -120,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-20,-1,0,11.44,11.44 -121,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-21,-1,17.199999999999886,5.38,11.819999999999887 -122,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-22,-1,17.499999999999886,3.36,14.139999999999887 -123,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,0,2.0999999999999392,2.65,0.5500000000000607 -124,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,-1,13.499999999999899,9.02,4.479999999999899 -125,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,0,14,2.54,11.46 -126,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 -127,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 -128,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 -129,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 -130,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 -131,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 -132,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-7,-1,4.999999999999929,6.63,1.630000000000071 -133,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 -134,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-9,-1,3.899999999999933,6.08,2.180000000000067 -135,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999914,7.71,1.489999999999914 -136,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-12,-1,14.299999999999896,6.98,7.3199999999998955 -137,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-1,7.299999999999921,7.27,0.0299999999999212 -138,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,6.999999999999922,2.54,4.459999999999922 -139,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 -140,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-17,-1,4.199999999999932,6.58,2.3800000000000683 -141,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-18,-1,4.999999999999929,2.72,2.2799999999999288 -142,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 -143,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 -144,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 -145,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,-1,0,11.44,11.44 -146,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-1,6.299999999999924,5.38,0.9199999999999244 -147,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-22,-1,5.199999999999928,3.36,1.8399999999999284 -148,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 -149,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 -150,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,0,14,2.54,11.46 -151,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,5.01,0.9100000000000676 -152,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-2,-1,6.099999999999925,4.41,1.689999999999925 -153,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-1,6.699999999999923,4.0,2.699999999999923 -154,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,-1,6.499999999999924,5.77,0.729999999999924 -155,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,-1,4.499999999999931,3.92,0.5799999999999308 -156,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 -157,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,-1,16.39999999999989,6.63,9.76999999999989 -158,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-8,0,4.399999999999931,2.78,1.6199999999999313 -159,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,-1,15.699999999999891,6.08,9.61999999999989 -160,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-10,0,5.599999999999927,7.71,2.110000000000073 -161,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-12,-1,19.09999999999988,6.98,12.11999999999988 -162,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-1,11.499999999999906,7.27,4.229999999999906 -163,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-15,0,4.299999999999931,2.54,1.7599999999999314 -164,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-16,0,4.69999999999993,5.1,0.40000000000006963 -165,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,-1,12.299999999999903,6.58,5.719999999999903 -166,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,-1,9.599999999999913,2.72,6.879999999999912 -167,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,4.93,4.2300000000000555 -168,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,6.99,4.109999999999907 -169,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,0,1.3999999999999417,2.44,1.0400000000000582 -170,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,-1,0,11.44,11.44 -171,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-1,13.699999999999898,5.38,8.319999999999897 -172,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-22,-1,13.899999999999897,3.36,10.539999999999898 -173,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.299999999999935,2.65,0.6499999999999351 -174,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,9.999999999999911,9.02,0.9799999999999116 -175,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-1,0,14,2.54,11.46 -176,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 -177,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-2,-1,4.899999999999929,4.41,0.48999999999992916 -178,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-3,-1,4.69999999999993,4.0,0.69999999999993 -179,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-4,-1,3.299999999999935,5.77,2.4700000000000646 -180,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-5,-1,0.29999999999994564,3.92,3.6200000000000543 -181,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-6,-1,-0.10000000000005294,4.17,4.270000000000053 -182,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-7,-1,7.59999999999992,6.63,0.9699999999999198 -183,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-8,0,3.9999999999999325,2.78,1.2199999999999327 -184,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-9,-1,7.999999999999918,6.08,1.9199999999999182 -185,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-10,0,6.399999999999924,7.71,1.310000000000076 -186,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-12,-1,13.1999999999999,6.98,6.219999999999899 -187,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-14,-1,4.099999999999932,7.27,3.1700000000000674 -188,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-15,0,5.499999999999927,2.54,2.959999999999927 -189,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-16,0,6.199999999999925,5.1,1.099999999999925 -190,pKa-RobertRaddi_RF,Random 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b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/Error_statistics.csv index f27e17f..13444a2 100644 --- a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/Error_statistics.csv +++ b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/Error_statistics.csv @@ -1,22 +1,22 @@ ,Molecule ID,Mean Error,Mean Absolute Error,Root Mean Squared Error -0,SAMPL8-1,0.8166666666666228,5.345000000000031,5.345000000000031 -1,SAMPL8-2,1.7899999999999245,2.5966666666666343,2.5966666666666343 -2,SAMPL8-3,1.0666666666665954,1.633333333333305,1.633333333333305 -3,SAMPL8-4,-0.6366666666667378,2.656666666666682,2.656666666666682 -4,SAMPL8-5,0.696666666666597,1.2766666666666397,1.2766666666666397 -5,SAMPL8-6,-0.103333333333401,0.8233333333333531,0.8233333333333531 -6,SAMPL8-7,5.469999999999921,6.013333333333279,6.013333333333279 -7,SAMPL8-8,0.08666666666660339,1.7666666666666604,1.7666666666666604 -8,SAMPL8-9,5.669999999999923,6.396666666666611,6.396666666666611 -9,SAMPL8-10,-0.7433333333334113,1.4366666666666885,1.4366666666666885 -10,SAMPL8-12,8.619999999999925,8.619999999999925,8.619999999999925 -11,SAMPL8-14,3.246666666666576,3.246666666666576,3.246666666666576 -12,SAMPL8-15,0.5933333333332689,1.9333333333333265,1.9333333333333265 -13,SAMPL8-16,0.09999999999992859,1.600000000000018,1.600000000000018 -14,SAMPL8-17,5.2699999999999045,6.063333333333261,6.063333333333261 -15,SAMPL8-18,8.613333333333257,8.613333333333257,8.613333333333257 -16,SAMPL8-19,0.5316666666665903,1.7816666666666592,1.7816666666666592 -17,SAMPL8-20,-3.898333333333379,5.001666666666688,5.001666666666688 -18,SAMPL8-21,4.753333333333244,4.753333333333244,4.753333333333244 -19,SAMPL8-22,9.606666666666586,9.606666666666586,9.606666666666586 -20,SAMPL8-23,0.5566666666665908,1.2049999999999816,1.2049999999999816 +0,SAMPL8-1,-2.7311111111111694,3.3066666666667066,5.121364835449428 +1,SAMPL8-2,1.7899999999999245,2.5966666666666343,3.382420238034644 +2,SAMPL8-3,1.0666666666665954,1.633333333333305,1.937352144896008 +3,SAMPL8-4,-0.6366666666667378,2.656666666666682,3.0617369797768976 +4,SAMPL8-5,0.696666666666597,1.2766666666666397,1.6862384173063685 +5,SAMPL8-6,-0.103333333333401,0.8233333333333531,1.030970416646378 +6,SAMPL8-7,5.089999999999906,5.741999999999933,6.471607219230701 +7,SAMPL8-8,0.08666666666660339,1.7666666666666604,1.9269319309894237 +8,SAMPL8-9,5.219999999999906,6.091999999999933,6.64803730434772 +9,SAMPL8-10,-0.7433333333334113,1.4366666666666885,1.615992986783493 +10,SAMPL8-12,9.419999999999888,9.419999999999888,9.6429456080597 +11,SAMPL8-14,3.246666666666576,3.246666666666576,4.15398202531812 +12,SAMPL8-15,0.5933333333332689,1.9333333333333265,2.2466864489732186 +13,SAMPL8-16,0.09999999999992859,1.600000000000018,1.856520042085899 +14,SAMPL8-17,5.2699999999999045,6.063333333333261,6.704878820679675 +15,SAMPL8-18,8.079999999999908,8.079999999999908,8.922241870740693 +16,SAMPL8-19,0.5316666666665903,1.7816666666666592,2.453874487417779 +17,SAMPL8-20,0.30999999999993705,1.8966666666666805,2.2357549060663886 +18,SAMPL8-21,4.753333333333244,4.753333333333244,6.192985279060957 +19,SAMPL8-22,9.399999999999903,9.399999999999903,10.26208555801393 +20,SAMPL8-23,0.5566666666665908,1.2049999999999816,1.6939942935755599 diff --git a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/abs_error_bymethod_plot.pdf b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/abs_error_bymethod_plot.pdf index 9c44ba0..5560832 100644 Binary files a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/abs_error_bymethod_plot.pdf and b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/abs_error_bymethod_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/abs_error_bymol_plot.pdf b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/abs_error_bymol_plot.pdf index 93e6904..3e80853 100644 Binary files a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/abs_error_bymol_plot.pdf and b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/abs_error_bymol_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/macrostate_pKa_data.csv b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/macrostate_pKa_data.csv index faf5335..523e6a9 100644 --- a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/macrostate_pKa_data.csv +++ b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/macrostate_pKa_data.csv @@ -1,273 +1,264 @@ ,Submission,Method Name,Method Type,Molecule ID,Formal Charge,Predicted pKa,Experimental pKa,Absolute Error -0,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 -1,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,-1,14.499999999999895,6.98,7.519999999999895 -2,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,0,8.499999999999917,6.98,1.519999999999916 -3,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,1,2.699999999999937,6.98,4.280000000000063 -4,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,-2,13.599999999999898,7.27,6.329999999999899 -5,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,-1,9.699999999999912,7.27,2.4299999999999127 -6,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,0,8.599999999999916,7.27,1.3299999999999166 -7,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,1,3.3999999999999346,7.27,3.870000000000065 -8,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 -9,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,-2,12.099999999999904,5.1,6.999999999999904 -10,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,-1,10.699999999999909,5.1,5.599999999999909 -11,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,0,6.699999999999923,5.1,1.5999999999999233 -12,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-17,-1,11.499999999999906,6.58,4.919999999999906 -13,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-17,0,7.299999999999921,6.58,0.7199999999999207 -14,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-18,-1,11.199999999999907,2.72,8.479999999999906 -15,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-18,0,5.199999999999928,2.72,2.479999999999928 -16,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,-1,6.699999999999923,4.93,1.7699999999999232 -17,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,-1,6.699999999999923,6.99,0.2900000000000773 -18,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,0,5.999999999999925,4.93,1.0699999999999257 -19,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,0,5.999999999999925,6.99,0.9900000000000748 -20,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,1,3.3999999999999346,4.93,1.530000000000065 -21,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,1,3.3999999999999346,6.99,3.5900000000000656 -22,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,-1,3.599999999999934,2.54,1.0599999999999339 -23,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,-1,3.599999999999934,5.01,1.4100000000000659 -24,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,0,-0.6000000000000512,2.54,3.140000000000051 -25,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,0,-0.6000000000000512,5.01,5.610000000000051 -26,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,-1,10.09999999999991,2.44,7.659999999999911 -27,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,-1,10.09999999999991,11.44,1.3400000000000887 -28,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,0,4.69999999999993,2.44,2.25999999999993 -29,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,0,4.69999999999993,11.44,6.7400000000000695 -30,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,1,0.199999999999946,2.44,2.240000000000054 -31,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,1,0.199999999999946,11.44,11.240000000000054 -32,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,-2,12.9999999999999,5.38,7.619999999999901 -33,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,-1,8.599999999999916,5.38,3.2199999999999163 -34,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,0,7.799999999999919,5.38,2.419999999999919 -35,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,1,2.8999999999999364,5.38,2.4800000000000635 -36,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,-1,12.499999999999902,3.36,9.139999999999903 -37,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,0,5.499999999999927,3.36,2.1399999999999273 -38,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,1,-0.9000000000000501,3.36,4.2600000000000495 -39,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,-1,8.899999999999915,2.65,6.249999999999915 -40,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,-1,8.899999999999915,9.02,0.12000000000008448 -41,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,0,4.399999999999931,2.65,1.7499999999999312 -42,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,0,4.399999999999931,9.02,4.6200000000000685 -43,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 -44,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-3,-2,7.299999999999921,4.0,3.2999999999999208 -45,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-3,-1,3.299999999999935,4.0,0.700000000000065 -46,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-3,0,-1.1000000000000494,4.0,5.100000000000049 -47,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 -48,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-4,0,2.399999999999938,5.77,3.3700000000000614 -49,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-5,-1,3.1999999999999353,3.92,0.7200000000000646 -50,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-5,0,-1.6000000000000476,3.92,5.5200000000000475 -51,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-6,-1,3.3999999999999346,4.17,0.7700000000000653 -52,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-6,0,3.3999999999999346,4.17,0.7700000000000653 -53,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-7,-1,11.899999999999904,6.63,5.2699999999999045 -54,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-7,0,7.899999999999919,6.63,1.2699999999999187 -55,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-8,0,1.7999999999999403,2.78,0.9800000000000595 -56,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-9,-1,12.199999999999903,6.08,6.119999999999903 -57,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-9,0,7.699999999999919,6.08,1.6199999999999193 -58,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999914,7.71,1.489999999999914 -59,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-12,-1,14.299999999999896,6.98,7.3199999999998955 -60,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-2,5.099999999999929,7.27,2.170000000000071 -61,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-1,7.299999999999921,7.27,0.0299999999999212 -62,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,6.999999999999922,2.54,4.459999999999922 -63,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 -64,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-17,-1,4.199999999999932,6.58,2.3800000000000683 -65,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-18,-1,4.999999999999929,2.72,2.2799999999999288 -66,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,4.93,4.269999999999914 -67,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 -68,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 -69,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,6.99,0.5900000000000762 -70,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,4.93,6.130000000000049 -71,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,6.99,8.19000000000005 -72,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,2.54,2.0599999999999303 -73,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 -74,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 -75,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,11.44,4.640000000000077 -76,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-2,19.399999999999878,5.38,14.019999999999879 -77,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-1,6.299999999999924,5.38,0.9199999999999244 -78,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-22,-1,5.199999999999928,3.36,1.8399999999999284 -79,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,2.65,6.549999999999914 -80,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 -81,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 -82,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,9.02,4.920000000000067 -83,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 -84,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 -85,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 -86,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 -87,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,0,14.599999999999895,3.92,10.679999999999895 -88,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 -89,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,0,13.1999999999999,4.17,9.0299999999999 -90,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-7,-1,4.999999999999929,6.63,1.630000000000071 -91,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 -92,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-9,-1,3.899999999999933,6.08,2.180000000000067 -93,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-10,0,5.599999999999927,7.71,2.110000000000073 -94,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-12,-1,19.09999999999988,6.98,12.11999999999988 -95,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-2,11.599999999999905,7.27,4.329999999999906 -96,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-1,11.499999999999906,7.27,4.229999999999906 -97,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-15,0,4.299999999999931,2.54,1.7599999999999314 -98,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-16,0,4.69999999999993,5.1,0.40000000000006963 -99,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,-1,12.299999999999903,6.58,5.719999999999903 -100,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,0,4.499999999999931,6.58,2.0800000000000693 -101,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,-1,9.599999999999913,2.72,6.879999999999912 -102,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,0,4.199999999999932,2.72,1.4799999999999316 -103,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,4.93,6.169999999999908 -104,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,6.99,4.109999999999907 -105,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,4.93,4.2300000000000555 -106,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,6.99,6.290000000000056 -107,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,1,-0.9000000000000501,4.93,5.83000000000005 -108,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,1,-0.9000000000000501,6.99,7.89000000000005 -109,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,2.54,1.559999999999932 -110,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,5.01,0.9100000000000676 -111,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,0,1.3999999999999417,2.44,1.0400000000000582 -112,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,0,1.3999999999999417,11.44,10.040000000000058 -113,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-3,19.899999999999878,5.38,14.519999999999879 -114,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-2,16.29999999999989,5.38,10.919999999999892 -115,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-1,13.699999999999898,5.38,8.319999999999897 -116,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-22,-1,13.899999999999897,3.36,10.539999999999898 -117,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,9.999999999999911,2.65,7.349999999999911 -118,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,9.999999999999911,9.02,0.9799999999999116 -119,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.299999999999935,2.65,0.6499999999999351 -120,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.299999999999935,9.02,5.720000000000065 -121,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-2,-1,6.099999999999925,4.41,1.689999999999925 -122,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-2,8.799999999999915,4.0,4.7999999999999154 -123,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-1,6.699999999999923,4.0,2.699999999999923 -124,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,-1,6.499999999999924,5.77,0.729999999999924 -125,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,0,-5.3290705182007514e-14,5.77,5.770000000000053 -126,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,-1,4.499999999999931,3.92,0.5799999999999308 -127,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,0,-1.200000000000049,3.92,5.120000000000049 -128,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 -129,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,0,1.9999999999999396,4.17,2.1700000000000603 -130,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,-1,16.39999999999989,6.63,9.76999999999989 -131,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,0,11.299999999999907,6.63,4.669999999999907 -132,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-8,0,4.399999999999931,2.78,1.6199999999999313 -133,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,-1,15.699999999999891,6.08,9.61999999999989 -134,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,0,4.499999999999931,6.08,1.5800000000000693 -135,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-10,0,7.0999999999999215,7.71,0.6100000000000785 -136,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-12,-1,17.699999999999882,6.98,10.719999999999882 -137,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-12,0,4.899999999999929,6.98,2.080000000000071 -138,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-12,1,-5.0000000000000355,6.98,11.980000000000036 -139,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-14,-3,20.799999999999873,7.27,13.529999999999873 -140,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-14,-2,16.29999999999989,7.27,9.029999999999891 -141,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-14,-1,11.499999999999906,7.27,4.229999999999906 -142,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-14,0,5.3999999999999275,7.27,1.870000000000072 -143,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-14,1,-3.80000000000004,7.27,11.07000000000004 -144,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-15,0,1.3999999999999417,2.54,1.1400000000000583 -145,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-16,0,3.9999999999999325,5.1,1.1000000000000671 -146,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-17,-1,14.199999999999896,6.58,7.619999999999896 -147,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-17,0,4.69999999999993,6.58,1.88000000000007 -148,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-18,-1,11.399999999999906,2.72,8.679999999999906 -149,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-18,0,1.6999999999999407,2.72,1.0200000000000595 -150,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-19,-1,6.999999999999922,4.93,2.069999999999922 -151,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-19,-1,6.999999999999922,6.99,0.009999999999921627 -152,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-19,0,4.099999999999932,4.93,0.8300000000000676 -153,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-19,0,4.099999999999932,6.99,2.890000000000068 -154,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-19,1,-2.2000000000000455,4.93,7.130000000000045 -155,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-19,1,-2.2000000000000455,6.99,9.190000000000046 -156,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-1,-1,4.59999999999993,2.54,2.0599999999999303 -157,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 -158,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-1,0,-2.5000000000000444,2.54,5.0400000000000444 -159,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-1,0,-2.5000000000000444,5.01,7.510000000000044 -160,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-20,0,1.4999999999999414,2.44,0.9400000000000586 -161,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-20,0,1.4999999999999414,11.44,9.940000000000058 -162,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-21,-3,20.399999999999874,5.38,15.019999999999875 -163,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-21,-2,17.199999999999886,5.38,11.819999999999887 -164,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-21,-1,8.199999999999918,5.38,2.8199999999999177 -165,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-21,0,3.799999999999933,5.38,1.5800000000000667 -166,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-21,1,-5.500000000000034,5.38,10.880000000000035 -167,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-22,-1,14.699999999999894,3.36,11.339999999999895 -168,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-22,0,2.0999999999999392,3.36,1.2600000000000606 -169,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-22,1,-7.700000000000026,3.36,11.060000000000025 -170,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-23,-1,10.09999999999991,2.65,7.4499999999999105 -171,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-23,-1,10.09999999999991,9.02,1.0799999999999113 -172,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-23,0,1.9999999999999396,2.65,0.6500000000000603 -173,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-23,0,1.9999999999999396,9.02,7.02000000000006 -174,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-2,-1,5.299999999999928,4.41,0.8899999999999277 -175,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-3,-2,10.39999999999991,4.0,6.39999999999991 -176,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-3,-1,4.199999999999932,4.0,0.1999999999999318 -177,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-3,0,-11.700000000000012,4.0,15.700000000000012 -178,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-4,-1,4.59999999999993,5.77,1.1700000000000692 -179,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-4,0,0.09999999999994635,5.77,5.670000000000053 -180,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-5,-1,5.099999999999929,3.92,1.1799999999999287 -181,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-5,0,-2.7000000000000437,3.92,6.620000000000044 -182,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-6,-1,4.69999999999993,4.17,0.5299999999999301 -183,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-6,0,2.7999999999999368,4.17,1.3700000000000632 -184,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-7,-1,14.999999999999893,6.63,8.369999999999894 -185,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-7,0,4.099999999999932,6.63,2.5300000000000678 -186,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-8,0,-0.40000000000005187,2.78,3.1800000000000517 -187,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-9,-1,14.299999999999896,6.08,8.219999999999896 -188,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-9,0,5.599999999999927,6.08,0.48000000000007326 -189,pKa_Chemaxon,Chemaxon,Other,SAMPL8-10,0,5.099999999999929,7.71,2.6100000000000714 -190,pKa_Chemaxon,Chemaxon,Other,SAMPL8-12,0,5.199999999999928,6.98,1.7800000000000722 -191,pKa_Chemaxon,Chemaxon,Other,SAMPL8-14,-1,7.999999999999918,7.27,0.7299999999999187 -192,pKa_Chemaxon,Chemaxon,Other,SAMPL8-14,0,5.499999999999927,7.27,1.7700000000000724 -193,pKa_Chemaxon,Chemaxon,Other,SAMPL8-15,0,1.0999999999999428,2.54,1.4400000000000572 -194,pKa_Chemaxon,Chemaxon,Other,SAMPL8-16,-1,8.299999999999917,5.1,3.1999999999999176 -195,pKa_Chemaxon,Chemaxon,Other,SAMPL8-16,0,3.599999999999934,5.1,1.5000000000000657 -196,pKa_Chemaxon,Chemaxon,Other,SAMPL8-17,-1,10.899999999999908,6.58,4.319999999999908 -197,pKa_Chemaxon,Chemaxon,Other,SAMPL8-17,0,5.499999999999927,6.58,1.080000000000073 -198,pKa_Chemaxon,Chemaxon,Other,SAMPL8-18,0,0.9999999999999432,2.72,1.720000000000057 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+234,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 +235,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-17,-1,4.199999999999932,6.58,2.3800000000000683 +236,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-18,-1,4.999999999999929,2.72,2.2799999999999288 +237,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,4.93,4.269999999999914 +238,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 +239,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 +240,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,6.99,0.5900000000000762 +241,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,4.93,6.130000000000049 +242,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,6.99,8.19000000000005 +243,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,2.54,2.0599999999999303 +244,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 +245,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 +246,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-2,19.399999999999878,5.38,14.019999999999879 +247,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-1,6.299999999999924,5.38,0.9199999999999244 +248,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-22,-1,5.199999999999928,3.36,1.8399999999999284 +249,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,2.65,6.549999999999914 +250,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 +251,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 +252,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,9.02,4.920000000000067 +253,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 +254,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 +255,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 +256,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 +257,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-5,0,14.599999999999895,3.92,10.679999999999895 +258,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 +259,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-6,0,13.1999999999999,4.17,9.0299999999999 +260,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-7,-1,4.999999999999929,6.63,1.630000000000071 +261,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 +262,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-9,-1,3.899999999999933,6.08,2.180000000000067 diff --git a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/mean_abs_error_plot.pdf b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/mean_abs_error_plot.pdf index 469a992..f59f309 100644 Binary files a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/mean_abs_error_plot.pdf and b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/mean_abs_error_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/mean_error_plot.pdf b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/mean_error_plot.pdf index 2d5e2ca..4bfcac4 100644 Binary files a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/mean_error_plot.pdf and b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/mean_error_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/popular_transitions_pKa_data.csv b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/popular_transitions_pKa_data.csv index 85141de..9fe86b4 100644 --- a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/popular_transitions_pKa_data.csv +++ b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/popular_transitions_pKa_data.csv @@ -1,151 +1,136 @@ ,Submission,Method Name,Method Type,Molecule ID,Formal Charge,Predicted pKa,Experimental pKa,Absolute Error -0,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,0,-0.6000000000000512,2.54,3.140000000000051 -1,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,-1,3.599999999999934,5.01,1.4100000000000659 -2,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 -3,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-3,-1,3.299999999999935,4.0,0.700000000000065 -4,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 -5,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-5,-1,3.1999999999999353,3.92,0.7200000000000646 -6,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-6,-1,3.3999999999999346,4.17,0.7700000000000653 -7,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-7,-1,11.899999999999904,6.63,5.2699999999999045 -8,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-8,0,1.7999999999999403,2.78,0.9800000000000595 -9,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-9,-1,12.199999999999903,6.08,6.119999999999903 -10,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 -11,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,-1,14.499999999999895,6.98,7.519999999999895 -12,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,-1,9.699999999999912,7.27,2.4299999999999127 -13,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 -14,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,0,6.699999999999923,5.1,1.5999999999999233 -15,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-17,-1,11.499999999999906,6.58,4.919999999999906 -16,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-18,-1,11.199999999999907,2.72,8.479999999999906 -17,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,0,5.999999999999925,4.93,1.0699999999999257 -18,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,-1,6.699999999999923,6.99,0.2900000000000773 -19,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,0,4.69999999999993,2.44,2.25999999999993 -20,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,-1,10.09999999999991,11.44,1.3400000000000887 -21,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,-1,8.599999999999916,5.38,3.2199999999999163 -22,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,-1,12.499999999999902,3.36,9.139999999999903 -23,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,0,4.399999999999931,2.65,1.7499999999999312 -24,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,-1,8.899999999999915,9.02,0.12000000000008448 -25,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,0,14.0,2.54,11.46 -26,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 -27,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 -28,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 -29,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 -30,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 -31,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 -32,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-7,-1,4.999999999999929,6.63,1.630000000000071 -33,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 -34,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-9,-1,3.899999999999933,6.08,2.180000000000067 -35,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999914,7.71,1.489999999999914 -36,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-12,-1,14.299999999999896,6.98,7.3199999999998955 -37,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-1,7.299999999999921,7.27,0.0299999999999212 -38,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,6.999999999999922,2.54,4.459999999999922 -39,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 -40,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-17,-1,4.199999999999932,6.58,2.3800000000000683 -41,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-18,-1,4.999999999999929,2.72,2.2799999999999288 -42,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 -43,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 -44,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 -45,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,-1,0.0,11.44,11.44 -46,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-1,6.299999999999924,5.38,0.9199999999999244 -47,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-22,-1,5.199999999999928,3.36,1.8399999999999284 -48,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 -49,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 -50,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,0,14.0,2.54,11.46 -51,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,5.01,0.9100000000000676 -52,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-2,-1,6.099999999999925,4.41,1.689999999999925 -53,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-1,6.699999999999923,4.0,2.699999999999923 -54,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,-1,6.499999999999924,5.77,0.729999999999924 -55,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,-1,4.499999999999931,3.92,0.5799999999999308 -56,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 -57,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,-1,16.39999999999989,6.63,9.76999999999989 -58,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-8,0,4.399999999999931,2.78,1.6199999999999313 -59,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,-1,15.699999999999891,6.08,9.61999999999989 -60,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-10,0,5.599999999999927,7.71,2.110000000000073 -61,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-12,-1,19.09999999999988,6.98,12.11999999999988 -62,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-1,11.499999999999906,7.27,4.229999999999906 -63,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-15,0,4.299999999999931,2.54,1.7599999999999314 -64,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-16,0,4.69999999999993,5.1,0.40000000000006963 -65,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,-1,12.299999999999903,6.58,5.719999999999903 -66,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,-1,9.599999999999913,2.72,6.879999999999912 -67,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,4.93,4.2300000000000555 -68,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,6.99,4.109999999999907 -69,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,0,1.3999999999999417,2.44,1.0400000000000582 -70,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,-1,0.0,11.44,11.44 -71,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-1,13.699999999999898,5.38,8.319999999999897 -72,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-22,-1,13.899999999999897,3.36,10.539999999999898 -73,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.299999999999935,2.65,0.6499999999999351 -74,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,9.999999999999911,9.02,0.9799999999999116 -75,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-1,0,-2.5000000000000444,2.54,5.0400000000000444 -76,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 -77,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-2,-1,5.299999999999928,4.41,0.8899999999999277 -78,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-3,-1,4.199999999999932,4.0,0.1999999999999318 -79,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-4,-1,4.59999999999993,5.77,1.1700000000000692 -80,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-5,-1,5.099999999999929,3.92,1.1799999999999287 -81,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-6,-1,4.69999999999993,4.17,0.5299999999999301 -82,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-7,-1,14.999999999999893,6.63,8.369999999999894 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Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 +130,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 +131,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-1,6.299999999999924,5.38,0.9199999999999244 +132,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-22,-1,5.199999999999928,3.36,1.8399999999999284 +133,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 +134,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 diff --git a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/rmse_plot.pdf b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/rmse_plot.pdf index 02220ae..2073ba2 100644 Binary files a/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/rmse_plot.pdf and b/physical_properties/pKa/macrostate_analysis/popular_transitions_analysis/analysis_outputs_ranked/rmse_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions.csv index 60f1ee7..5e4f156 100644 --- a/physical_properties/pKa/macrostate_analysis/selected_transitions.csv +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions.csv @@ -19,7 +19,6 @@ SAMPL8-18, 2.72, 0 SAMPL8-19, 4.93, 0 SAMPL8-19,6.99,-1 SAMPL8-20, 2.44, 0 -SAMPL8-20, 11.44, -1 SAMPL8-21, 5.38, 0 SAMPL8-22, 3.36, 0 SAMPL8-23, 2.65, 0 diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/README.md b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/README.md index fe33e05..fdc4ca0 100644 --- a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/README.md +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/README.md @@ -1,4 +1,4 @@ ## Manifest -[`analysis_outputs_all/`](analysis_outputs_all/)- This directory contains bar plots and correlation plots associated with the performance statistics for all submissions. -[`analysis_outputs_ranked/`](analysis_outputs_ranked/)- This directory contains bar plots and correlation plots associated with the performance statistics for all ranked submissions. - +-[`supplementary_figures/`](supplementary_figures/)-This directory contains tables and figures which will be included in the supplementary material for the publication. diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/Correlation_Plots/Correlation_statistics.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/Correlation_Plots/Correlation_statistics.csv index 44c4ea4..65cbf23 100644 --- a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/Correlation_Plots/Correlation_statistics.csv +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/Correlation_Plots/Correlation_statistics.csv @@ -1,13 +1,13 @@ ,Submission,R-squared,Slope,Kendall Tau -0,pKa-3DS-1,0.8060107999090355,0.9186706651772883,0.6398668943087059 -1,pKa-RobertRaddi_AdaBoost,-0.1554763438592885,-0.34721724893693445,-0.049364677205182415 -2,pKa-3DS-2,0.782840531545755,1.0553936995159576,0.6174531409332867 -3,pKa-3DS-3,0.7849780477326276,0.8568085111731772,0.6197663635974378 -4,pKa_SabatinoRodriguezPaluch_uESE,0.08933929143362386,0.18697042300667957,0.16583227554105334 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Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/Correlation_Plots/pKa_SabatinoRodriguezPaluch_uESE_modifiedCorr_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/Error_statistics.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/Error_statistics.csv index 2cf187b..75e1cc3 100644 --- a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/Error_statistics.csv +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/Error_statistics.csv @@ -1,22 +1,22 @@ ,Molecule ID,Mean Error,Mean Absolute Error,Root Mean Squared Error -0,SAMPL8-1,1.9208333333332905,5.195833333333364,5.195833333333364 -1,SAMPL8-2,1.2316666666665932,2.188333333333303,2.1883333333333024 -2,SAMPL8-3,0.7249999999999299,1.391666666666639,1.391666666666639 -3,SAMPL8-4,-0.9116666666667368,2.8100000000000267,2.8100000000000267 -4,SAMPL8-5,-0.45333333333339887,2.053333333333337,2.053333333333337 -5,SAMPL8-6,-1.1783333333333972,1.8150000000000162,1.8150000000000162 -6,SAMPL8-7,3.2116666666666127,3.8383333333333027,3.8383333333333027 -7,SAMPL8-8,0.7283333333332679,1.7316666666666396,1.7316666666666396 -8,SAMPL8-9,2.7783333333332827,3.29500000000001,3.29500000000001 -9,SAMPL8-10,-0.5850000000000786,1.326666666666675,1.326666666666675 -10,SAMPL8-12,3.5116666666666276,4.284999999999997,4.284999999999997 -11,SAMPL8-14,-3.428333333333373,4.448333333333317,4.448333333333317 -12,SAMPL8-15,1.4183333333332657,2.3283333333333043,2.3283333333333043 -13,SAMPL8-16,0.5999999999999268,1.5999999999999825,1.5999999999999825 -14,SAMPL8-17,1.9949999999999506,3.2950000000000093,3.2950000000000093 -15,SAMPL8-18,4.046666666666623,4.8766666666666625,4.8766666666666625 -16,SAMPL8-19,0.439999999999924,1.6641666666666544,1.6641666666666548 -17,SAMPL8-20,-3.206666666666715,5.350000000000005,5.350000000000005 -18,SAMPL8-21,4.703333333333297,5.1099999999999985,5.1099999999999985 -19,SAMPL8-22,6.106666666666631,6.526666666666652,6.526666666666652 -20,SAMPL8-23,0.16083333333325903,1.4541666666666613,1.4541666666666615 +0,SAMPL8-1,-2.007058823529473,2.6164705882353365,4.116789154326051 +1,SAMPL8-2,1.2316666666665932,2.188333333333303,2.86637401606974 +2,SAMPL8-3,0.7249999999999299,1.391666666666639,1.7066048165875665 +3,SAMPL8-4,-0.9116666666667368,2.8100000000000267,3.146993274010405 +4,SAMPL8-5,-0.45333333333339887,2.0533333333333377,2.512846990964634 +5,SAMPL8-6,-1.1783333333333972,1.8150000000000162,2.4040036050999283 +6,SAMPL8-8,0.7283333333332679,1.7316666666666396,1.8707128765971943 +7,SAMPL8-10,-0.5850000000000786,1.3266666666666753,1.5239531926320478 +8,SAMPL8-15,1.4183333333332657,2.3283333333333043,2.588583911459399 +9,SAMPL8-16,0.5999999999999268,1.5999999999999825,1.7781076082921863 +10,SAMPL8-19,0.439999999999924,1.6641666666666548,2.2484068433744877 +11,SAMPL8-20,1.6433333333332658,2.6433333333333136,3.148322304550959 +12,SAMPL8-23,0.16083333333325903,1.4541666666666615,1.9661595391354398 +13,SAMPL8-7,1.1324999999999192,2.0724999999999545,2.3637681781426423 +14,SAMPL8-9,0.2074999999999243,0.9825000000000153,1.2069175613934693 +15,SAMPL8-17,-0.7175000000000742,1.2325000000000148,1.3737357824560357 +16,SAMPL8-18,0.4299999999999353,1.674999999999994,1.8234308322499986 +17,SAMPL8-12,0.0033333333332548065,1.5499999999999945,1.630357833932983 +18,SAMPL8-14,0.4133333333332532,1.6266666666666347,1.6799503960930657 +19,SAMPL8-21,0.7866666666665916,1.5999999999999943,1.8621850964211895 +20,SAMPL8-22,1.5733333333332629,2.4133333333333034,2.9957080409589985 diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/abs_error_bymethod_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/abs_error_bymethod_plot.pdf index 6a68a13..a2e1c18 100644 Binary files a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/abs_error_bymethod_plot.pdf and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/abs_error_bymethod_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/abs_error_bymol_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/abs_error_bymol_plot.pdf index 9b2c60e..f865760 100644 Binary files a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/abs_error_bymol_plot.pdf and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/abs_error_bymol_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/macrostate_pKa_data.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/macrostate_pKa_data.csv index 383ddac..abb5fd4 100644 --- a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/macrostate_pKa_data.csv +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/macrostate_pKa_data.csv @@ -1,529 +1,510 @@ ,Submission,Method Name,Method Type,Molecule ID,Formal Charge,Predicted pKa,Experimental pKa,Absolute Error -0,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 -1,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,-1,14.499999999999895,6.98,7.519999999999895 -2,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,0,8.499999999999917,6.98,1.519999999999916 -3,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,1,2.699999999999937,6.98,4.280000000000063 -4,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,-2,13.599999999999898,7.27,6.329999999999899 -5,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,-1,9.699999999999912,7.27,2.4299999999999127 -6,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,0,8.599999999999916,7.27,1.3299999999999166 -7,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,1,3.3999999999999346,7.27,3.870000000000065 -8,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 -9,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,-2,12.099999999999904,5.1,6.999999999999904 -10,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,-1,10.699999999999909,5.1,5.599999999999909 -11,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,0,6.699999999999923,5.1,1.5999999999999233 -12,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-17,-1,11.499999999999906,6.58,4.919999999999906 -13,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-17,0,7.299999999999921,6.58,0.7199999999999207 -14,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-18,-1,11.199999999999907,2.72,8.479999999999906 -15,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-18,0,5.199999999999928,2.72,2.479999999999928 -16,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,-1,6.699999999999923,4.93,1.7699999999999232 -17,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,-1,6.699999999999923,6.99,0.2900000000000773 -18,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,0,5.999999999999925,4.93,1.0699999999999257 -19,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,0,5.999999999999925,6.99,0.9900000000000748 -20,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,1,3.3999999999999346,4.93,1.530000000000065 -21,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,1,3.3999999999999346,6.99,3.5900000000000656 -22,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,-1,3.599999999999934,2.54,1.0599999999999339 -23,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,-1,3.599999999999934,5.01,1.4100000000000659 -24,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,0,-0.6000000000000512,2.54,3.140000000000051 -25,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,0,-0.6000000000000512,5.01,5.610000000000051 -26,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,-1,10.09999999999991,2.44,7.659999999999911 -27,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,-1,10.09999999999991,11.44,1.3400000000000887 -28,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,0,4.69999999999993,2.44,2.25999999999993 -29,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,0,4.69999999999993,11.44,6.7400000000000695 -30,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,1,0.199999999999946,2.44,2.240000000000054 -31,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,1,0.199999999999946,11.44,11.240000000000054 -32,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,-2,12.9999999999999,5.38,7.619999999999901 -33,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,-1,8.599999999999916,5.38,3.2199999999999163 -34,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,0,7.799999999999919,5.38,2.419999999999919 -35,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,1,2.8999999999999364,5.38,2.4800000000000635 -36,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,-1,12.499999999999902,3.36,9.139999999999903 -37,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,0,5.499999999999927,3.36,2.1399999999999273 -38,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,1,-0.9000000000000501,3.36,4.2600000000000495 -39,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,-1,8.899999999999915,2.65,6.249999999999915 -40,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,-1,8.899999999999915,9.02,0.12000000000008448 -41,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,0,4.399999999999931,2.65,1.7499999999999312 -42,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,0,4.399999999999931,9.02,4.6200000000000685 -43,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 -44,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-3,-2,7.299999999999921,4.0,3.2999999999999208 -45,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-3,-1,3.299999999999935,4.0,0.700000000000065 -46,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-3,0,-1.1000000000000494,4.0,5.100000000000049 -47,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 -48,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-4,0,2.399999999999938,5.77,3.3700000000000614 -49,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-5,-1,3.1999999999999353,3.92,0.7200000000000646 -50,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-5,0,-1.6000000000000476,3.92,5.5200000000000475 -51,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-6,-1,3.3999999999999346,4.17,0.7700000000000653 -52,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-6,0,3.3999999999999346,4.17,0.7700000000000653 -53,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-7,-1,11.899999999999904,6.63,5.2699999999999045 -54,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-7,0,7.899999999999919,6.63,1.2699999999999187 -55,pKa-3DS-1,COSMO-RS one pKa 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pKa fit,LFER,SAMPL8-4,0,3.1999999999999353,5.77,2.5700000000000642 -200,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-5,-1,3.899999999999933,3.92,0.020000000000067075 -201,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-5,0,-0.8000000000000504,3.92,4.72000000000005 -202,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-6,-1,4.199999999999932,4.17,0.02999999999993186 -203,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-6,0,4.099999999999932,4.17,0.07000000000006779 -204,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-7,-1,12.499999999999902,6.63,5.869999999999902 -205,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-7,0,8.499999999999917,6.63,1.8699999999999166 -206,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-8,0,4.099999999999932,2.78,1.3199999999999323 -207,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-9,-1,12.699999999999902,6.08,6.6199999999999015 -208,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-9,0,8.299999999999917,6.08,2.219999999999917 -209,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-10,0,6.499999999999924,7.71,1.2100000000000763 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-219,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,-1,11.999999999999904,4.93,7.069999999999904 -220,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,-1,11.999999999999904,6.99,5.009999999999904 -221,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,0,3.0999999999999357,4.93,1.830000000000064 -222,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,0,3.0999999999999357,6.99,3.8900000000000645 -223,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-1,-1,7.59999999999992,2.54,5.05999999999992 -224,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-1,-1,7.59999999999992,5.01,2.58999999999992 -225,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-20,0,1.1999999999999424,2.44,1.2400000000000575 -226,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-20,0,1.1999999999999424,11.44,10.240000000000057 -227,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-21,-1,17.199999999999886,5.38,11.819999999999887 -228,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-22,-1,17.499999999999886,3.36,14.139999999999887 -229,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,-1,13.499999999999899,2.65,10.849999999999898 -230,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,-1,13.499999999999899,9.02,4.479999999999899 -231,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,0,2.0999999999999392,2.65,0.5500000000000607 -232,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,0,2.0999999999999392,9.02,6.92000000000006 -233,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-2,-1,8.099999999999918,4.41,3.689999999999918 -234,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-3,-1,6.299999999999924,4.0,2.2999999999999243 -235,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-4,-1,11.099999999999907,5.77,5.329999999999908 -236,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-4,0,-8.000000000000025,5.77,13.770000000000024 -237,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-5,-1,7.59999999999992,3.92,3.67999999999992 -238,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-5,0,-10.100000000000017,3.92,14.020000000000017 -239,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-6,-1,5.799999999999926,4.17,1.6299999999999262 -240,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-6,0,-5.3000000000000345,4.17,9.470000000000034 -241,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-7,0,8.799999999999915,6.63,2.1699999999999156 -242,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-8,0,4.59999999999993,2.78,1.8199999999999306 -243,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-9,0,5.899999999999926,6.08,0.18000000000007432 -244,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999914,7.71,1.489999999999914 -245,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-12,-1,14.299999999999896,6.98,7.3199999999998955 -246,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-2,5.099999999999929,7.27,2.170000000000071 -247,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-1,7.299999999999921,7.27,0.0299999999999212 -248,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,6.999999999999922,2.54,4.459999999999922 -249,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 -250,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-17,-1,4.199999999999932,6.58,2.3800000000000683 -251,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-18,-1,4.999999999999929,2.72,2.2799999999999288 -252,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,4.93,4.269999999999914 -253,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 -254,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 -255,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,6.99,0.5900000000000762 -256,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,4.93,6.130000000000049 -257,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,6.99,8.19000000000005 -258,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,2.54,2.0599999999999303 -259,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 -260,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 -261,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,11.44,4.640000000000077 -262,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-2,19.399999999999878,5.38,14.019999999999879 -263,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-1,6.299999999999924,5.38,0.9199999999999244 -264,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-22,-1,5.199999999999928,3.36,1.8399999999999284 -265,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,2.65,6.549999999999914 -266,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 -267,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 -268,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,9.02,4.920000000000067 -269,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 -270,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 -271,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 -272,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 -273,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,0,14.599999999999895,3.92,10.679999999999895 -274,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 -275,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,0,13.1999999999999,4.17,9.0299999999999 -276,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-7,-1,4.999999999999929,6.63,1.630000000000071 -277,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 -278,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-9,-1,3.899999999999933,6.08,2.180000000000067 -279,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-10,0,5.599999999999927,7.71,2.110000000000073 -280,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-12,-1,19.09999999999988,6.98,12.11999999999988 -281,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-2,11.599999999999905,7.27,4.329999999999906 -282,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-1,11.499999999999906,7.27,4.229999999999906 -283,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-15,0,4.299999999999931,2.54,1.7599999999999314 -284,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-16,0,4.69999999999993,5.1,0.40000000000006963 -285,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,-1,12.299999999999903,6.58,5.719999999999903 -286,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,0,4.499999999999931,6.58,2.0800000000000693 -287,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,-1,9.599999999999913,2.72,6.879999999999912 -288,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,0,4.199999999999932,2.72,1.4799999999999316 -289,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,4.93,6.169999999999908 -290,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,6.99,4.109999999999907 -291,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,4.93,4.2300000000000555 -292,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,6.99,6.290000000000056 -293,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,1,-0.9000000000000501,4.93,5.83000000000005 -294,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,1,-0.9000000000000501,6.99,7.89000000000005 -295,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,2.54,1.559999999999932 -296,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,5.01,0.9100000000000676 -297,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,0,1.3999999999999417,2.44,1.0400000000000582 -298,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,0,1.3999999999999417,11.44,10.040000000000058 -299,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-3,19.899999999999878,5.38,14.519999999999879 -300,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-2,16.29999999999989,5.38,10.919999999999892 -301,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-1,13.699999999999898,5.38,8.319999999999897 -302,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-22,-1,13.899999999999897,3.36,10.539999999999898 -303,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,9.999999999999911,2.65,7.349999999999911 -304,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,9.999999999999911,9.02,0.9799999999999116 -305,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.299999999999935,2.65,0.6499999999999351 -306,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.299999999999935,9.02,5.720000000000065 -307,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-2,-1,6.099999999999925,4.41,1.689999999999925 -308,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-2,8.799999999999915,4.0,4.7999999999999154 -309,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-1,6.699999999999923,4.0,2.699999999999923 -310,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,-1,6.499999999999924,5.77,0.729999999999924 -311,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,0,-5.3290705182007514e-14,5.77,5.770000000000053 -312,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,-1,4.499999999999931,3.92,0.5799999999999308 -313,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,0,-1.200000000000049,3.92,5.120000000000049 -314,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 -315,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,0,1.9999999999999396,4.17,2.1700000000000603 -316,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,-1,16.39999999999989,6.63,9.76999999999989 -317,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,0,11.299999999999907,6.63,4.669999999999907 -318,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-8,0,4.399999999999931,2.78,1.6199999999999313 -319,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,-1,15.699999999999891,6.08,9.61999999999989 -320,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,0,4.499999999999931,6.08,1.5800000000000693 -321,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-10,0,6.399999999999924,7.71,1.310000000000076 -322,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-12,-1,13.1999999999999,6.98,6.219999999999899 -323,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-14,-2,3.9999999999999325,7.27,3.270000000000067 -324,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-14,-1,4.099999999999932,7.27,3.1700000000000674 -325,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-15,0,5.499999999999927,2.54,2.959999999999927 -326,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-16,0,6.199999999999925,5.1,1.099999999999925 -327,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-17,-1,4.499999999999931,6.58,2.0800000000000693 -328,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-18,-1,4.499999999999931,2.72,1.7799999999999305 -329,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,-1,5.299999999999928,4.93,0.36999999999992816 -330,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,-1,5.299999999999928,6.99,1.6900000000000723 -331,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,0,5.899999999999926,4.93,0.969999999999926 -332,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,0,5.899999999999926,6.99,1.0900000000000745 -333,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,1,-1.3000000000000487,4.93,6.230000000000048 -334,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,1,-1.3000000000000487,6.99,8.290000000000049 -335,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-1,-1,4.59999999999993,2.54,2.0599999999999303 -336,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 -337,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-20,0,7.699999999999919,2.44,5.25999999999992 -338,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-20,0,7.699999999999919,11.44,3.74000000000008 -339,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-21,-2,9.999999999999911,5.38,4.619999999999911 -340,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-21,-1,2.399999999999938,5.38,2.9800000000000617 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100644 Binary files a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/mean_abs_error_plot.pdf and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/mean_abs_error_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/mean_error_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/mean_error_plot.pdf index c603d0d..37d0173 100644 Binary files a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/mean_error_plot.pdf and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/mean_error_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/popular_transitions_pKa_data.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/popular_transitions_pKa_data.csv index f7bdc8d..1f8af3c 100644 --- a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/popular_transitions_pKa_data.csv +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/popular_transitions_pKa_data.csv @@ -1,301 +1,289 @@ ,Submission,Method Name,Method Type,Molecule ID,Formal Charge,Predicted pKa,Experimental pKa,Absolute Error -0,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,0,-0.6000000000000512,2.54,3.140000000000051 -1,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,-1,3.599999999999934,5.01,1.4100000000000659 -2,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 -3,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-3,-1,3.299999999999935,4.0,0.700000000000065 -4,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 -5,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-5,-1,3.1999999999999353,3.92,0.7200000000000646 -6,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-6,-1,3.3999999999999346,4.17,0.7700000000000653 -7,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-7,0,7.899999999999919,6.63,1.2699999999999187 -8,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-8,0,1.7999999999999403,2.78,0.9800000000000595 -9,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-9,0,7.699999999999919,6.08,1.6199999999999193 -10,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 -11,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,0,8.499999999999917,6.98,1.519999999999916 -12,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,0,8.599999999999916,7.27,1.3299999999999166 -13,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 -14,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,0,6.699999999999923,5.1,1.5999999999999233 -15,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-17,0,7.299999999999921,6.58,0.7199999999999207 -16,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-18,0,5.199999999999928,2.72,2.479999999999928 -17,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,0,5.999999999999925,4.93,1.0699999999999257 -18,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,-1,6.699999999999923,6.99,0.2900000000000773 -19,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,0,4.69999999999993,2.44,2.25999999999993 -20,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,-1,10.09999999999991,11.44,1.3400000000000887 -21,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,0,7.799999999999919,5.38,2.419999999999919 -22,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,0,5.499999999999927,3.36,2.1399999999999273 -23,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,0,4.399999999999931,2.65,1.7499999999999312 -24,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,-1,8.899999999999915,9.02,0.12000000000008448 -25,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-1,0,14,2.54,11.46 -26,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-1,-1,4.999999999999929,5.01,0.010000000000070841 -27,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-2,-1,7.199999999999921,4.41,2.789999999999921 -28,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-3,-1,4.999999999999929,4.0,0.999999999999929 -29,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 -30,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-5,-1,0.29999999999994564,3.92,3.6200000000000543 -31,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-6,-1,-0.10000000000005294,4.17,4.270000000000053 -32,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-7,0,14,6.63,7.37 -33,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-8,0,5.6999999999999265,2.78,2.9199999999999267 -34,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-9,0,14,6.08,7.92 -35,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-10,0,5.299999999999928,7.71,2.410000000000072 -36,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-12,0,14,6.98,7.02 -37,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-14,0,0,7.27,7.27 -38,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-15,0,6.299999999999924,2.54,3.7599999999999243 -39,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-16,0,7.199999999999921,5.1,2.0999999999999215 -40,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-17,0,14,6.58,7.42 -41,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-18,0,14,2.72,11.28 -42,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-19,0,7.799999999999919,4.93,2.8699999999999193 -43,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-19,-1,5.199999999999928,6.99,1.790000000000072 -44,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-20,0,7.59999999999992,2.44,5.15999999999992 -45,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-20,-1,0,11.44,11.44 -46,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-21,0,14,5.38,8.620000000000001 -47,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-22,0,14,3.36,10.64 -48,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-23,0,3.599999999999934,2.65,0.949999999999934 -49,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-23,-1,7.999999999999918,9.02,1.0200000000000813 -50,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-1,0,-3.0000000000000426,2.54,5.540000000000043 -51,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-1,-1,2.0999999999999392,5.01,2.9100000000000605 -52,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-2,-1,1.599999999999941,4.41,2.810000000000059 -53,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-3,-1,1.6999999999999407,4.0,2.3000000000000593 -54,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-4,-1,1.7999999999999403,5.77,3.9700000000000593 -55,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-5,-1,1.4999999999999414,3.92,2.4200000000000585 -56,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-6,-1,1.7999999999999403,4.17,2.3700000000000596 -57,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-7,0,7.299999999999921,6.63,0.6699999999999209 -58,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-8,0,1.7999999999999403,2.78,0.9800000000000595 -59,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-9,0,6.999999999999922,6.08,0.9199999999999218 -60,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 -61,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-12,0,7.999999999999918,6.98,1.0199999999999179 -62,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-14,0,8.099999999999918,7.27,0.8299999999999184 -63,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 -64,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-16,0,5.799999999999926,5.1,0.6999999999999265 -65,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-17,0,6.599999999999923,6.58,0.01999999999992319 -66,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-18,0,3.9999999999999325,2.72,1.2799999999999323 -67,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-19,0,4.999999999999929,4.93,0.06999999999992923 -68,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-19,-1,5.6999999999999265,6.99,1.2900000000000738 -69,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-20,0,3.299999999999935,2.44,0.859999999999935 -70,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-20,-1,9.899999999999912,11.44,1.540000000000088 -71,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-21,0,7.0999999999999215,5.38,1.7199999999999216 -72,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-22,0,4.299999999999931,3.36,0.9399999999999316 -73,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-23,0,3.0999999999999357,2.65,0.4499999999999358 -74,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-23,-1,8.399999999999917,9.02,0.6200000000000827 -75,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-1,0,0.199999999999946,2.54,2.340000000000054 -76,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-1,-1,4.299999999999931,5.01,0.7100000000000684 -77,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 -78,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-3,-1,3.9999999999999325,4.0,6.750155989720952e-14 -79,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-4,-1,4.199999999999932,5.77,1.5700000000000678 -80,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-5,-1,3.899999999999933,3.92,0.020000000000067075 -81,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-6,-1,4.199999999999932,4.17,0.02999999999993186 -82,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-7,0,8.499999999999917,6.63,1.8699999999999166 -83,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-8,0,4.099999999999932,2.78,1.3199999999999323 -84,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-9,0,8.299999999999917,6.08,2.219999999999917 -85,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-10,0,9.399999999999913,7.71,1.6899999999999133 -86,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-12,0,9.099999999999914,6.98,2.119999999999914 -87,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-14,0,9.199999999999914,7.27,1.9299999999999145 -88,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-15,0,5.799999999999926,2.54,3.259999999999926 -89,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-16,0,7.39999999999992,5.1,2.2999999999999208 -90,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-17,0,7.899999999999919,6.58,1.3199999999999186 -91,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-18,0,5.899999999999926,2.72,3.1799999999999256 -92,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-19,0,6.699999999999923,4.93,1.7699999999999232 -93,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-19,-1,7.299999999999921,6.99,0.30999999999992056 -94,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-20,0,5.3999999999999275,2.44,2.9599999999999276 -95,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-20,-1,10.699999999999909,11.44,0.7400000000000908 -96,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-21,0,8.399999999999917,5.38,3.019999999999917 -97,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-22,0,6.099999999999925,3.36,2.739999999999925 -98,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-23,0,5.099999999999929,2.65,2.4499999999999287 -99,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-23,-1,9.499999999999913,9.02,0.4799999999999134 -100,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-1,0,14,2.54,11.46 -101,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-1,-1,7.59999999999992,5.01,2.58999999999992 -102,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-2,-1,8.099999999999918,4.41,3.689999999999918 -103,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-3,-1,6.299999999999924,4.0,2.2999999999999243 -104,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-4,-1,11.099999999999907,5.77,5.329999999999908 -105,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-5,-1,7.59999999999992,3.92,3.67999999999992 -106,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-6,-1,5.799999999999926,4.17,1.6299999999999262 -107,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-7,0,8.799999999999915,6.63,2.1699999999999156 -108,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-8,0,4.59999999999993,2.78,1.8199999999999306 -109,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-9,0,5.899999999999926,6.08,0.18000000000007432 -110,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-10,0,6.499999999999924,7.71,1.2100000000000763 -111,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-12,0,14,6.98,7.02 -112,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-14,0,0,7.27,7.27 -113,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-15,0,1.0999999999999428,2.54,1.4400000000000572 -114,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-16,0,3.599999999999934,5.1,1.5000000000000657 -115,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-17,0,5.199999999999928,6.58,1.3800000000000718 -116,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-18,0,1.599999999999941,2.72,1.1200000000000592 -117,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,0,3.0999999999999357,4.93,1.830000000000064 -118,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,-1,11.999999999999904,6.99,5.009999999999904 -119,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-20,0,1.1999999999999424,2.44,1.2400000000000575 -120,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-20,-1,0,11.44,11.44 -121,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-21,0,14,5.38,8.620000000000001 -122,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-22,0,14,3.36,10.64 -123,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,0,2.0999999999999392,2.65,0.5500000000000607 -124,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,-1,13.499999999999899,9.02,4.479999999999899 -125,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,0,14,2.54,11.46 -126,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 -127,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 -128,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 -129,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 -130,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 -131,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 -132,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-7,0,14,6.63,7.37 -133,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 -134,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-9,0,14,6.08,7.92 -135,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999914,7.71,1.489999999999914 -136,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-12,0,14,6.98,7.02 -137,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,0,0,7.27,7.27 -138,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,6.999999999999922,2.54,4.459999999999922 -139,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 -140,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-17,0,14,6.58,7.42 -141,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-18,0,14,2.72,11.28 -142,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 -143,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 -144,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 -145,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,-1,0,11.44,11.44 -146,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,0,14,5.38,8.620000000000001 -147,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-22,0,14,3.36,10.64 -148,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 -149,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 -150,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,0,14,2.54,11.46 -151,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,5.01,0.9100000000000676 -152,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-2,-1,6.099999999999925,4.41,1.689999999999925 -153,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-1,6.699999999999923,4.0,2.699999999999923 -154,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,-1,6.499999999999924,5.77,0.729999999999924 -155,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,-1,4.499999999999931,3.92,0.5799999999999308 -156,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 -157,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,0,11.299999999999907,6.63,4.669999999999907 -158,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-8,0,4.399999999999931,2.78,1.6199999999999313 -159,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,0,4.499999999999931,6.08,1.5800000000000693 -160,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-10,0,5.599999999999927,7.71,2.110000000000073 -161,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-12,0,14,6.98,7.02 -162,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,0,0,7.27,7.27 -163,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-15,0,4.299999999999931,2.54,1.7599999999999314 -164,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-16,0,4.69999999999993,5.1,0.40000000000006963 -165,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,0,4.499999999999931,6.58,2.0800000000000693 -166,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,0,4.199999999999932,2.72,1.4799999999999316 -167,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,4.93,4.2300000000000555 -168,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,6.99,4.109999999999907 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Forest,QSPR/ML,SAMPL8-18,0,14,2.72,11.28 -192,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,0,5.899999999999926,4.93,0.969999999999926 -193,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,-1,5.299999999999928,6.99,1.6900000000000723 -194,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-20,0,7.699999999999919,2.44,5.25999999999992 -195,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-20,-1,0,11.44,11.44 -196,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-21,0,14,5.38,8.620000000000001 -197,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-22,0,14,3.36,10.64 -198,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-23,0,1.6999999999999407,2.65,0.9500000000000592 -199,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-23,-1,5.499999999999927,9.02,3.5200000000000724 -200,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-1,0,-2.5000000000000444,2.54,5.0400000000000444 -201,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 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fit,QM+LEC,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 +5,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-5,-1,3.1999999999999353,3.92,0.7200000000000646 +6,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-6,-1,3.3999999999999346,4.17,0.7700000000000653 +7,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-7,0,7.899999999999919,6.63,1.2699999999999187 +8,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-8,0,1.7999999999999403,2.78,0.9800000000000595 +9,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-9,0,7.699999999999919,6.08,1.6199999999999193 +10,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 +11,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-12,0,8.499999999999917,6.98,1.519999999999916 +12,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,0,8.599999999999916,7.27,1.3299999999999166 +13,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 +14,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-16,0,6.699999999999923,5.1,1.5999999999999233 +15,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-17,0,7.299999999999921,6.58,0.7199999999999207 +16,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-18,0,5.199999999999928,2.72,2.479999999999928 +17,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,0,5.999999999999925,4.93,1.0699999999999257 +18,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,-1,6.699999999999923,6.99,0.2900000000000773 +19,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-20,0,4.69999999999993,2.44,2.25999999999993 +20,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-21,0,7.799999999999919,5.38,2.419999999999919 +21,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-22,0,5.499999999999927,3.36,2.1399999999999273 +22,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-23,0,4.399999999999931,2.65,1.7499999999999312 +23,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-23,-1,8.899999999999915,9.02,0.12000000000008448 +24,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-1,0,14,2.54,11.46 +25,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-1,-1,4.999999999999929,5.01,0.010000000000070841 +26,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-2,-1,7.199999999999921,4.41,2.789999999999921 +27,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-3,-1,4.999999999999929,4.0,0.999999999999929 +28,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 +29,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-5,-1,0.29999999999994564,3.92,3.6200000000000543 +30,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-6,-1,-0.10000000000005294,4.17,4.270000000000053 +31,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-7,0,14,6.63,7.37 +32,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-8,0,5.6999999999999265,2.78,2.9199999999999267 +33,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-9,0,14,6.08,7.92 +34,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-10,0,5.299999999999928,7.71,2.410000000000072 +35,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-12,0,14,6.98,7.02 +36,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-14,0,0,7.27,7.27 +37,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-15,0,6.299999999999924,2.54,3.7599999999999243 +38,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-16,0,7.199999999999921,5.1,2.0999999999999215 +39,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-17,0,14,6.58,7.42 +40,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-18,0,14,2.72,11.28 +41,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-19,0,7.799999999999919,4.93,2.8699999999999193 +42,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-19,-1,5.199999999999928,6.99,1.790000000000072 +43,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-20,0,7.59999999999992,2.44,5.15999999999992 +44,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-21,0,14,5.38,8.620000000000001 +45,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-22,0,14,3.36,10.64 +46,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-23,0,3.599999999999934,2.65,0.949999999999934 +47,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-23,-1,7.999999999999918,9.02,1.0200000000000813 +48,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-1,0,-3.0000000000000426,2.54,5.540000000000043 +49,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-1,-1,2.0999999999999392,5.01,2.9100000000000605 +50,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-2,-1,1.599999999999941,4.41,2.810000000000059 +51,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-3,-1,1.6999999999999407,4.0,2.3000000000000593 +52,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-4,-1,1.7999999999999403,5.77,3.9700000000000593 +53,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-5,-1,1.4999999999999414,3.92,2.4200000000000585 +54,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-6,-1,1.7999999999999403,4.17,2.3700000000000596 +55,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-7,0,7.299999999999921,6.63,0.6699999999999209 +56,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-8,0,1.7999999999999403,2.78,0.9800000000000595 +57,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-9,0,6.999999999999922,6.08,0.9199999999999218 +58,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 +59,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-12,0,7.999999999999918,6.98,1.0199999999999179 +60,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-14,0,8.099999999999918,7.27,0.8299999999999184 +61,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 +62,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-16,0,5.799999999999926,5.1,0.6999999999999265 +63,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-17,0,6.599999999999923,6.58,0.01999999999992319 +64,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-18,0,3.9999999999999325,2.72,1.2799999999999323 +65,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-19,0,4.999999999999929,4.93,0.06999999999992923 +66,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-19,-1,5.6999999999999265,6.99,1.2900000000000738 +67,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-20,0,3.299999999999935,2.44,0.859999999999935 +68,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-21,0,7.0999999999999215,5.38,1.7199999999999216 +69,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-22,0,4.299999999999931,3.36,0.9399999999999316 +70,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-23,0,3.0999999999999357,2.65,0.4499999999999358 +71,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-23,-1,8.399999999999917,9.02,0.6200000000000827 +72,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-1,0,0.199999999999946,2.54,2.340000000000054 +73,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-1,-1,4.299999999999931,5.01,0.7100000000000684 +74,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 +75,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-3,-1,3.9999999999999325,4.0,6.750155989720952e-14 +76,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-4,-1,4.199999999999932,5.77,1.5700000000000678 +77,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-5,-1,3.899999999999933,3.92,0.020000000000067075 +78,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-6,-1,4.199999999999932,4.17,0.02999999999993186 +79,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-7,0,8.499999999999917,6.63,1.8699999999999166 +80,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-8,0,4.099999999999932,2.78,1.3199999999999323 +81,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-9,0,8.299999999999917,6.08,2.219999999999917 +82,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-10,0,9.399999999999913,7.71,1.6899999999999133 +83,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-12,0,9.099999999999914,6.98,2.119999999999914 +84,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-14,0,9.199999999999914,7.27,1.9299999999999145 +85,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-15,0,5.799999999999926,2.54,3.259999999999926 +86,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-16,0,7.39999999999992,5.1,2.2999999999999208 +87,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-17,0,7.899999999999919,6.58,1.3199999999999186 +88,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-18,0,5.899999999999926,2.72,3.1799999999999256 +89,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-19,0,6.699999999999923,4.93,1.7699999999999232 +90,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-19,-1,7.299999999999921,6.99,0.30999999999992056 +91,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-20,0,5.3999999999999275,2.44,2.9599999999999276 +92,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-21,0,8.399999999999917,5.38,3.019999999999917 +93,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-22,0,6.099999999999925,3.36,2.739999999999925 +94,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-23,0,5.099999999999929,2.65,2.4499999999999287 +95,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-23,-1,9.499999999999913,9.02,0.4799999999999134 +96,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-1,0,14,2.54,11.46 +97,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-1,-1,7.59999999999992,5.01,2.58999999999992 +98,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-2,-1,8.099999999999918,4.41,3.689999999999918 +99,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-3,-1,6.299999999999924,4.0,2.2999999999999243 +100,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-4,-1,11.099999999999907,5.77,5.329999999999908 +101,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-5,-1,7.59999999999992,3.92,3.67999999999992 +102,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-6,-1,5.799999999999926,4.17,1.6299999999999262 +103,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-7,0,8.799999999999915,6.63,2.1699999999999156 +104,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-8,0,4.59999999999993,2.78,1.8199999999999306 +105,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-9,0,5.899999999999926,6.08,0.18000000000007432 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+116,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-21,0,14,5.38,8.620000000000001 +117,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-22,0,14,3.36,10.64 +118,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,0,2.0999999999999392,2.65,0.5500000000000607 +119,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,-1,13.499999999999899,9.02,4.479999999999899 +120,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,0,14,2.54,11.46 +121,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 +122,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 +123,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 +124,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 +125,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 +126,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 +127,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-7,0,14,6.63,7.37 +128,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 +129,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-9,0,14,6.08,7.92 +130,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999914,7.71,1.489999999999914 +131,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-12,0,14,6.98,7.02 +132,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,0,0,7.27,7.27 +133,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,6.999999999999922,2.54,4.459999999999922 +134,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 +135,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-17,0,14,6.58,7.42 +136,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-18,0,14,2.72,11.28 +137,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 +138,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 +139,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 +140,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,0,14,5.38,8.620000000000001 +141,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-22,0,14,3.36,10.64 +142,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 +143,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 +144,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,0,14,2.54,11.46 +145,pKa-ZhiyiWu-1,QM with linear 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a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/rmse_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/rmse_plot.pdf index 825f690..707a5d7 100644 Binary files a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/rmse_plot.pdf and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/rmse_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/selected_transitions_pKa_data.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/selected_transitions_pKa_data.csv new file mode 100644 index 0000000..22e495e --- /dev/null +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_all/selected_transitions_pKa_data.csv @@ -0,0 +1,242 @@ +,Submission,Method Name,Method Type,Molecule ID,Formal Charge,Predicted pKa,Experimental pKa,Absolute Error +0,pKa-RobertRaddi_AdaBoost_modified,AdaBoost,QSPR/ML,SAMPL8-1,-1,4.999999999999929,5.01,0.010000000000070841 +1,pKa-RobertRaddi_AdaBoost_modified,AdaBoost,QSPR/ML,SAMPL8-2,-1,7.199999999999921,4.41,2.789999999999921 +2,pKa-RobertRaddi_AdaBoost_modified,AdaBoost,QSPR/ML,SAMPL8-3,-1,4.999999999999929,4.0,0.999999999999929 +3,pKa-RobertRaddi_AdaBoost_modified,AdaBoost,QSPR/ML,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 +4,pKa-RobertRaddi_AdaBoost_modified,AdaBoost,QSPR/ML,SAMPL8-5,-1,0.29999999999994564,3.92,3.6200000000000543 +5,pKa-RobertRaddi_AdaBoost_modified,AdaBoost,QSPR/ML,SAMPL8-6,-1,-0.10000000000005294,4.17,4.270000000000053 +6,pKa-RobertRaddi_AdaBoost_modified,AdaBoost,QSPR/ML,SAMPL8-8,0,5.6999999999999265,2.78,2.9199999999999267 +7,pKa-RobertRaddi_AdaBoost_modified,AdaBoost,QSPR/ML,SAMPL8-10,0,5.299999999999928,7.71,2.410000000000072 +8,pKa-RobertRaddi_AdaBoost_modified,AdaBoost,QSPR/ML,SAMPL8-15,0,6.299999999999924,2.54,3.7599999999999243 +9,pKa-RobertRaddi_AdaBoost_modified,AdaBoost,QSPR/ML,SAMPL8-16,0,7.199999999999921,5.1,2.0999999999999215 +10,pKa-RobertRaddi_AdaBoost_modified,AdaBoost,QSPR/ML,SAMPL8-19,0,7.799999999999919,4.93,2.8699999999999193 +11,pKa-RobertRaddi_AdaBoost_modified,AdaBoost,QSPR/ML,SAMPL8-19,-1,5.199999999999928,6.99,1.790000000000072 +12,pKa-RobertRaddi_AdaBoost_modified,AdaBoost,QSPR/ML,SAMPL8-20,0,7.59999999999992,2.44,5.15999999999992 +13,pKa-RobertRaddi_AdaBoost_modified,AdaBoost,QSPR/ML,SAMPL8-23,0,3.599999999999934,2.65,0.949999999999934 +14,pKa-RobertRaddi_AdaBoost_modified,AdaBoost,QSPR/ML,SAMPL8-23,-1,7.999999999999918,9.02,1.0200000000000813 +15,pKa_SabatinoRodriguezPaluch_uESE_modified,RFE-uESE,QM,SAMPL8-1,-1,7.59999999999992,5.01,2.58999999999992 +16,pKa_SabatinoRodriguezPaluch_uESE_modified,RFE-uESE,QM,SAMPL8-2,-1,8.099999999999918,4.41,3.689999999999918 +17,pKa_SabatinoRodriguezPaluch_uESE_modified,RFE-uESE,QM,SAMPL8-3,-1,6.299999999999924,4.0,2.2999999999999243 +18,pKa_SabatinoRodriguezPaluch_uESE_modified,RFE-uESE,QM,SAMPL8-4,-1,11.099999999999907,5.77,5.329999999999908 +19,pKa_SabatinoRodriguezPaluch_uESE_modified,RFE-uESE,QM,SAMPL8-5,-1,7.59999999999992,3.92,3.67999999999992 +20,pKa_SabatinoRodriguezPaluch_uESE_modified,RFE-uESE,QM,SAMPL8-6,-1,5.799999999999926,4.17,1.6299999999999262 +21,pKa_SabatinoRodriguezPaluch_uESE_modified,RFE-uESE,QM,SAMPL8-7,0,8.799999999999915,6.63,2.1699999999999156 +22,pKa_SabatinoRodriguezPaluch_uESE_modified,RFE-uESE,QM,SAMPL8-8,0,4.59999999999993,2.78,1.8199999999999306 +23,pKa_SabatinoRodriguezPaluch_uESE_modified,RFE-uESE,QM,SAMPL8-9,0,5.899999999999926,6.08,0.18000000000007432 +24,pKa_SabatinoRodriguezPaluch_uESE_modified,RFE-uESE,QM,SAMPL8-10,0,6.499999999999924,7.71,1.2100000000000763 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a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/Correlation_Plots/Correlation_statistics.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/Correlation_Plots/Correlation_statistics.csv index 3242054..3090563 100644 --- a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/Correlation_Plots/Correlation_statistics.csv +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/Correlation_Plots/Correlation_statistics.csv @@ -1,7 +1,7 @@ ,Submission,R-squared,Slope,Kendall Tau -0,pKa-3DS-1,0.8060107999090355,0.9186706651772883,0.6398668943087059 -1,pKa-RobertRaddi_DeepGP,-0.1412526525239042,-0.29180176186549595,-0.010597862085190504 -2,pKa-ZhiyiWu-1,-0.020581050801808363,-0.04038207379238602,0.11885937745424623 -3,PKA_ECRISM,0.4939794402818,0.5754309343193519,0.5234928803564822 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a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/Correlation_Plots/pKa_SabatinoRodriguezPaluch_uESE_extra_modifiedCorr_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/Correlation_Plots/pKa_SabatinoRodriguezPaluch_uESE_extra_modifiedCorr_plot.pdf new file mode 100644 index 0000000..b6c75a7 Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/Correlation_Plots/pKa_SabatinoRodriguezPaluch_uESE_extra_modifiedCorr_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/Error_statistics.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/Error_statistics.csv index 110b88c..c54d60f 100644 --- a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/Error_statistics.csv +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/Error_statistics.csv @@ -1,22 +1,22 @@ ,Molecule ID,Mean Error,Mean Absolute Error,Root Mean Squared Error -0,SAMPL8-1,0.8166666666666228,5.345000000000031,5.345000000000031 -1,SAMPL8-2,1.7899999999999245,2.5966666666666343,2.5966666666666343 -2,SAMPL8-3,1.0666666666665954,1.633333333333305,1.633333333333305 -3,SAMPL8-4,-0.6366666666667378,2.656666666666682,2.656666666666682 -4,SAMPL8-5,0.696666666666597,1.2766666666666397,1.2766666666666397 -5,SAMPL8-6,-0.103333333333401,0.8233333333333531,0.8233333333333531 -6,SAMPL8-7,1.9533333333332668,3.206666666666647,3.206666666666647 -7,SAMPL8-8,0.08666666666660339,1.7666666666666604,1.7666666666666604 -8,SAMPL8-9,1.1033333333332715,2.0766666666667013,2.0766666666667013 -9,SAMPL8-10,-0.7433333333334113,1.4366666666666885,1.4366666666666885 -10,SAMPL8-12,1.8199999999999494,3.366666666666689,3.366666666666689 -11,SAMPL8-14,-2.4700000000000526,3.5899999999999963,3.5899999999999963 -12,SAMPL8-15,0.5933333333332689,1.9333333333333265,1.9333333333333265 -13,SAMPL8-16,0.09999999999992859,1.600000000000018,1.600000000000018 -14,SAMPL8-17,0.28666666666660606,2.426666666666701,2.426666666666701 -15,SAMPL8-18,1.8966666666666134,3.1833333333333385,3.1833333333333385 -16,SAMPL8-19,0.5316666666665903,1.7816666666666592,1.7816666666666592 -17,SAMPL8-20,-3.898333333333379,5.001666666666688,5.001666666666688 -18,SAMPL8-21,2.8699999999999526,3.683333333333355,3.683333333333355 -19,SAMPL8-22,4.506666666666621,5.346666666666661,5.346666666666661 -20,SAMPL8-23,0.5566666666665908,1.2049999999999816,1.2049999999999816 +0,SAMPL8-1,-2.7311111111111694,3.3066666666667066,5.121364835449428 +1,SAMPL8-2,1.7899999999999245,2.5966666666666343,3.382420238034644 +2,SAMPL8-3,1.0666666666665954,1.633333333333305,1.937352144896008 +3,SAMPL8-4,-0.6366666666667378,2.656666666666682,3.0617369797768976 +4,SAMPL8-5,0.696666666666597,1.2766666666666397,1.6862384173063685 +5,SAMPL8-6,-0.103333333333401,0.8233333333333531,1.030970416646378 +6,SAMPL8-7,0.8699999999999202,2.373999999999976,2.6849394779025872 +7,SAMPL8-8,0.08666666666660339,1.7666666666666604,1.9269319309894237 +8,SAMPL8-9,-0.26000000000007406,0.9080000000000418,1.0812955192730758 +9,SAMPL8-10,-0.7433333333334113,1.4366666666666885,1.615992986783493 +10,SAMPL8-15,0.5933333333332689,1.9333333333333265,2.2466864489732186 +11,SAMPL8-16,0.09999999999992859,1.600000000000018,1.856520042085899 +12,SAMPL8-17,-1.1400000000000727,1.428000000000041,1.513274595042208 +13,SAMPL8-18,0.01999999999993678,1.5640000000000072,1.6488784066752702 +14,SAMPL8-19,0.5316666666665903,1.7816666666666592,2.453874487417779 +15,SAMPL8-20,0.30999999999993705,1.8966666666666805,2.2357549060663886 +16,SAMPL8-23,0.5566666666665908,1.2049999999999816,1.6939942935755599 +17,SAMPL8-12,-0.7800000000000757,1.5400000000000338,1.6135055004554848 +18,SAMPL8-14,-0.07000000000007844,1.7499999999999938,1.7691523393987272 +19,SAMPL8-21,-0.00500000000007228,1.2150000000000318,1.4771255870778168 +20,SAMPL8-22,1.4399999999999298,2.6999999999999904,3.3709939187129563 diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/abs_error_bymethod_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/abs_error_bymethod_plot.pdf index 067d50f..08ff36f 100644 Binary files a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/abs_error_bymethod_plot.pdf and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/abs_error_bymethod_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/abs_error_bymol_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/abs_error_bymol_plot.pdf index 7d1fe82..14fce1d 100644 Binary files a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/abs_error_bymol_plot.pdf and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/abs_error_bymol_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/macrostate_pKa_data.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/macrostate_pKa_data.csv index faf5335..523e6a9 100644 --- a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/macrostate_pKa_data.csv +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/macrostate_pKa_data.csv @@ -1,273 +1,264 @@ ,Submission,Method Name,Method Type,Molecule ID,Formal Charge,Predicted pKa,Experimental pKa,Absolute Error -0,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 -1,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,-1,14.499999999999895,6.98,7.519999999999895 -2,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,0,8.499999999999917,6.98,1.519999999999916 -3,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,1,2.699999999999937,6.98,4.280000000000063 -4,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,-2,13.599999999999898,7.27,6.329999999999899 -5,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,-1,9.699999999999912,7.27,2.4299999999999127 -6,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,0,8.599999999999916,7.27,1.3299999999999166 -7,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,1,3.3999999999999346,7.27,3.870000000000065 -8,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 -9,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,-2,12.099999999999904,5.1,6.999999999999904 -10,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,-1,10.699999999999909,5.1,5.599999999999909 -11,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,0,6.699999999999923,5.1,1.5999999999999233 -12,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-17,-1,11.499999999999906,6.58,4.919999999999906 -13,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-17,0,7.299999999999921,6.58,0.7199999999999207 -14,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-18,-1,11.199999999999907,2.72,8.479999999999906 -15,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-18,0,5.199999999999928,2.72,2.479999999999928 -16,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,-1,6.699999999999923,4.93,1.7699999999999232 -17,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,-1,6.699999999999923,6.99,0.2900000000000773 -18,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,0,5.999999999999925,4.93,1.0699999999999257 -19,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,0,5.999999999999925,6.99,0.9900000000000748 -20,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,1,3.3999999999999346,4.93,1.530000000000065 -21,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,1,3.3999999999999346,6.99,3.5900000000000656 -22,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,-1,3.599999999999934,2.54,1.0599999999999339 -23,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,-1,3.599999999999934,5.01,1.4100000000000659 -24,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,0,-0.6000000000000512,2.54,3.140000000000051 -25,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,0,-0.6000000000000512,5.01,5.610000000000051 -26,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,-1,10.09999999999991,2.44,7.659999999999911 -27,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,-1,10.09999999999991,11.44,1.3400000000000887 -28,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,0,4.69999999999993,2.44,2.25999999999993 -29,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,0,4.69999999999993,11.44,6.7400000000000695 -30,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,1,0.199999999999946,2.44,2.240000000000054 -31,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,1,0.199999999999946,11.44,11.240000000000054 -32,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,-2,12.9999999999999,5.38,7.619999999999901 -33,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,-1,8.599999999999916,5.38,3.2199999999999163 -34,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,0,7.799999999999919,5.38,2.419999999999919 -35,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,1,2.8999999999999364,5.38,2.4800000000000635 -36,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,-1,12.499999999999902,3.36,9.139999999999903 -37,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,0,5.499999999999927,3.36,2.1399999999999273 -38,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,1,-0.9000000000000501,3.36,4.2600000000000495 -39,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,-1,8.899999999999915,2.65,6.249999999999915 -40,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,-1,8.899999999999915,9.02,0.12000000000008448 -41,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,0,4.399999999999931,2.65,1.7499999999999312 -42,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,0,4.399999999999931,9.02,4.6200000000000685 -43,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 -44,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-3,-2,7.299999999999921,4.0,3.2999999999999208 -45,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-3,-1,3.299999999999935,4.0,0.700000000000065 -46,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-3,0,-1.1000000000000494,4.0,5.100000000000049 -47,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 -48,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-4,0,2.399999999999938,5.77,3.3700000000000614 -49,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-5,-1,3.1999999999999353,3.92,0.7200000000000646 -50,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-5,0,-1.6000000000000476,3.92,5.5200000000000475 -51,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-6,-1,3.3999999999999346,4.17,0.7700000000000653 -52,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-6,0,3.3999999999999346,4.17,0.7700000000000653 -53,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-7,-1,11.899999999999904,6.63,5.2699999999999045 -54,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-7,0,7.899999999999919,6.63,1.2699999999999187 -55,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-8,0,1.7999999999999403,2.78,0.9800000000000595 -56,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-9,-1,12.199999999999903,6.08,6.119999999999903 -57,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-9,0,7.699999999999919,6.08,1.6199999999999193 -58,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999914,7.71,1.489999999999914 -59,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-12,-1,14.299999999999896,6.98,7.3199999999998955 -60,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-2,5.099999999999929,7.27,2.170000000000071 -61,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-1,7.299999999999921,7.27,0.0299999999999212 -62,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,6.999999999999922,2.54,4.459999999999922 -63,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 -64,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-17,-1,4.199999999999932,6.58,2.3800000000000683 -65,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-18,-1,4.999999999999929,2.72,2.2799999999999288 -66,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,4.93,4.269999999999914 -67,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 -68,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 -69,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,6.99,0.5900000000000762 -70,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,4.93,6.130000000000049 -71,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,6.99,8.19000000000005 -72,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,2.54,2.0599999999999303 -73,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 -74,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 -75,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,11.44,4.640000000000077 -76,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-2,19.399999999999878,5.38,14.019999999999879 -77,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-1,6.299999999999924,5.38,0.9199999999999244 -78,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-22,-1,5.199999999999928,3.36,1.8399999999999284 -79,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,2.65,6.549999999999914 -80,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 -81,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 -82,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,9.02,4.920000000000067 -83,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 -84,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 -85,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 -86,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 -87,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,0,14.599999999999895,3.92,10.679999999999895 -88,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 -89,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,0,13.1999999999999,4.17,9.0299999999999 -90,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-7,-1,4.999999999999929,6.63,1.630000000000071 -91,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 -92,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-9,-1,3.899999999999933,6.08,2.180000000000067 -93,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-10,0,5.599999999999927,7.71,2.110000000000073 -94,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-12,-1,19.09999999999988,6.98,12.11999999999988 -95,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-2,11.599999999999905,7.27,4.329999999999906 -96,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-1,11.499999999999906,7.27,4.229999999999906 -97,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-15,0,4.299999999999931,2.54,1.7599999999999314 -98,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-16,0,4.69999999999993,5.1,0.40000000000006963 -99,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,-1,12.299999999999903,6.58,5.719999999999903 -100,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,0,4.499999999999931,6.58,2.0800000000000693 -101,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,-1,9.599999999999913,2.72,6.879999999999912 -102,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,0,4.199999999999932,2.72,1.4799999999999316 -103,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,4.93,6.169999999999908 -104,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,6.99,4.109999999999907 -105,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,4.93,4.2300000000000555 -106,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,6.99,6.290000000000056 -107,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,1,-0.9000000000000501,4.93,5.83000000000005 -108,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,1,-0.9000000000000501,6.99,7.89000000000005 -109,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,2.54,1.559999999999932 -110,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,5.01,0.9100000000000676 -111,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,0,1.3999999999999417,2.44,1.0400000000000582 -112,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,0,1.3999999999999417,11.44,10.040000000000058 -113,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-3,19.899999999999878,5.38,14.519999999999879 -114,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-2,16.29999999999989,5.38,10.919999999999892 -115,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-1,13.699999999999898,5.38,8.319999999999897 -116,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-22,-1,13.899999999999897,3.36,10.539999999999898 -117,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,9.999999999999911,2.65,7.349999999999911 -118,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,9.999999999999911,9.02,0.9799999999999116 -119,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.299999999999935,2.65,0.6499999999999351 -120,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.299999999999935,9.02,5.720000000000065 -121,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-2,-1,6.099999999999925,4.41,1.689999999999925 -122,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-2,8.799999999999915,4.0,4.7999999999999154 -123,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-1,6.699999999999923,4.0,2.699999999999923 -124,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,-1,6.499999999999924,5.77,0.729999999999924 -125,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,0,-5.3290705182007514e-14,5.77,5.770000000000053 -126,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,-1,4.499999999999931,3.92,0.5799999999999308 -127,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,0,-1.200000000000049,3.92,5.120000000000049 -128,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 -129,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,0,1.9999999999999396,4.17,2.1700000000000603 -130,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,-1,16.39999999999989,6.63,9.76999999999989 -131,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,0,11.299999999999907,6.63,4.669999999999907 -132,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-8,0,4.399999999999931,2.78,1.6199999999999313 -133,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,-1,15.699999999999891,6.08,9.61999999999989 -134,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,0,4.499999999999931,6.08,1.5800000000000693 -135,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-10,0,7.0999999999999215,7.71,0.6100000000000785 -136,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-12,-1,17.699999999999882,6.98,10.719999999999882 -137,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-12,0,4.899999999999929,6.98,2.080000000000071 -138,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-12,1,-5.0000000000000355,6.98,11.980000000000036 -139,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-14,-3,20.799999999999873,7.27,13.529999999999873 -140,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-14,-2,16.29999999999989,7.27,9.029999999999891 -141,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-14,-1,11.499999999999906,7.27,4.229999999999906 -142,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-14,0,5.3999999999999275,7.27,1.870000000000072 -143,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-14,1,-3.80000000000004,7.27,11.07000000000004 -144,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-15,0,1.3999999999999417,2.54,1.1400000000000583 -145,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-16,0,3.9999999999999325,5.1,1.1000000000000671 -146,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-17,-1,14.199999999999896,6.58,7.619999999999896 -147,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-17,0,4.69999999999993,6.58,1.88000000000007 -148,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-18,-1,11.399999999999906,2.72,8.679999999999906 -149,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-18,0,1.6999999999999407,2.72,1.0200000000000595 -150,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-19,-1,6.999999999999922,4.93,2.069999999999922 -151,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-19,-1,6.999999999999922,6.99,0.009999999999921627 -152,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-19,0,4.099999999999932,4.93,0.8300000000000676 -153,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-19,0,4.099999999999932,6.99,2.890000000000068 -154,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-19,1,-2.2000000000000455,4.93,7.130000000000045 -155,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-19,1,-2.2000000000000455,6.99,9.190000000000046 -156,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-1,-1,4.59999999999993,2.54,2.0599999999999303 -157,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 -158,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-1,0,-2.5000000000000444,2.54,5.0400000000000444 -159,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-1,0,-2.5000000000000444,5.01,7.510000000000044 -160,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-20,0,1.4999999999999414,2.44,0.9400000000000586 -161,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-20,0,1.4999999999999414,11.44,9.940000000000058 -162,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-21,-3,20.399999999999874,5.38,15.019999999999875 -163,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-21,-2,17.199999999999886,5.38,11.819999999999887 -164,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-21,-1,8.199999999999918,5.38,2.8199999999999177 -165,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-21,0,3.799999999999933,5.38,1.5800000000000667 -166,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-21,1,-5.500000000000034,5.38,10.880000000000035 -167,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-22,-1,14.699999999999894,3.36,11.339999999999895 -168,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-22,0,2.0999999999999392,3.36,1.2600000000000606 -169,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-22,1,-7.700000000000026,3.36,11.060000000000025 -170,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-23,-1,10.09999999999991,2.65,7.4499999999999105 -171,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-23,-1,10.09999999999991,9.02,1.0799999999999113 -172,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-23,0,1.9999999999999396,2.65,0.6500000000000603 -173,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-23,0,1.9999999999999396,9.02,7.02000000000006 -174,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-2,-1,5.299999999999928,4.41,0.8899999999999277 -175,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-3,-2,10.39999999999991,4.0,6.39999999999991 -176,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-3,-1,4.199999999999932,4.0,0.1999999999999318 -177,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-3,0,-11.700000000000012,4.0,15.700000000000012 -178,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-4,-1,4.59999999999993,5.77,1.1700000000000692 -179,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-4,0,0.09999999999994635,5.77,5.670000000000053 -180,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-5,-1,5.099999999999929,3.92,1.1799999999999287 -181,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-5,0,-2.7000000000000437,3.92,6.620000000000044 -182,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-6,-1,4.69999999999993,4.17,0.5299999999999301 -183,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-6,0,2.7999999999999368,4.17,1.3700000000000632 -184,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-7,-1,14.999999999999893,6.63,8.369999999999894 -185,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-7,0,4.099999999999932,6.63,2.5300000000000678 -186,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-8,0,-0.40000000000005187,2.78,3.1800000000000517 -187,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-9,-1,14.299999999999896,6.08,8.219999999999896 -188,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-9,0,5.599999999999927,6.08,0.48000000000007326 -189,pKa_Chemaxon,Chemaxon,Other,SAMPL8-10,0,5.099999999999929,7.71,2.6100000000000714 -190,pKa_Chemaxon,Chemaxon,Other,SAMPL8-12,0,5.199999999999928,6.98,1.7800000000000722 -191,pKa_Chemaxon,Chemaxon,Other,SAMPL8-14,-1,7.999999999999918,7.27,0.7299999999999187 -192,pKa_Chemaxon,Chemaxon,Other,SAMPL8-14,0,5.499999999999927,7.27,1.7700000000000724 -193,pKa_Chemaxon,Chemaxon,Other,SAMPL8-15,0,1.0999999999999428,2.54,1.4400000000000572 -194,pKa_Chemaxon,Chemaxon,Other,SAMPL8-16,-1,8.299999999999917,5.1,3.1999999999999176 -195,pKa_Chemaxon,Chemaxon,Other,SAMPL8-16,0,3.599999999999934,5.1,1.5000000000000657 -196,pKa_Chemaxon,Chemaxon,Other,SAMPL8-17,-1,10.899999999999908,6.58,4.319999999999908 -197,pKa_Chemaxon,Chemaxon,Other,SAMPL8-17,0,5.499999999999927,6.58,1.080000000000073 -198,pKa_Chemaxon,Chemaxon,Other,SAMPL8-18,0,0.9999999999999432,2.72,1.720000000000057 -199,pKa_Chemaxon,Chemaxon,Other,SAMPL8-19,-1,6.899999999999922,4.93,1.9699999999999225 -200,pKa_Chemaxon,Chemaxon,Other,SAMPL8-19,-1,6.899999999999922,6.99,0.09000000000007802 -201,pKa_Chemaxon,Chemaxon,Other,SAMPL8-19,0,4.69999999999993,4.93,0.2300000000000697 -202,pKa_Chemaxon,Chemaxon,Other,SAMPL8-19,0,4.69999999999993,6.99,2.29000000000007 -203,pKa_Chemaxon,Chemaxon,Other,SAMPL8-1,-1,2.7999999999999368,2.54,0.2599999999999367 -204,pKa_Chemaxon,Chemaxon,Other,SAMPL8-1,-1,2.7999999999999368,5.01,2.210000000000063 -205,pKa_Chemaxon,Chemaxon,Other,SAMPL8-20,-1,9.899999999999912,2.44,7.459999999999912 -206,pKa_Chemaxon,Chemaxon,Other,SAMPL8-20,-1,9.899999999999912,11.44,1.540000000000088 -207,pKa_Chemaxon,Chemaxon,Other,SAMPL8-20,0,0.8999999999999435,2.44,1.5400000000000564 -208,pKa_Chemaxon,Chemaxon,Other,SAMPL8-20,0,0.8999999999999435,11.44,10.540000000000056 -209,pKa_Chemaxon,Chemaxon,Other,SAMPL8-21,-1,6.7999999999999226,5.38,1.4199999999999227 -210,pKa_Chemaxon,Chemaxon,Other,SAMPL8-21,0,4.899999999999929,5.38,0.4800000000000706 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+234,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 +235,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-17,-1,4.199999999999932,6.58,2.3800000000000683 +236,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-18,-1,4.999999999999929,2.72,2.2799999999999288 +237,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,4.93,4.269999999999914 +238,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 +239,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 +240,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,6.99,0.5900000000000762 +241,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,4.93,6.130000000000049 +242,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,6.99,8.19000000000005 +243,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,2.54,2.0599999999999303 +244,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 +245,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 +246,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-2,19.399999999999878,5.38,14.019999999999879 +247,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-1,6.299999999999924,5.38,0.9199999999999244 +248,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-22,-1,5.199999999999928,3.36,1.8399999999999284 +249,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,2.65,6.549999999999914 +250,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 +251,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 +252,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,9.02,4.920000000000067 +253,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 +254,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 +255,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 +256,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 +257,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-5,0,14.599999999999895,3.92,10.679999999999895 +258,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 +259,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-6,0,13.1999999999999,4.17,9.0299999999999 +260,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-7,-1,4.999999999999929,6.63,1.630000000000071 +261,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 +262,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-9,-1,3.899999999999933,6.08,2.180000000000067 diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/mean_abs_error_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/mean_abs_error_plot.pdf index a8f77ae..ef8c607 100644 Binary files a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/mean_abs_error_plot.pdf and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/mean_abs_error_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/mean_error_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/mean_error_plot.pdf index 3dbabe3..fb71e7b 100644 Binary files a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/mean_error_plot.pdf and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/mean_error_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/popular_transitions_pKa_data.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/popular_transitions_pKa_data.csv index 9cf0538..f33c105 100644 --- a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/popular_transitions_pKa_data.csv +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/popular_transitions_pKa_data.csv @@ -1,151 +1,145 @@ ,Submission,Method Name,Method Type,Molecule ID,Formal Charge,Predicted pKa,Experimental pKa,Absolute Error -0,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,0,-0.6000000000000512,2.54,3.140000000000051 -1,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,-1,3.599999999999934,5.01,1.4100000000000659 -2,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 -3,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-3,-1,3.299999999999935,4.0,0.700000000000065 -4,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 -5,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-5,-1,3.1999999999999353,3.92,0.7200000000000646 -6,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-6,-1,3.3999999999999346,4.17,0.7700000000000653 -7,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-7,0,7.899999999999919,6.63,1.2699999999999187 -8,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-8,0,1.7999999999999403,2.78,0.9800000000000595 -9,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-9,0,7.699999999999919,6.08,1.6199999999999193 -10,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 -11,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,0,8.499999999999917,6.98,1.519999999999916 -12,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,0,8.599999999999916,7.27,1.3299999999999166 -13,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 -14,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,0,6.699999999999923,5.1,1.5999999999999233 -15,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-17,0,7.299999999999921,6.58,0.7199999999999207 -16,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-18,0,5.199999999999928,2.72,2.479999999999928 -17,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,0,5.999999999999925,4.93,1.0699999999999257 -18,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,-1,6.699999999999923,6.99,0.2900000000000773 -19,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,0,4.69999999999993,2.44,2.25999999999993 -20,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,-1,10.09999999999991,11.44,1.3400000000000887 -21,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,0,7.799999999999919,5.38,2.419999999999919 -22,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,0,5.499999999999927,3.36,2.1399999999999273 -23,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,0,4.399999999999931,2.65,1.7499999999999312 -24,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,-1,8.899999999999915,9.02,0.12000000000008448 -25,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,0,14.0,2.54,11.46 -26,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 -27,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 -28,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 -29,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 -30,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 -31,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 -32,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-7,0,14.0,6.63,7.37 -33,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 -34,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-9,0,14.0,6.08,7.92 -35,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999914,7.71,1.489999999999914 -36,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-12,0,14.0,6.98,7.02 -37,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,0,0.0,7.27,7.27 -38,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,6.999999999999922,2.54,4.459999999999922 -39,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 -40,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-17,0,14.0,6.58,7.42 -41,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-18,0,14.0,2.72,11.28 -42,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 -43,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 -44,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 -45,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,-1,0.0,11.44,11.44 -46,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,0,14.0,5.38,8.620000000000001 -47,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-22,0,14.0,3.36,10.64 -48,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 -49,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 -50,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,0,14.0,2.54,11.46 -51,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,5.01,0.9100000000000676 -52,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-2,-1,6.099999999999925,4.41,1.689999999999925 -53,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-1,6.699999999999923,4.0,2.699999999999923 -54,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,-1,6.499999999999924,5.77,0.729999999999924 -55,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,-1,4.499999999999931,3.92,0.5799999999999308 -56,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 -57,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,0,11.299999999999907,6.63,4.669999999999907 -58,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-8,0,4.399999999999931,2.78,1.6199999999999313 -59,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,0,4.499999999999931,6.08,1.5800000000000693 -60,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-10,0,5.599999999999927,7.71,2.110000000000073 -61,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-12,0,14.0,6.98,7.02 -62,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,0,0.0,7.27,7.27 -63,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-15,0,4.299999999999931,2.54,1.7599999999999314 -64,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-16,0,4.69999999999993,5.1,0.40000000000006963 -65,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,0,4.499999999999931,6.58,2.0800000000000693 -66,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,0,4.199999999999932,2.72,1.4799999999999316 -67,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,4.93,4.2300000000000555 -68,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,6.99,4.109999999999907 -69,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,0,1.3999999999999417,2.44,1.0400000000000582 -70,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,-1,0.0,11.44,11.44 -71,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,0,14.0,5.38,8.620000000000001 -72,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-22,0,14.0,3.36,10.64 -73,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.299999999999935,2.65,0.6499999999999351 -74,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,9.999999999999911,9.02,0.9799999999999116 -75,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-1,0,-2.5000000000000444,2.54,5.0400000000000444 -76,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 -77,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-2,-1,5.299999999999928,4.41,0.8899999999999277 -78,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-3,-1,4.199999999999932,4.0,0.1999999999999318 -79,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-4,-1,4.59999999999993,5.77,1.1700000000000692 -80,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-5,-1,5.099999999999929,3.92,1.1799999999999287 -81,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-6,-1,4.69999999999993,4.17,0.5299999999999301 -82,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-7,0,4.099999999999932,6.63,2.5300000000000678 -83,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-8,0,-0.40000000000005187,2.78,3.1800000000000517 -84,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-9,0,5.599999999999927,6.08,0.48000000000007326 -85,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-10,0,7.0999999999999215,7.71,0.6100000000000785 -86,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-12,0,4.899999999999929,6.98,2.080000000000071 -87,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-14,0,5.3999999999999275,7.27,1.870000000000072 -88,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-15,0,1.3999999999999417,2.54,1.1400000000000583 -89,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-16,0,3.9999999999999325,5.1,1.1000000000000671 -90,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-17,0,4.69999999999993,6.58,1.88000000000007 -91,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-18,0,1.6999999999999407,2.72,1.0200000000000595 -92,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-19,0,4.099999999999932,4.93,0.8300000000000676 -93,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-19,-1,6.999999999999922,6.99,0.009999999999921627 -94,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-20,0,1.4999999999999414,2.44,0.9400000000000586 -95,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-20,-1,0.0,11.44,11.44 -96,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-21,0,3.799999999999933,5.38,1.5800000000000667 -97,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-22,0,2.0999999999999392,3.36,1.2600000000000606 -98,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-23,0,1.9999999999999396,2.65,0.6500000000000603 -99,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-23,-1,10.09999999999991,9.02,1.0799999999999113 -100,pKa_Chemaxon,Chemaxon,Other,SAMPL8-1,0,14.0,2.54,11.46 -101,pKa_Chemaxon,Chemaxon,Other,SAMPL8-1,-1,2.7999999999999368,5.01,2.210000000000063 -102,pKa_Chemaxon,Chemaxon,Other,SAMPL8-2,-1,2.499999999999938,4.41,1.9100000000000623 -103,pKa_Chemaxon,Chemaxon,Other,SAMPL8-3,-1,2.999999999999936,4.0,1.000000000000064 -104,pKa_Chemaxon,Chemaxon,Other,SAMPL8-4,-1,2.699999999999937,5.77,3.0700000000000625 -105,pKa_Chemaxon,Chemaxon,Other,SAMPL8-5,-1,2.8999999999999364,3.92,1.0200000000000635 -106,pKa_Chemaxon,Chemaxon,Other,SAMPL8-6,-1,2.499999999999938,4.17,1.670000000000062 -107,pKa_Chemaxon,Chemaxon,Other,SAMPL8-7,0,5.3999999999999275,6.63,1.2300000000000724 -108,pKa_Chemaxon,Chemaxon,Other,SAMPL8-8,0,1.89999999999994,2.78,0.8800000000000598 -109,pKa_Chemaxon,Chemaxon,Other,SAMPL8-9,0,5.3999999999999275,6.08,0.6800000000000725 -110,pKa_Chemaxon,Chemaxon,Other,SAMPL8-10,0,5.099999999999929,7.71,2.6100000000000714 -111,pKa_Chemaxon,Chemaxon,Other,SAMPL8-12,0,5.199999999999928,6.98,1.7800000000000722 -112,pKa_Chemaxon,Chemaxon,Other,SAMPL8-14,0,5.499999999999927,7.27,1.7700000000000724 -113,pKa_Chemaxon,Chemaxon,Other,SAMPL8-15,0,1.0999999999999428,2.54,1.4400000000000572 -114,pKa_Chemaxon,Chemaxon,Other,SAMPL8-16,0,3.599999999999934,5.1,1.5000000000000657 -115,pKa_Chemaxon,Chemaxon,Other,SAMPL8-17,0,5.499999999999927,6.58,1.080000000000073 -116,pKa_Chemaxon,Chemaxon,Other,SAMPL8-18,0,0.9999999999999432,2.72,1.720000000000057 -117,pKa_Chemaxon,Chemaxon,Other,SAMPL8-19,0,4.69999999999993,4.93,0.2300000000000697 -118,pKa_Chemaxon,Chemaxon,Other,SAMPL8-19,-1,6.899999999999922,6.99,0.09000000000007802 -119,pKa_Chemaxon,Chemaxon,Other,SAMPL8-20,0,0.8999999999999435,2.44,1.5400000000000564 -120,pKa_Chemaxon,Chemaxon,Other,SAMPL8-20,-1,9.899999999999912,11.44,1.540000000000088 -121,pKa_Chemaxon,Chemaxon,Other,SAMPL8-21,0,4.899999999999929,5.38,0.4800000000000706 -122,pKa_Chemaxon,Chemaxon,Other,SAMPL8-22,0,2.0999999999999392,3.36,1.2600000000000606 -123,pKa_Chemaxon,Chemaxon,Other,SAMPL8-23,0,2.499999999999938,2.65,0.15000000000006208 -124,pKa_Chemaxon,Chemaxon,Other,SAMPL8-23,-1,6.599999999999923,9.02,2.4200000000000763 -125,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-1,0,-11.100000000000014,2.54,13.640000000000015 -126,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-1,-1,7.59999999999992,5.01,2.58999999999992 -127,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-2,-1,8.099999999999918,4.41,3.689999999999918 -128,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-3,-1,6.299999999999924,4.0,2.2999999999999243 -129,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-4,-1,11.099999999999907,5.77,5.329999999999908 -130,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-5,-1,7.59999999999992,3.92,3.67999999999992 -131,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-6,-1,5.799999999999926,4.17,1.6299999999999262 -132,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-7,0,8.799999999999915,6.63,2.1699999999999156 -133,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-8,0,4.59999999999993,2.78,1.8199999999999306 -134,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-9,0,5.899999999999926,6.08,0.18000000000007432 -135,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-10,0,6.499999999999924,7.71,1.2100000000000763 -136,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-12,0,6.199999999999925,6.98,0.7800000000000757 -137,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-14,0,9.299999999999914,7.27,2.029999999999914 -138,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-15,0,1.0999999999999428,2.54,1.4400000000000572 -139,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-16,0,3.599999999999934,5.1,1.5000000000000657 -140,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-17,0,5.199999999999928,6.58,1.3800000000000718 -141,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-18,0,1.599999999999941,2.72,1.1200000000000592 -142,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-19,0,3.0999999999999357,4.93,1.830000000000064 -143,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-19,-1,11.999999999999904,6.99,5.009999999999904 -144,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-20,0,1.1999999999999424,2.44,1.2400000000000575 -145,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-20,-1,0.0,11.44,11.44 -146,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-21,0,4.999999999999929,5.38,0.38000000000007095 -147,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-22,0,9.499999999999913,3.36,6.1399999999999135 -148,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-23,0,2.0999999999999392,2.65,0.5500000000000607 -149,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-23,-1,13.499999999999899,9.02,4.479999999999899 +0,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,0,-0.6000000000000512,2.54,3.140000000000051 +1,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,-1,3.599999999999934,5.01,1.4100000000000659 +2,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 +3,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-3,-1,3.299999999999935,4.0,0.700000000000065 +4,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 +5,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-5,-1,3.1999999999999353,3.92,0.7200000000000646 +6,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-6,-1,3.3999999999999346,4.17,0.7700000000000653 +7,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-7,0,7.899999999999919,6.63,1.2699999999999187 +8,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-8,0,1.7999999999999403,2.78,0.9800000000000595 +9,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-9,0,7.699999999999919,6.08,1.6199999999999193 +10,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 +11,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-12,0,8.499999999999917,6.98,1.519999999999916 +12,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,0,8.599999999999916,7.27,1.3299999999999166 +13,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 +14,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-16,0,6.699999999999923,5.1,1.5999999999999233 +15,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-17,0,7.299999999999921,6.58,0.7199999999999207 +16,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-18,0,5.199999999999928,2.72,2.479999999999928 +17,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,0,5.999999999999925,4.93,1.0699999999999257 +18,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,-1,6.699999999999923,6.99,0.2900000000000773 +19,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-20,0,4.69999999999993,2.44,2.25999999999993 +20,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-21,0,7.799999999999919,5.38,2.419999999999919 +21,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-22,0,5.499999999999927,3.36,2.1399999999999273 +22,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-23,0,4.399999999999931,2.65,1.7499999999999312 +23,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-23,-1,8.899999999999915,9.02,0.12000000000008448 +24,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,0,14.0,2.54,11.46 +25,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 +26,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 +27,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 +28,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 +29,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 +30,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 +31,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-7,0,14.0,6.63,7.37 +32,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 +33,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-9,0,14.0,6.08,7.92 +34,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999914,7.71,1.489999999999914 +35,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-12,0,14.0,6.98,7.02 +36,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,0,0.0,7.27,7.27 +37,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,6.999999999999922,2.54,4.459999999999922 +38,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 +39,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-17,0,14.0,6.58,7.42 +40,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-18,0,14.0,2.72,11.28 +41,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 +42,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 +43,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 +44,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,0,14.0,5.38,8.620000000000001 +45,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-22,0,14.0,3.36,10.64 +46,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 +47,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 +48,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,0,14.0,2.54,11.46 +49,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,5.01,0.9100000000000676 +50,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-2,-1,6.099999999999925,4.41,1.689999999999925 +51,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-1,6.699999999999923,4.0,2.699999999999923 +52,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,-1,6.499999999999924,5.77,0.729999999999924 +53,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,-1,4.499999999999931,3.92,0.5799999999999308 +54,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 +55,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,0,11.299999999999907,6.63,4.669999999999907 +56,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-8,0,4.399999999999931,2.78,1.6199999999999313 +57,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,0,4.499999999999931,6.08,1.5800000000000693 +58,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-10,0,5.599999999999927,7.71,2.110000000000073 +59,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-12,0,14.0,6.98,7.02 +60,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,0,0.0,7.27,7.27 +61,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-15,0,4.299999999999931,2.54,1.7599999999999314 +62,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-16,0,4.69999999999993,5.1,0.40000000000006963 +63,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,0,4.499999999999931,6.58,2.0800000000000693 +64,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,0,4.199999999999932,2.72,1.4799999999999316 +65,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,4.93,4.2300000000000555 +66,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,6.99,4.109999999999907 +67,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,0,1.3999999999999417,2.44,1.0400000000000582 +68,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,0,14.0,5.38,8.620000000000001 +69,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-22,0,14.0,3.36,10.64 +70,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.299999999999935,2.65,0.6499999999999351 +71,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,9.999999999999911,9.02,0.9799999999999116 +72,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-1,0,-2.5000000000000444,2.54,5.0400000000000444 +73,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 +74,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-2,-1,5.299999999999928,4.41,0.8899999999999277 +75,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-3,-1,4.199999999999932,4.0,0.1999999999999318 +76,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-4,-1,4.59999999999993,5.77,1.1700000000000692 +77,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-5,-1,5.099999999999929,3.92,1.1799999999999287 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a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/rmse_plot.pdf and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/rmse_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/selected_transitions_pKa_data.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/selected_transitions_pKa_data.csv new file mode 100644 index 0000000..ddbf40b --- /dev/null +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/analysis_outputs_ranked/selected_transitions_pKa_data.csv @@ -0,0 +1,130 @@ +,Submission,Method Name,Method Type,Molecule ID,Formal Charge,Predicted pKa,Experimental pKa,Absolute Error +0,pKa-ZhiyiWu-1_modified,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,5.01,0.9100000000000676 +1,pKa-ZhiyiWu-1_modified,QM with linear 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+83,pKa_SabatinoRodriguezPaluch_uESE_extra_modified,RFE-uESE-extra,QM,SAMPL8-18,0,1.599999999999941,2.72,1.1200000000000592 +84,pKa_SabatinoRodriguezPaluch_uESE_extra_modified,RFE-uESE-extra,QM,SAMPL8-19,0,3.0999999999999357,4.93,1.830000000000064 +85,pKa_SabatinoRodriguezPaluch_uESE_extra_modified,RFE-uESE-extra,QM,SAMPL8-19,-1,11.999999999999904,6.99,5.009999999999904 +86,pKa_SabatinoRodriguezPaluch_uESE_extra_modified,RFE-uESE-extra,QM,SAMPL8-20,0,1.1999999999999424,2.44,1.2400000000000575 +87,pKa_SabatinoRodriguezPaluch_uESE_extra_modified,RFE-uESE-extra,QM,SAMPL8-21,0,4.999999999999929,5.38,0.38000000000007095 +88,pKa_SabatinoRodriguezPaluch_uESE_extra_modified,RFE-uESE-extra,QM,SAMPL8-22,0,9.499999999999913,3.36,6.1399999999999135 +89,pKa_SabatinoRodriguezPaluch_uESE_extra_modified,RFE-uESE-extra,QM,SAMPL8-23,0,2.0999999999999392,2.65,0.5500000000000607 +90,pKa_SabatinoRodriguezPaluch_uESE_extra_modified,RFE-uESE-extra,QM,SAMPL8-23,-1,13.499999999999899,9.02,4.479999999999899 +91,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-1,-1,2.7999999999999368,5.01,2.210000000000063 +92,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-2,-1,2.499999999999938,4.41,1.9100000000000623 +93,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-3,-1,2.999999999999936,4.0,1.000000000000064 +94,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-4,-1,2.699999999999937,5.77,3.0700000000000625 +95,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-5,-1,2.8999999999999364,3.92,1.0200000000000635 +96,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-6,-1,2.499999999999938,4.17,1.670000000000062 +97,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-7,0,5.3999999999999275,6.63,1.2300000000000724 +98,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-8,0,1.89999999999994,2.78,0.8800000000000598 +99,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-9,0,5.3999999999999275,6.08,0.6800000000000725 +100,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-10,0,5.099999999999929,7.71,2.6100000000000714 +101,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-12,0,5.199999999999928,6.98,1.7800000000000722 +102,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-14,0,5.499999999999927,7.27,1.7700000000000724 +103,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-15,0,1.0999999999999428,2.54,1.4400000000000572 +104,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-16,0,3.599999999999934,5.1,1.5000000000000657 +105,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-17,0,5.499999999999927,6.58,1.080000000000073 +106,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-18,0,0.9999999999999432,2.72,1.720000000000057 +107,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-19,0,4.69999999999993,4.93,0.2300000000000697 +108,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-19,-1,6.899999999999922,6.99,0.09000000000007802 +109,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-20,0,0.8999999999999435,2.44,1.5400000000000564 +110,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-21,0,4.899999999999929,5.38,0.4800000000000706 +111,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-22,0,2.0999999999999392,3.36,1.2600000000000606 +112,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-23,0,2.499999999999938,2.65,0.15000000000006208 +113,pKa_Chemaxon_modified,Chemaxon,Other,SAMPL8-23,-1,6.599999999999923,9.02,2.4200000000000763 +114,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 +115,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 +116,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 +117,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 +118,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 +119,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 +120,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 +121,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999914,7.71,1.489999999999914 +122,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,6.999999999999922,2.54,4.459999999999922 +123,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 +124,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 +125,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 +126,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 +127,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 +128,pKa-RobertRaddi_DeepGP_modified,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/README.md b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/README.md new file mode 100644 index 0000000..f519de6 --- /dev/null +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/README.md @@ -0,0 +1,4 @@ +## Manifest +This folder is for figures and tables that will go into the supplementary material. In this run we change the assigned predicted $pKa$ for submissions missing a designated $pKa$ with the designated formal charge to 40 when the experimental $pKa$ is closer to 0. +-[`analysis_outputs_all/`](analysis_outputs_all/)- This directory contains bar plots and correlation plots associated with the performance statistics for all submissions. +-[`analysis_outputs_ranked/`](analysis_outputs_ranked/)- This directory contains bar plots and correlation plots associated with the performance statistics for all ranked submissions. diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/Correlation_Plots/Correlation_statistics.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/Correlation_Plots/Correlation_statistics.csv new file mode 100644 index 0000000..604eb0b --- /dev/null +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/Correlation_Plots/Correlation_statistics.csv @@ -0,0 +1,13 @@ +,Submission,R-squared,Slope,Kendall Tau +0,pKa-3DS-1,0.7834943477469948,1.0137866774745936,0.6083798799280435 +1,pKa-RobertRaddi_AdaBoost,0.02927004955589373,0.2618137625625803,0.026913125683807732 +2,pKa-3DS-2,0.7536231507883856,1.1538261805405876,0.5839454948814495 +3,pKa-3DS-3,0.7552485515279517,0.9351327184830505,0.5865219201701498 +4,pKa_SabatinoRodriguezPaluch_uESE,0.04551592065531991,0.32120863384931336,0.2647219842825437 +5,pKa-RobertRaddi_DeepGP,0.04757007716520839,0.41016216074250195,0.07705141285294194 +6,pKa-ZhiyiWu-1,-0.00820901109920531,-0.058356259397499374,0.21404545767263877 +7,pKa-RobertRaddi_RF,0.03412671510204557,0.3109478646676795,0.06139106381413451 +8,PKA_ECRISM,0.8477227975324197,1.1469468690328275,0.6423400443695945 +9,pKa-RobertRaddi_XGBoost,0.039429067693559264,0.35750035963429105,0.06906494679090133 +10,pKa_Chemaxon,-0.05804112161070563,-0.23184025910382575,0.615401130013483 +11,pKa_SabatinoRodriguezPaluch_uESE_extra,0.6422746474157303,1.6417529142315437,0.5236363636363636 diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/Correlation_Plots/PKA_ECRISMCorr_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/Correlation_Plots/PKA_ECRISMCorr_plot.pdf new file mode 100644 index 0000000..8810193 Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/Correlation_Plots/PKA_ECRISMCorr_plot.pdf differ diff --git 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b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/Correlation_Plots/pKa_SabatinoRodriguezPaluch_uESECorr_plot.pdf new file mode 100644 index 0000000..4a98ab2 Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/Correlation_Plots/pKa_SabatinoRodriguezPaluch_uESECorr_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/Correlation_Plots/pKa_SabatinoRodriguezPaluch_uESE_extraCorr_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/Correlation_Plots/pKa_SabatinoRodriguezPaluch_uESE_extraCorr_plot.pdf new file mode 100644 index 0000000..1bebba6 Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/Correlation_Plots/pKa_SabatinoRodriguezPaluch_uESE_extraCorr_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/Error_statistics.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/Error_statistics.csv new file mode 100644 index 0000000..0cdb1d8 --- /dev/null +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/Error_statistics.csv @@ -0,0 +1,22 @@ +,Molecule ID,Mean Error,Mean Absolute Error,Root Mean Squared Error +0,SAMPL8-1,9.504166666666622,12.779166666666697,20.525265325122273 +1,SAMPL8-2,1.2316666666665932,2.188333333333303,2.86637401606974 +2,SAMPL8-3,0.7249999999999299,1.391666666666639,1.7066048165875667 +3,SAMPL8-4,-0.9116666666667368,2.8100000000000267,3.146993274010405 +4,SAMPL8-5,-0.45333333333339887,2.053333333333337,2.512846990964634 +5,SAMPL8-6,-1.1783333333333972,1.8150000000000162,2.4040036050999287 +6,SAMPL8-7,11.878333333333275,12.504999999999967,19.36260743460618 +7,SAMPL8-8,0.7283333333332679,1.7316666666666396,1.8707128765971943 +8,SAMPL8-9,11.44499999999995,11.961666666666678,19.60849900765822 +9,SAMPL8-10,-0.5850000000000786,1.326666666666675,1.5239531926320478 +10,SAMPL8-12,16.511666666666624,17.284999999999997,23.37710917400467 +11,SAMPL8-14,-3.428333333333373,4.448333333333317,5.276131790115427 +12,SAMPL8-15,1.4183333333332657,2.3283333333333043,2.5885839114593994 +13,SAMPL8-16,0.5999999999999268,1.5999999999999825,1.7781076082921863 +14,SAMPL8-17,10.661666666666617,11.961666666666678,19.327620132856506 +15,SAMPL8-18,12.71333333333329,13.54333333333333,21.575048860508595 +16,SAMPL8-19,0.439999999999924,1.6641666666666544,2.2484068433744877 +17,SAMPL8-20,1.643333333333266,2.643333333333314,3.148322304550959 +18,SAMPL8-21,17.703333333333294,18.11,24.515425076197772 +19,SAMPL8-22,19.106666666666634,19.52666666666665,25.994844360629152 +20,SAMPL8-23,0.16083333333325903,1.4541666666666613,1.9661595391354398 diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/abs_error_bymethod_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/abs_error_bymethod_plot.pdf new file mode 100644 index 0000000..f8eee7d Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/abs_error_bymethod_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/abs_error_bymol_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/abs_error_bymol_plot.pdf new file mode 100644 index 0000000..09be0c1 Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/abs_error_bymol_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/macrostate_pKa_data.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/macrostate_pKa_data.csv new file mode 100644 index 0000000..4009c94 --- /dev/null +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_all/macrostate_pKa_data.csv @@ -0,0 +1,510 @@ +,Submission,Method Name,Method Type,Molecule ID,Formal Charge,Predicted pKa,Experimental pKa,Absolute Error +0,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 +1,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-12,-1,14.499999999999895,6.98,7.519999999999895 +2,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-12,0,8.499999999999917,6.98,1.519999999999916 +3,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-12,1,2.699999999999937,6.98,4.280000000000063 +4,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,-2,13.599999999999898,7.27,6.329999999999899 +5,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,-1,9.699999999999912,7.27,2.4299999999999127 +6,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,0,8.599999999999916,7.27,1.3299999999999166 +7,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,1,3.3999999999999346,7.27,3.870000000000065 +8,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 +9,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-16,-2,12.099999999999904,5.1,6.999999999999904 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fit,QM+LEC,SAMPL8-19,1,3.3999999999999346,4.93,1.530000000000065 +21,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,1,3.3999999999999346,6.99,3.5900000000000656 +22,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,-1,3.599999999999934,2.54,1.0599999999999339 +23,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,-1,3.599999999999934,5.01,1.4100000000000659 +24,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,0,-0.6000000000000512,2.54,3.140000000000051 +25,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,0,-0.6000000000000512,5.01,5.610000000000051 +26,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-20,-1,10.09999999999991,2.44,7.659999999999911 +27,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-20,0,4.69999999999993,2.44,2.25999999999993 +28,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-20,1,0.199999999999946,2.44,2.240000000000054 +29,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-21,-2,12.9999999999999,5.38,7.619999999999901 +30,pKa-3DS-1,COSMO-RS one pKa 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fit,QM+LEC,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 +41,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-3,-2,7.299999999999921,4.0,3.2999999999999208 +42,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-3,-1,3.299999999999935,4.0,0.700000000000065 +43,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-3,0,-1.1000000000000494,4.0,5.100000000000049 +44,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 +45,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-4,0,2.399999999999938,5.77,3.3700000000000614 +46,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-5,-1,3.1999999999999353,3.92,0.7200000000000646 +47,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-5,0,-1.6000000000000476,3.92,5.5200000000000475 +48,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-6,-1,3.3999999999999346,4.17,0.7700000000000653 +49,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-6,0,3.3999999999999346,4.17,0.7700000000000653 +50,pKa-3DS-1,COSMO-RS one pKa 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fit,QM+LEC,SAMPL8-7,0,7.299999999999921,6.63,0.6699999999999209 +141,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-8,0,1.7999999999999403,2.78,0.9800000000000595 +142,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-9,-1,12.399999999999903,6.08,6.319999999999903 +143,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-9,0,6.999999999999922,6.08,0.9199999999999218 +144,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-10,0,9.399999999999913,7.71,1.6899999999999133 +145,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-12,-1,14.999999999999893,6.98,8.019999999999893 +146,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-12,0,9.099999999999914,6.98,2.119999999999914 +147,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-12,1,3.3999999999999346,6.98,3.580000000000066 +148,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-14,-2,14.099999999999897,7.27,6.829999999999897 +149,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-14,-1,10.29999999999991,7.27,3.0299999999999105 +150,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-14,0,9.199999999999914,7.27,1.9299999999999145 +151,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-14,1,4.199999999999932,7.27,3.070000000000068 +152,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-15,0,5.799999999999926,2.54,3.259999999999926 +153,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-16,-2,12.699999999999902,5.1,7.599999999999902 +154,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-16,-1,11.299999999999907,5.1,6.199999999999907 +155,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-16,0,7.39999999999992,5.1,2.2999999999999208 +156,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-17,-1,11.999999999999904,6.58,5.419999999999904 +157,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-17,0,7.899999999999919,6.58,1.3199999999999186 +158,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-18,-1,11.799999999999905,2.72,9.079999999999904 +159,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-18,0,5.899999999999926,2.72,3.1799999999999256 +160,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-19,-1,7.299999999999921,4.93,2.369999999999921 +161,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-19,-1,7.299999999999921,6.99,0.30999999999992056 +162,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-19,0,6.699999999999923,4.93,1.7699999999999232 +163,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-19,0,6.699999999999923,6.99,0.2900000000000773 +164,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-19,1,4.099999999999932,4.93,0.8300000000000676 +165,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-19,1,4.099999999999932,6.99,2.890000000000068 +166,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-1,-1,4.299999999999931,2.54,1.7599999999999314 +167,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-1,-1,4.299999999999931,5.01,0.7100000000000684 +168,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-1,0,0.199999999999946,2.54,2.340000000000054 +169,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-1,0,0.199999999999946,5.01,4.810000000000054 +170,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-20,-1,10.699999999999909,2.44,8.25999999999991 +171,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-20,0,5.3999999999999275,2.44,2.9599999999999276 +172,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-20,1,0.9999999999999432,2.44,1.4400000000000568 +173,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-21,-2,13.499999999999899,5.38,8.119999999999898 +174,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-21,-1,9.199999999999914,5.38,3.819999999999914 +175,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-21,0,8.399999999999917,5.38,3.019999999999917 +176,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-21,1,3.599999999999934,5.38,1.780000000000066 +177,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-22,-1,12.9999999999999,3.36,9.639999999999901 +178,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-22,0,6.099999999999925,3.36,2.739999999999925 +179,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-22,1,-0.10000000000005294,3.36,3.460000000000053 +180,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-23,-1,9.499999999999913,2.65,6.849999999999913 +181,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-23,-1,9.499999999999913,9.02,0.4799999999999134 +182,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-23,0,5.099999999999929,2.65,2.4499999999999287 +183,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-23,0,5.099999999999929,9.02,3.920000000000071 +184,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 +185,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-3,-2,7.999999999999918,4.0,3.9999999999999183 +186,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-3,-1,3.9999999999999325,4.0,6.750155989720952e-14 +187,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-3,0,-0.3000000000000522,4.0,4.300000000000052 +188,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-4,-1,4.199999999999932,5.77,1.5700000000000678 +189,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-4,0,3.1999999999999353,5.77,2.5700000000000642 +190,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-5,-1,3.899999999999933,3.92,0.020000000000067075 +191,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-5,0,-0.8000000000000504,3.92,4.72000000000005 +192,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-6,-1,4.199999999999932,4.17,0.02999999999993186 +193,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-6,0,4.099999999999932,4.17,0.07000000000006779 +194,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-7,-1,12.499999999999902,6.63,5.869999999999902 +195,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-7,0,8.499999999999917,6.63,1.8699999999999166 +196,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-8,0,4.099999999999932,2.78,1.3199999999999323 +197,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-9,-1,12.699999999999902,6.08,6.6199999999999015 +198,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-9,0,8.299999999999917,6.08,2.219999999999917 +199,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-10,0,6.499999999999924,7.71,1.2100000000000763 +200,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-12,-1,14,6.98,7.02 +201,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-14,-3,-9.20000000000002,7.27,16.47000000000002 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Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,6.99,8.19000000000005 +247,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,2.54,2.0599999999999303 +248,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 +249,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 +250,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-2,19.399999999999878,5.38,14.019999999999879 +251,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-1,6.299999999999924,5.38,0.9199999999999244 +252,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-22,-1,5.199999999999928,3.36,1.8399999999999284 +253,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,2.65,6.549999999999914 +254,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 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Process,QSPR/ML,SAMPL8-6,0,13.1999999999999,4.17,9.0299999999999 +264,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-7,-1,4.999999999999929,6.63,1.630000000000071 +265,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 +266,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-9,-1,3.899999999999933,6.08,2.180000000000067 +267,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-10,0,5.599999999999927,7.71,2.110000000000073 +268,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-12,-1,19.09999999999988,6.98,12.11999999999988 +269,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-2,11.599999999999905,7.27,4.329999999999906 +270,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-1,11.499999999999906,7.27,4.229999999999906 +271,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-15,0,4.299999999999931,2.54,1.7599999999999314 +272,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-16,0,4.69999999999993,5.1,0.40000000000006963 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+34,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-10,0,5.299999999999928,7.71,2.410000000000072 +35,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-12,0,40,6.98,33.019999999999996 +36,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-14,0,0,7.27,7.27 +37,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-15,0,6.299999999999924,2.54,3.7599999999999243 +38,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-16,0,7.199999999999921,5.1,2.0999999999999215 +39,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-17,0,40,6.58,33.42 +40,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-18,0,40,2.72,37.28 +41,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-19,0,7.799999999999919,4.93,2.8699999999999193 +42,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-19,-1,5.199999999999928,6.99,1.790000000000072 +43,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-20,0,7.59999999999992,2.44,5.15999999999992 +44,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-21,0,40,5.38,34.62 +45,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-22,0,40,3.36,36.64 +46,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-23,0,3.599999999999934,2.65,0.949999999999934 +47,pKa-RobertRaddi_AdaBoost,AdaBoost,QSPR/ML,SAMPL8-23,-1,7.999999999999918,9.02,1.0200000000000813 +48,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-1,0,-3.0000000000000426,2.54,5.540000000000043 +49,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-1,-1,2.0999999999999392,5.01,2.9100000000000605 +50,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-2,-1,1.599999999999941,4.41,2.810000000000059 +51,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-3,-1,1.6999999999999407,4.0,2.3000000000000593 +52,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-4,-1,1.7999999999999403,5.77,3.9700000000000593 +53,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-5,-1,1.4999999999999414,3.92,2.4200000000000585 +54,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-6,-1,1.7999999999999403,4.17,2.3700000000000596 +55,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-7,0,7.299999999999921,6.63,0.6699999999999209 +56,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-8,0,1.7999999999999403,2.78,0.9800000000000595 +57,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-9,0,6.999999999999922,6.08,0.9199999999999218 +58,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 +59,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-12,0,7.999999999999918,6.98,1.0199999999999179 +60,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-14,0,8.099999999999918,7.27,0.8299999999999184 +61,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 +62,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-16,0,5.799999999999926,5.1,0.6999999999999265 +63,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-17,0,6.599999999999923,6.58,0.01999999999992319 +64,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-18,0,3.9999999999999325,2.72,1.2799999999999323 +65,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-19,0,4.999999999999929,4.93,0.06999999999992923 +66,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-19,-1,5.6999999999999265,6.99,1.2900000000000738 +67,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-20,0,3.299999999999935,2.44,0.859999999999935 +68,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-21,0,7.0999999999999215,5.38,1.7199999999999216 +69,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-22,0,4.299999999999931,3.36,0.9399999999999316 +70,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-23,0,3.0999999999999357,2.65,0.4499999999999358 +71,pKa-3DS-2,COSMO-RS base pKa fit,QM+LEC,SAMPL8-23,-1,8.399999999999917,9.02,0.6200000000000827 +72,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-1,0,0.199999999999946,2.54,2.340000000000054 +73,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-1,-1,4.299999999999931,5.01,0.7100000000000684 +74,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 +75,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-3,-1,3.9999999999999325,4.0,6.750155989720952e-14 +76,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-4,-1,4.199999999999932,5.77,1.5700000000000678 +77,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-5,-1,3.899999999999933,3.92,0.020000000000067075 +78,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-6,-1,4.199999999999932,4.17,0.02999999999993186 +79,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-7,0,8.499999999999917,6.63,1.8699999999999166 +80,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-8,0,4.099999999999932,2.78,1.3199999999999323 +81,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-9,0,8.299999999999917,6.08,2.219999999999917 +82,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-10,0,9.399999999999913,7.71,1.6899999999999133 +83,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-12,0,9.099999999999914,6.98,2.119999999999914 +84,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-14,0,9.199999999999914,7.27,1.9299999999999145 +85,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-15,0,5.799999999999926,2.54,3.259999999999926 +86,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-16,0,7.39999999999992,5.1,2.2999999999999208 +87,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-17,0,7.899999999999919,6.58,1.3199999999999186 +88,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-18,0,5.899999999999926,2.72,3.1799999999999256 +89,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-19,0,6.699999999999923,4.93,1.7699999999999232 +90,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-19,-1,7.299999999999921,6.99,0.30999999999992056 +91,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-20,0,5.3999999999999275,2.44,2.9599999999999276 +92,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-21,0,8.399999999999917,5.38,3.019999999999917 +93,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-22,0,6.099999999999925,3.36,2.739999999999925 +94,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-23,0,5.099999999999929,2.65,2.4499999999999287 +95,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-23,-1,9.499999999999913,9.02,0.4799999999999134 +96,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-1,0,40,2.54,37.46 +97,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-1,-1,7.59999999999992,5.01,2.58999999999992 +98,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-2,-1,8.099999999999918,4.41,3.689999999999918 +99,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-3,-1,6.299999999999924,4.0,2.2999999999999243 +100,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-4,-1,11.099999999999907,5.77,5.329999999999908 +101,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-5,-1,7.59999999999992,3.92,3.67999999999992 +102,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-6,-1,5.799999999999926,4.17,1.6299999999999262 +103,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-7,0,8.799999999999915,6.63,2.1699999999999156 +104,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-8,0,4.59999999999993,2.78,1.8199999999999306 +105,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-9,0,5.899999999999926,6.08,0.18000000000007432 +106,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-10,0,6.499999999999924,7.71,1.2100000000000763 +107,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-12,0,40,6.98,33.019999999999996 +108,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-14,0,0,7.27,7.27 +109,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-15,0,1.0999999999999428,2.54,1.4400000000000572 +110,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-16,0,3.599999999999934,5.1,1.5000000000000657 +111,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-17,0,5.199999999999928,6.58,1.3800000000000718 +112,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-18,0,1.599999999999941,2.72,1.1200000000000592 +113,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,0,3.0999999999999357,4.93,1.830000000000064 +114,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,-1,11.999999999999904,6.99,5.009999999999904 +115,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-20,0,1.1999999999999424,2.44,1.2400000000000575 +116,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-21,0,40,5.38,34.62 +117,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-22,0,40,3.36,36.64 +118,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,0,2.0999999999999392,2.65,0.5500000000000607 +119,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,-1,13.499999999999899,9.02,4.479999999999899 +120,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,0,40,2.54,37.46 +121,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 +122,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 +123,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 +124,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 +125,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 +126,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 +127,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-7,0,40,6.63,33.37 +128,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 +129,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-9,0,40,6.08,33.92 +130,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999914,7.71,1.489999999999914 +131,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-12,0,40,6.98,33.019999999999996 +132,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,0,0,7.27,7.27 +133,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,6.999999999999922,2.54,4.459999999999922 +134,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 +135,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-17,0,40,6.58,33.42 +136,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-18,0,40,2.72,37.28 +137,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 +138,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 +139,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 +140,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,0,40,5.38,34.62 +141,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-22,0,40,3.36,36.64 +142,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 +143,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 +144,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,0,40,2.54,37.46 +145,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,5.01,0.9100000000000676 +146,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-2,-1,6.099999999999925,4.41,1.689999999999925 +147,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-1,6.699999999999923,4.0,2.699999999999923 +148,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,-1,6.499999999999924,5.77,0.729999999999924 +149,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,-1,4.499999999999931,3.92,0.5799999999999308 +150,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 +151,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,0,11.299999999999907,6.63,4.669999999999907 +152,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-8,0,4.399999999999931,2.78,1.6199999999999313 +153,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,0,4.499999999999931,6.08,1.5800000000000693 +154,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-10,0,5.599999999999927,7.71,2.110000000000073 +155,pKa-ZhiyiWu-1,QM with linear 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a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/Error_statistics.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/Error_statistics.csv new file mode 100644 index 0000000..e729970 --- /dev/null +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/Error_statistics.csv @@ -0,0 +1,22 @@ +,Molecule ID,Mean Error,Mean Absolute Error,Root Mean Squared Error +0,SAMPL8-1,7.316666666666623,11.845000000000033,19.247965693374805 +1,SAMPL8-2,1.7899999999999245,2.5966666666666343,3.382420238034644 +2,SAMPL8-3,1.0666666666665954,1.633333333333305,1.937352144896008 +3,SAMPL8-4,-0.6366666666667378,2.656666666666682,3.0617369797768976 +4,SAMPL8-5,0.696666666666597,1.2766666666666397,1.6862384173063683 +5,SAMPL8-6,-0.103333333333401,0.8233333333333531,1.030970416646378 +6,SAMPL8-7,6.2866666666666005,7.5399999999999805,13.841973606871715 +7,SAMPL8-8,0.08666666666660339,1.7666666666666604,1.9269319309894237 +8,SAMPL8-9,5.436666666666606,6.410000000000035,13.882917560801118 +9,SAMPL8-10,-0.7433333333334113,1.4366666666666885,1.615992986783493 +10,SAMPL8-12,10.486666666666617,12.033333333333355,19.109571772630947 +11,SAMPL8-14,-2.4700000000000526,3.5899999999999963,4.438945069871143 +12,SAMPL8-15,0.5933333333332689,1.9333333333333265,2.2466864489732186 +13,SAMPL8-16,0.09999999999992859,1.600000000000018,1.8565200420858992 +14,SAMPL8-17,4.61999999999994,6.760000000000034,13.713414357239172 +15,SAMPL8-18,6.229999999999947,7.516666666666673,15.29374817804103 +16,SAMPL8-19,0.5316666666665903,1.7816666666666592,2.453874487417779 +17,SAMPL8-20,0.30999999999993727,1.8966666666666805,2.2357549060663886 +18,SAMPL8-21,11.536666666666617,12.350000000000021,20.024220334385053 +19,SAMPL8-22,13.173333333333288,14.013333333333328,21.332422897239464 +20,SAMPL8-23,0.5566666666665908,1.2049999999999816,1.6939942935755603 diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/abs_error_bymethod_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/abs_error_bymethod_plot.pdf new file mode 100644 index 0000000..7393106 Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/abs_error_bymethod_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/abs_error_bymol_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/abs_error_bymol_plot.pdf new file mode 100644 index 0000000..2b7b0b3 Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/abs_error_bymol_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/macrostate_pKa_data.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/macrostate_pKa_data.csv new file mode 100644 index 0000000..d720fbe --- /dev/null +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/macrostate_pKa_data.csv @@ -0,0 +1,264 @@ +,Submission,Method Name,Method Type,Molecule ID,Formal Charge,Predicted pKa,Experimental pKa,Absolute Error +0,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 +1,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-12,-1,14.499999999999895,6.98,7.519999999999895 +2,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-12,0,8.499999999999917,6.98,1.519999999999916 +3,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-12,1,2.699999999999937,6.98,4.280000000000063 +4,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,-2,13.599999999999898,7.27,6.329999999999899 +5,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,-1,9.699999999999912,7.27,2.4299999999999127 +6,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,0,8.599999999999916,7.27,1.3299999999999166 +7,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,1,3.3999999999999346,7.27,3.870000000000065 +8,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 +9,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-16,-2,12.099999999999904,5.1,6.999999999999904 +10,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-16,-1,10.699999999999909,5.1,5.599999999999909 +11,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-16,0,6.699999999999923,5.1,1.5999999999999233 +12,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-17,-1,11.499999999999906,6.58,4.919999999999906 +13,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-17,0,7.299999999999921,6.58,0.7199999999999207 +14,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-18,-1,11.199999999999907,2.72,8.479999999999906 +15,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-18,0,5.199999999999928,2.72,2.479999999999928 +16,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,-1,6.699999999999923,4.93,1.7699999999999232 +17,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,-1,6.699999999999923,6.99,0.2900000000000773 +18,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,0,5.999999999999925,4.93,1.0699999999999257 +19,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,0,5.999999999999925,6.99,0.9900000000000748 +20,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,1,3.3999999999999346,4.93,1.530000000000065 +21,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,1,3.3999999999999346,6.99,3.5900000000000656 +22,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,-1,3.599999999999934,2.54,1.0599999999999339 +23,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,-1,3.599999999999934,5.01,1.4100000000000659 +24,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,0,-0.6000000000000512,2.54,3.140000000000051 +25,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,0,-0.6000000000000512,5.01,5.610000000000051 +26,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-20,-1,10.09999999999991,2.44,7.659999999999911 +27,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-20,0,4.69999999999993,2.44,2.25999999999993 +28,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-20,1,0.199999999999946,2.44,2.240000000000054 +29,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-21,-2,12.9999999999999,5.38,7.619999999999901 +30,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-21,-1,8.599999999999916,5.38,3.2199999999999163 +31,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-21,0,7.799999999999919,5.38,2.419999999999919 +32,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-21,1,2.8999999999999364,5.38,2.4800000000000635 +33,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-22,-1,12.499999999999902,3.36,9.139999999999903 +34,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-22,0,5.499999999999927,3.36,2.1399999999999273 +35,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-22,1,-0.9000000000000501,3.36,4.2600000000000495 +36,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-23,-1,8.899999999999915,2.65,6.249999999999915 +37,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-23,-1,8.899999999999915,9.02,0.12000000000008448 +38,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-23,0,4.399999999999931,2.65,1.7499999999999312 +39,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-23,0,4.399999999999931,9.02,4.6200000000000685 +40,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 +41,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-3,-2,7.299999999999921,4.0,3.2999999999999208 +42,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-3,-1,3.299999999999935,4.0,0.700000000000065 +43,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-3,0,-1.1000000000000494,4.0,5.100000000000049 +44,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 +45,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-4,0,2.399999999999938,5.77,3.3700000000000614 +46,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-5,-1,3.1999999999999353,3.92,0.7200000000000646 +47,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-5,0,-1.6000000000000476,3.92,5.5200000000000475 +48,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-6,-1,3.3999999999999346,4.17,0.7700000000000653 +49,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-6,0,3.3999999999999346,4.17,0.7700000000000653 +50,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-7,-1,11.899999999999904,6.63,5.2699999999999045 +51,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-7,0,7.899999999999919,6.63,1.2699999999999187 +52,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-8,0,1.7999999999999403,2.78,0.9800000000000595 +53,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-9,-1,12.199999999999903,6.08,6.119999999999903 +54,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-9,0,7.699999999999919,6.08,1.6199999999999193 +55,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999914,7.71,1.489999999999914 +56,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-12,-1,14.299999999999896,6.98,7.3199999999998955 +57,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-2,5.099999999999929,7.27,2.170000000000071 +58,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-1,7.299999999999921,7.27,0.0299999999999212 +59,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,6.999999999999922,2.54,4.459999999999922 +60,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 +61,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-17,-1,4.199999999999932,6.58,2.3800000000000683 +62,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-18,-1,4.999999999999929,2.72,2.2799999999999288 +63,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,4.93,4.269999999999914 +64,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 +65,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 +66,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,6.99,0.5900000000000762 +67,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,4.93,6.130000000000049 +68,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,6.99,8.19000000000005 +69,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,2.54,2.0599999999999303 +70,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 +71,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 +72,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-2,19.399999999999878,5.38,14.019999999999879 +73,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-1,6.299999999999924,5.38,0.9199999999999244 +74,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-22,-1,5.199999999999928,3.36,1.8399999999999284 +75,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,2.65,6.549999999999914 +76,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 +77,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 +78,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,9.02,4.920000000000067 +79,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 +80,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 +81,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 +82,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 +83,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,0,14.599999999999895,3.92,10.679999999999895 +84,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 +85,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,0,13.1999999999999,4.17,9.0299999999999 +86,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-7,-1,4.999999999999929,6.63,1.630000000000071 +87,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 +88,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-9,-1,3.899999999999933,6.08,2.180000000000067 +89,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-10,0,5.599999999999927,7.71,2.110000000000073 +90,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-12,-1,19.09999999999988,6.98,12.11999999999988 +91,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-2,11.599999999999905,7.27,4.329999999999906 +92,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-1,11.499999999999906,7.27,4.229999999999906 +93,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-15,0,4.299999999999931,2.54,1.7599999999999314 +94,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-16,0,4.69999999999993,5.1,0.40000000000006963 +95,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,-1,12.299999999999903,6.58,5.719999999999903 +96,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,0,4.499999999999931,6.58,2.0800000000000693 +97,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,-1,9.599999999999913,2.72,6.879999999999912 +98,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,0,4.199999999999932,2.72,1.4799999999999316 +99,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,4.93,6.169999999999908 +100,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,6.99,4.109999999999907 +101,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,4.93,4.2300000000000555 +102,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,6.99,6.290000000000056 +103,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,1,-0.9000000000000501,4.93,5.83000000000005 +104,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,1,-0.9000000000000501,6.99,7.89000000000005 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a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/mean_abs_error_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/mean_abs_error_plot.pdf new file mode 100644 index 0000000..1020f03 Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/mean_abs_error_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/mean_error_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/mean_error_plot.pdf new file mode 100644 index 0000000..5a1f706 Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/mean_error_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/popular_transitions_pKa_data.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/popular_transitions_pKa_data.csv new file mode 100644 index 0000000..15ab0f6 --- /dev/null +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/popular_transitions_pKa_data.csv @@ -0,0 +1,145 @@ +,Submission,Method Name,Method Type,Molecule ID,Formal Charge,Predicted pKa,Experimental pKa,Absolute Error +0,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,0,-0.6000000000000512,2.54,3.140000000000051 +1,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,-1,3.599999999999934,5.01,1.4100000000000659 +2,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 +3,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-3,-1,3.299999999999935,4.0,0.700000000000065 +4,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 +5,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-5,-1,3.1999999999999353,3.92,0.7200000000000646 +6,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-6,-1,3.3999999999999346,4.17,0.7700000000000653 +7,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-7,0,7.899999999999919,6.63,1.2699999999999187 +8,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-8,0,1.7999999999999403,2.78,0.9800000000000595 +9,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-9,0,7.699999999999919,6.08,1.6199999999999193 +10,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 +11,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-12,0,8.499999999999917,6.98,1.519999999999916 +12,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,0,8.599999999999916,7.27,1.3299999999999166 +13,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 +14,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-16,0,6.699999999999923,5.1,1.5999999999999233 +15,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-17,0,7.299999999999921,6.58,0.7199999999999207 +16,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-18,0,5.199999999999928,2.72,2.479999999999928 +17,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,0,5.999999999999925,4.93,1.0699999999999257 +18,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,-1,6.699999999999923,6.99,0.2900000000000773 +19,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-20,0,4.69999999999993,2.44,2.25999999999993 +20,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-21,0,7.799999999999919,5.38,2.419999999999919 +21,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-22,0,5.499999999999927,3.36,2.1399999999999273 +22,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-23,0,4.399999999999931,2.65,1.7499999999999312 +23,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-23,-1,8.899999999999915,9.02,0.12000000000008448 +24,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,0,40.0,2.54,37.46 +25,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 +26,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 +27,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 +28,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 +29,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 +30,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 +31,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-7,0,40.0,6.63,33.37 +32,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 +33,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-9,0,40.0,6.08,33.92 +34,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999914,7.71,1.489999999999914 +35,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-12,0,40.0,6.98,33.019999999999996 +36,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,0,0.0,7.27,7.27 +37,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,6.999999999999922,2.54,4.459999999999922 +38,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 +39,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-17,0,40.0,6.58,33.42 +40,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-18,0,40.0,2.72,37.28 +41,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 +42,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 +43,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 +44,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,0,40.0,5.38,34.62 +45,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-22,0,40.0,3.36,36.64 +46,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 +47,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 +48,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,0,40.0,2.54,37.46 +49,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,5.01,0.9100000000000676 +50,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-2,-1,6.099999999999925,4.41,1.689999999999925 +51,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-1,6.699999999999923,4.0,2.699999999999923 +52,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,-1,6.499999999999924,5.77,0.729999999999924 +53,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,-1,4.499999999999931,3.92,0.5799999999999308 +54,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 +55,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,0,11.299999999999907,6.63,4.669999999999907 +56,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-8,0,4.399999999999931,2.78,1.6199999999999313 +57,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,0,4.499999999999931,6.08,1.5800000000000693 +58,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-10,0,5.599999999999927,7.71,2.110000000000073 +59,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-12,0,40.0,6.98,33.019999999999996 +60,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,0,0.0,7.27,7.27 +61,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-15,0,4.299999999999931,2.54,1.7599999999999314 +62,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-16,0,4.69999999999993,5.1,0.40000000000006963 +63,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,0,4.499999999999931,6.58,2.0800000000000693 +64,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,0,4.199999999999932,2.72,1.4799999999999316 +65,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,4.93,4.2300000000000555 +66,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,6.99,4.109999999999907 +67,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,0,1.3999999999999417,2.44,1.0400000000000582 +68,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,0,40.0,5.38,34.62 +69,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-22,0,40.0,3.36,36.64 +70,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.299999999999935,2.65,0.6499999999999351 +71,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,9.999999999999911,9.02,0.9799999999999116 +72,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-1,0,-2.5000000000000444,2.54,5.0400000000000444 +73,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 +74,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-2,-1,5.299999999999928,4.41,0.8899999999999277 +75,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-3,-1,4.199999999999932,4.0,0.1999999999999318 +76,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-4,-1,4.59999999999993,5.77,1.1700000000000692 +77,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-5,-1,5.099999999999929,3.92,1.1799999999999287 +78,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-6,-1,4.69999999999993,4.17,0.5299999999999301 +79,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-7,0,4.099999999999932,6.63,2.5300000000000678 +80,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-8,0,-0.40000000000005187,2.78,3.1800000000000517 +81,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-9,0,5.599999999999927,6.08,0.48000000000007326 +82,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-10,0,7.0999999999999215,7.71,0.6100000000000785 +83,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-12,0,4.899999999999929,6.98,2.080000000000071 +84,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-14,0,5.3999999999999275,7.27,1.870000000000072 +85,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-15,0,1.3999999999999417,2.54,1.1400000000000583 +86,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-16,0,3.9999999999999325,5.1,1.1000000000000671 +87,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-17,0,4.69999999999993,6.58,1.88000000000007 +88,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-18,0,1.6999999999999407,2.72,1.0200000000000595 +89,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-19,0,4.099999999999932,4.93,0.8300000000000676 +90,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-19,-1,6.999999999999922,6.99,0.009999999999921627 +91,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-20,0,1.4999999999999414,2.44,0.9400000000000586 +92,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-21,0,3.799999999999933,5.38,1.5800000000000667 +93,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-22,0,2.0999999999999392,3.36,1.2600000000000606 +94,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-23,0,1.9999999999999396,2.65,0.6500000000000603 +95,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-23,-1,10.09999999999991,9.02,1.0799999999999113 +96,pKa_Chemaxon,Chemaxon,Other,SAMPL8-1,0,40.0,2.54,37.46 +97,pKa_Chemaxon,Chemaxon,Other,SAMPL8-1,-1,2.7999999999999368,5.01,2.210000000000063 +98,pKa_Chemaxon,Chemaxon,Other,SAMPL8-2,-1,2.499999999999938,4.41,1.9100000000000623 +99,pKa_Chemaxon,Chemaxon,Other,SAMPL8-3,-1,2.999999999999936,4.0,1.000000000000064 +100,pKa_Chemaxon,Chemaxon,Other,SAMPL8-4,-1,2.699999999999937,5.77,3.0700000000000625 +101,pKa_Chemaxon,Chemaxon,Other,SAMPL8-5,-1,2.8999999999999364,3.92,1.0200000000000635 +102,pKa_Chemaxon,Chemaxon,Other,SAMPL8-6,-1,2.499999999999938,4.17,1.670000000000062 +103,pKa_Chemaxon,Chemaxon,Other,SAMPL8-7,0,5.3999999999999275,6.63,1.2300000000000724 +104,pKa_Chemaxon,Chemaxon,Other,SAMPL8-8,0,1.89999999999994,2.78,0.8800000000000598 +105,pKa_Chemaxon,Chemaxon,Other,SAMPL8-9,0,5.3999999999999275,6.08,0.6800000000000725 +106,pKa_Chemaxon,Chemaxon,Other,SAMPL8-10,0,5.099999999999929,7.71,2.6100000000000714 +107,pKa_Chemaxon,Chemaxon,Other,SAMPL8-12,0,5.199999999999928,6.98,1.7800000000000722 +108,pKa_Chemaxon,Chemaxon,Other,SAMPL8-14,0,5.499999999999927,7.27,1.7700000000000724 +109,pKa_Chemaxon,Chemaxon,Other,SAMPL8-15,0,1.0999999999999428,2.54,1.4400000000000572 +110,pKa_Chemaxon,Chemaxon,Other,SAMPL8-16,0,3.599999999999934,5.1,1.5000000000000657 +111,pKa_Chemaxon,Chemaxon,Other,SAMPL8-17,0,5.499999999999927,6.58,1.080000000000073 +112,pKa_Chemaxon,Chemaxon,Other,SAMPL8-18,0,0.9999999999999432,2.72,1.720000000000057 +113,pKa_Chemaxon,Chemaxon,Other,SAMPL8-19,0,4.69999999999993,4.93,0.2300000000000697 +114,pKa_Chemaxon,Chemaxon,Other,SAMPL8-19,-1,6.899999999999922,6.99,0.09000000000007802 +115,pKa_Chemaxon,Chemaxon,Other,SAMPL8-20,0,0.8999999999999435,2.44,1.5400000000000564 +116,pKa_Chemaxon,Chemaxon,Other,SAMPL8-21,0,4.899999999999929,5.38,0.4800000000000706 +117,pKa_Chemaxon,Chemaxon,Other,SAMPL8-22,0,2.0999999999999392,3.36,1.2600000000000606 +118,pKa_Chemaxon,Chemaxon,Other,SAMPL8-23,0,2.499999999999938,2.65,0.15000000000006208 +119,pKa_Chemaxon,Chemaxon,Other,SAMPL8-23,-1,6.599999999999923,9.02,2.4200000000000763 +120,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-1,0,-11.100000000000014,2.54,13.640000000000015 +121,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-1,-1,7.59999999999992,5.01,2.58999999999992 +122,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-2,-1,8.099999999999918,4.41,3.689999999999918 +123,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-3,-1,6.299999999999924,4.0,2.2999999999999243 +124,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-4,-1,11.099999999999907,5.77,5.329999999999908 +125,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-5,-1,7.59999999999992,3.92,3.67999999999992 +126,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-6,-1,5.799999999999926,4.17,1.6299999999999262 +127,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-7,0,8.799999999999915,6.63,2.1699999999999156 +128,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-8,0,4.59999999999993,2.78,1.8199999999999306 +129,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-9,0,5.899999999999926,6.08,0.18000000000007432 +130,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-10,0,6.499999999999924,7.71,1.2100000000000763 +131,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-12,0,6.199999999999925,6.98,0.7800000000000757 +132,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-14,0,9.299999999999914,7.27,2.029999999999914 +133,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-15,0,1.0999999999999428,2.54,1.4400000000000572 +134,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-16,0,3.599999999999934,5.1,1.5000000000000657 +135,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-17,0,5.199999999999928,6.58,1.3800000000000718 +136,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-18,0,1.599999999999941,2.72,1.1200000000000592 +137,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-19,0,3.0999999999999357,4.93,1.830000000000064 +138,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-19,-1,11.999999999999904,6.99,5.009999999999904 +139,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-20,0,1.1999999999999424,2.44,1.2400000000000575 +140,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-21,0,4.999999999999929,5.38,0.38000000000007095 +141,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-22,0,9.499999999999913,3.36,6.1399999999999135 +142,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-23,0,2.0999999999999392,2.65,0.5500000000000607 +143,pKa_SabatinoRodriguezPaluch_uESE_extra,RFE-uESE-extra,QM,SAMPL8-23,-1,13.499999999999899,9.02,4.479999999999899 diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/rmse_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/rmse_plot.pdf new file mode 100644 index 0000000..730a351 Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-1/analysis_outputs_ranked/rmse_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/README.md b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/README.md new file mode 100644 index 0000000..444f5f8 --- /dev/null +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/README.md @@ -0,0 +1,4 @@ +## Manifest +This folder is for figures and tables that will go into the supplementary material. In this run we change the assigned predicted $pKa$ for submissions missing a designated $pKa$ with the designated formal charge to -20 when the experimental $pKa$ is closer to 14. +-[`analysis_outputs_all/`](analysis_outputs_all/)- This directory contains bar plots and correlation plots associated with the performance statistics for all submissions. +-[`analysis_outputs_ranked/`](analysis_outputs_ranked/)- This directory contains bar plots and correlation plots associated with the performance statistics for all ranked submissions. diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/Correlation_Plots/Correlation_statistics.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/Correlation_Plots/Correlation_statistics.csv new file mode 100644 index 0000000..d481cd4 --- /dev/null +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/Correlation_Plots/Correlation_statistics.csv @@ -0,0 +1,13 @@ +,Submission,R-squared,Slope,Kendall Tau +0,pKa-3DS-1,0.7834943477469948,1.0137866774745936,0.6083798799280435 +1,pKa-RobertRaddi_AdaBoost,-0.12375362743146529,-0.4796596218139512,0.01922366120271981 +2,pKa-3DS-2,0.7536231507883856,1.1538261805405876,0.5839454948814495 +3,pKa-3DS-3,0.7552485515279517,0.9351327184830505,0.5865219201701498 +4,pKa_SabatinoRodriguezPaluch_uESE,0.06877969576035531,0.25638492627944426,0.2647219842825437 +5,pKa-RobertRaddi_DeepGP,-0.08788518642814273,-0.3313112236340298,0.07705141285294194 +6,pKa-ZhiyiWu-1,-0.03426186958205091,-0.12317996696736858,0.21404545767263877 +7,pKa-RobertRaddi_RF,-0.1097766476200591,-0.4305255197088526,0.053717180837367706 +8,PKA_ECRISM,0.8477227975324197,1.1469468690328275,0.6423400443695945 +9,pKa-RobertRaddi_XGBoost,-0.09803523697127486,-0.3839730247422404,0.06139106381413451 +10,pKa_Chemaxon,0.35923113141641155,0.5185269857035623,0.615401130013483 +11,pKa_SabatinoRodriguezPaluch_uESE_extra,0.6422746474157303,1.6417529142315437,0.5236363636363636 diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/Correlation_Plots/PKA_ECRISMCorr_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/Correlation_Plots/PKA_ECRISMCorr_plot.pdf new file mode 100644 index 0000000..8375f8b Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/Correlation_Plots/PKA_ECRISMCorr_plot.pdf differ diff --git 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b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/Correlation_Plots/pKa_SabatinoRodriguezPaluch_uESECorr_plot.pdf new file mode 100644 index 0000000..80539d2 Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/Correlation_Plots/pKa_SabatinoRodriguezPaluch_uESECorr_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/Correlation_Plots/pKa_SabatinoRodriguezPaluch_uESE_extraCorr_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/Correlation_Plots/pKa_SabatinoRodriguezPaluch_uESE_extraCorr_plot.pdf new file mode 100644 index 0000000..7003368 Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/Correlation_Plots/pKa_SabatinoRodriguezPaluch_uESE_extraCorr_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/Error_statistics.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/Error_statistics.csv new file mode 100644 index 0000000..29bc39f --- /dev/null +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/Error_statistics.csv @@ -0,0 +1,22 @@ +,Molecule ID,Mean Error,Mean Absolute Error,Root Mean Squared Error +0,SAMPL8-1,1.9208333333332905,5.195833333333364,7.092943676640898 +1,SAMPL8-2,1.2316666666665932,2.188333333333303,2.86637401606974 +2,SAMPL8-3,0.7249999999999299,1.391666666666639,1.7066048165875667 +3,SAMPL8-4,-0.9116666666667368,2.8100000000000267,3.146993274010405 +4,SAMPL8-5,-0.45333333333339887,2.053333333333337,2.512846990964634 +5,SAMPL8-6,-1.1783333333333972,1.8150000000000162,2.4040036050999287 +6,SAMPL8-7,3.2116666666666127,3.8383333333333027,4.672319195717105 +7,SAMPL8-8,0.7283333333332679,1.7316666666666396,1.8707128765971943 +8,SAMPL8-9,2.7783333333332827,3.29500000000001,4.677595536170263 +9,SAMPL8-10,-0.5850000000000786,1.326666666666675,1.5239531926320478 +10,SAMPL8-12,3.5116666666666276,4.284999999999997,5.096001700679987 +11,SAMPL8-14,-13.428333333333372,14.448333333333316,19.319357304700034 +12,SAMPL8-15,1.4183333333332657,2.3283333333333043,2.5885839114593994 +13,SAMPL8-16,0.5999999999999268,1.5999999999999825,1.7781076082921863 +14,SAMPL8-17,1.9949999999999506,3.2950000000000093,4.428344310612421 +15,SAMPL8-18,4.046666666666623,4.8766666666666625,6.680523931549078 +16,SAMPL8-19,0.439999999999924,1.6641666666666544,2.2484068433744877 +17,SAMPL8-20,1.643333333333266,2.643333333333314,3.148322304550959 +18,SAMPL8-21,4.703333333333297,5.1099999999999985,6.235869359332876 +19,SAMPL8-22,6.106666666666631,6.526666666666652,7.816132888668999 +20,SAMPL8-23,0.16083333333325903,1.4541666666666613,1.9661595391354398 diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/abs_error_bymethod_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/abs_error_bymethod_plot.pdf new file mode 100644 index 0000000..859f33d Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/abs_error_bymethod_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/abs_error_bymol_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/abs_error_bymol_plot.pdf new file mode 100644 index 0000000..c9ae123 Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/abs_error_bymol_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/macrostate_pKa_data.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/macrostate_pKa_data.csv new file mode 100644 index 0000000..4009c94 --- /dev/null +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_all/macrostate_pKa_data.csv @@ -0,0 +1,510 @@ +,Submission,Method Name,Method Type,Molecule ID,Formal Charge,Predicted pKa,Experimental pKa,Absolute Error +0,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-10,0,8.299999999999917,7.71,0.5899999999999173 +1,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-12,-1,14.499999999999895,6.98,7.519999999999895 +2,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-12,0,8.499999999999917,6.98,1.519999999999916 +3,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-12,1,2.699999999999937,6.98,4.280000000000063 +4,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,-2,13.599999999999898,7.27,6.329999999999899 +5,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,-1,9.699999999999912,7.27,2.4299999999999127 +6,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,0,8.599999999999916,7.27,1.3299999999999166 +7,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-14,1,3.3999999999999346,7.27,3.870000000000065 +8,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-15,0,3.899999999999933,2.54,1.3599999999999328 +9,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-16,-2,12.099999999999904,5.1,6.999999999999904 +10,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-16,-1,10.699999999999909,5.1,5.599999999999909 +11,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-16,0,6.699999999999923,5.1,1.5999999999999233 +12,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-17,-1,11.499999999999906,6.58,4.919999999999906 +13,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-17,0,7.299999999999921,6.58,0.7199999999999207 +14,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-18,-1,11.199999999999907,2.72,8.479999999999906 +15,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-18,0,5.199999999999928,2.72,2.479999999999928 +16,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,-1,6.699999999999923,4.93,1.7699999999999232 +17,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,-1,6.699999999999923,6.99,0.2900000000000773 +18,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,0,5.999999999999925,4.93,1.0699999999999257 +19,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,0,5.999999999999925,6.99,0.9900000000000748 +20,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,1,3.3999999999999346,4.93,1.530000000000065 +21,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,1,3.3999999999999346,6.99,3.5900000000000656 +22,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,-1,3.599999999999934,2.54,1.0599999999999339 +23,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,-1,3.599999999999934,5.01,1.4100000000000659 +24,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,0,-0.6000000000000512,2.54,3.140000000000051 +25,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,0,-0.6000000000000512,5.01,5.610000000000051 +26,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-20,-1,10.09999999999991,2.44,7.659999999999911 +27,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-20,0,4.69999999999993,2.44,2.25999999999993 +28,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-20,1,0.199999999999946,2.44,2.240000000000054 +29,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-21,-2,12.9999999999999,5.38,7.619999999999901 +30,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-21,-1,8.599999999999916,5.38,3.2199999999999163 +31,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-21,0,7.799999999999919,5.38,2.419999999999919 +32,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-21,1,2.8999999999999364,5.38,2.4800000000000635 +33,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-22,-1,12.499999999999902,3.36,9.139999999999903 +34,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-22,0,5.499999999999927,3.36,2.1399999999999273 +35,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-22,1,-0.9000000000000501,3.36,4.2600000000000495 +36,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-23,-1,8.899999999999915,2.65,6.249999999999915 +37,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-23,-1,8.899999999999915,9.02,0.12000000000008448 +38,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-23,0,4.399999999999931,2.65,1.7499999999999312 +39,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-23,0,4.399999999999931,9.02,4.6200000000000685 +40,pKa-3DS-1,COSMO-RS one pKa 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fit,QM+LEC,SAMPL8-6,-1,4.199999999999932,4.17,0.02999999999993186 +193,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-6,0,4.099999999999932,4.17,0.07000000000006779 +194,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-7,-1,12.499999999999902,6.63,5.869999999999902 +195,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-7,0,8.499999999999917,6.63,1.8699999999999166 +196,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-8,0,4.099999999999932,2.78,1.3199999999999323 +197,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-9,-1,12.699999999999902,6.08,6.6199999999999015 +198,pKa-3DS-3,COSMO-RS pKa fit,QM+LEC,SAMPL8-9,0,8.299999999999917,6.08,2.219999999999917 +199,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-10,0,6.499999999999924,7.71,1.2100000000000763 +200,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-12,-1,14,6.98,7.02 +201,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-14,-3,-9.20000000000002,7.27,16.47000000000002 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+211,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,0,3.0999999999999357,4.93,1.830000000000064 +212,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,0,3.0999999999999357,6.99,3.8900000000000645 +213,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-1,-1,7.59999999999992,2.54,5.05999999999992 +214,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-1,-1,7.59999999999992,5.01,2.58999999999992 +215,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-20,0,1.1999999999999424,2.44,1.2400000000000575 +216,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-21,-1,17.199999999999886,5.38,11.819999999999887 +217,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-22,-1,17.499999999999886,3.36,14.139999999999887 +218,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,-1,13.499999999999899,2.65,10.849999999999898 +219,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,-1,13.499999999999899,9.02,4.479999999999899 +220,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,0,2.0999999999999392,2.65,0.5500000000000607 +221,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,0,2.0999999999999392,9.02,6.92000000000006 +222,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-2,-1,8.099999999999918,4.41,3.689999999999918 +223,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-3,-1,6.299999999999924,4.0,2.2999999999999243 +224,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-4,-1,11.099999999999907,5.77,5.329999999999908 +225,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-4,0,-8.000000000000025,5.77,13.770000000000024 +226,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-5,-1,7.59999999999992,3.92,3.67999999999992 +227,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-5,0,-10.100000000000017,3.92,14.020000000000017 +228,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-6,-1,5.799999999999926,4.17,1.6299999999999262 +229,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-6,0,-5.3000000000000345,4.17,9.470000000000034 +230,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-7,0,8.799999999999915,6.63,2.1699999999999156 +231,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-8,0,4.59999999999993,2.78,1.8199999999999306 +232,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-9,0,5.899999999999926,6.08,0.18000000000007432 +233,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999914,7.71,1.489999999999914 +234,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-12,-1,14.299999999999896,6.98,7.3199999999998955 +235,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-2,5.099999999999929,7.27,2.170000000000071 +236,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-1,7.299999999999921,7.27,0.0299999999999212 +237,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,6.999999999999922,2.54,4.459999999999922 +238,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 +239,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-17,-1,4.199999999999932,6.58,2.3800000000000683 +240,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-18,-1,4.999999999999929,2.72,2.2799999999999288 +241,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,4.93,4.269999999999914 +242,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 +243,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 +244,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,6.99,0.5900000000000762 +245,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,4.93,6.130000000000049 +246,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,6.99,8.19000000000005 +247,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,2.54,2.0599999999999303 +248,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 +249,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 +250,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-2,19.399999999999878,5.38,14.019999999999879 +251,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-1,6.299999999999924,5.38,0.9199999999999244 +252,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-22,-1,5.199999999999928,3.36,1.8399999999999284 +253,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,2.65,6.549999999999914 +254,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 +255,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 +256,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,9.02,4.920000000000067 +257,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 +258,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 +259,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 +260,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 +261,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,0,14.599999999999895,3.92,10.679999999999895 +262,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 +263,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,0,13.1999999999999,4.17,9.0299999999999 +264,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-7,-1,4.999999999999929,6.63,1.630000000000071 +265,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 +266,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-9,-1,3.899999999999933,6.08,2.180000000000067 +267,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-10,0,5.599999999999927,7.71,2.110000000000073 +268,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-12,-1,19.09999999999988,6.98,12.11999999999988 +269,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-2,11.599999999999905,7.27,4.329999999999906 +270,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-1,11.499999999999906,7.27,4.229999999999906 +271,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-15,0,4.299999999999931,2.54,1.7599999999999314 +272,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-16,0,4.69999999999993,5.1,0.40000000000006963 +273,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,-1,12.299999999999903,6.58,5.719999999999903 +274,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,0,4.499999999999931,6.58,2.0800000000000693 +275,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,-1,9.599999999999913,2.72,6.879999999999912 +276,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,0,4.199999999999932,2.72,1.4799999999999316 +277,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,4.93,6.169999999999908 +278,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,6.99,4.109999999999907 +279,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,4.93,4.2300000000000555 +280,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,6.99,6.290000000000056 +281,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,1,-0.9000000000000501,4.93,5.83000000000005 +282,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,1,-0.9000000000000501,6.99,7.89000000000005 +283,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,2.54,1.559999999999932 +284,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,5.01,0.9100000000000676 +285,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,0,1.3999999999999417,2.44,1.0400000000000582 +286,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-3,19.899999999999878,5.38,14.519999999999879 +287,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-2,16.29999999999989,5.38,10.919999999999892 +288,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-1,13.699999999999898,5.38,8.319999999999897 +289,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-22,-1,13.899999999999897,3.36,10.539999999999898 +290,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,9.999999999999911,2.65,7.349999999999911 +291,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,9.999999999999911,9.02,0.9799999999999116 +292,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.299999999999935,2.65,0.6499999999999351 +293,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.299999999999935,9.02,5.720000000000065 +294,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-2,-1,6.099999999999925,4.41,1.689999999999925 +295,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-2,8.799999999999915,4.0,4.7999999999999154 +296,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-1,6.699999999999923,4.0,2.699999999999923 +297,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,-1,6.499999999999924,5.77,0.729999999999924 +298,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,0,-5.3290705182007514e-14,5.77,5.770000000000053 +299,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,-1,4.499999999999931,3.92,0.5799999999999308 +300,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,0,-1.200000000000049,3.92,5.120000000000049 +301,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 +302,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,0,1.9999999999999396,4.17,2.1700000000000603 +303,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,-1,16.39999999999989,6.63,9.76999999999989 +304,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,0,11.299999999999907,6.63,4.669999999999907 +305,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-8,0,4.399999999999931,2.78,1.6199999999999313 +306,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,-1,15.699999999999891,6.08,9.61999999999989 +307,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,0,4.499999999999931,6.08,1.5800000000000693 +308,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-10,0,6.399999999999924,7.71,1.310000000000076 +309,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-12,-1,13.1999999999999,6.98,6.219999999999899 +310,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-14,-2,3.9999999999999325,7.27,3.270000000000067 +311,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-14,-1,4.099999999999932,7.27,3.1700000000000674 +312,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-15,0,5.499999999999927,2.54,2.959999999999927 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Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 +126,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 +127,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-7,0,14,6.63,7.37 +128,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 +129,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-9,0,14,6.08,7.92 +130,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999914,7.71,1.489999999999914 +131,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-12,0,14,6.98,7.02 +132,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,0,-20,7.27,27.27 +133,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,6.999999999999922,2.54,4.459999999999922 +134,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 +135,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-17,0,14,6.58,7.42 +136,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-18,0,14,2.72,11.28 +137,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 +138,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 +139,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 +140,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,0,14,5.38,8.620000000000001 +141,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-22,0,14,3.36,10.64 +142,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 +143,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 +144,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,0,14,2.54,11.46 +145,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,5.01,0.9100000000000676 +146,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-2,-1,6.099999999999925,4.41,1.689999999999925 +147,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-1,6.699999999999923,4.0,2.699999999999923 +148,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,-1,6.499999999999924,5.77,0.729999999999924 +149,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,-1,4.499999999999931,3.92,0.5799999999999308 +150,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 +151,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,0,11.299999999999907,6.63,4.669999999999907 +152,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-8,0,4.399999999999931,2.78,1.6199999999999313 +153,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,0,4.499999999999931,6.08,1.5800000000000693 +154,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-10,0,5.599999999999927,7.71,2.110000000000073 +155,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-12,0,14,6.98,7.02 +156,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,0,-20,7.27,27.27 +157,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-15,0,4.299999999999931,2.54,1.7599999999999314 +158,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-16,0,4.69999999999993,5.1,0.40000000000006963 +159,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,0,4.499999999999931,6.58,2.0800000000000693 +160,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,0,4.199999999999932,2.72,1.4799999999999316 +161,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,4.93,4.2300000000000555 +162,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,6.99,4.109999999999907 +163,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,0,1.3999999999999417,2.44,1.0400000000000582 +164,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,0,14,5.38,8.620000000000001 +165,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-22,0,14,3.36,10.64 +166,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.299999999999935,2.65,0.6499999999999351 +167,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,9.999999999999911,9.02,0.9799999999999116 +168,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-1,0,14,2.54,11.46 +169,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 +170,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-2,-1,4.899999999999929,4.41,0.48999999999992916 +171,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-3,-1,4.69999999999993,4.0,0.69999999999993 +172,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-4,-1,3.299999999999935,5.77,2.4700000000000646 +173,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-5,-1,0.29999999999994564,3.92,3.6200000000000543 +174,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-6,-1,-0.10000000000005294,4.17,4.270000000000053 +175,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-7,0,14,6.63,7.37 +176,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-8,0,3.9999999999999325,2.78,1.2199999999999327 +177,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-9,0,14,6.08,7.92 +178,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-10,0,6.399999999999924,7.71,1.310000000000076 +179,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-12,0,14,6.98,7.02 +180,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-14,0,-20,7.27,27.27 +181,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-15,0,5.499999999999927,2.54,2.959999999999927 +182,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-16,0,6.199999999999925,5.1,1.099999999999925 +183,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-17,0,14,6.58,7.42 +184,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-18,0,14,2.72,11.28 +185,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,0,5.899999999999926,4.93,0.969999999999926 +186,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,-1,5.299999999999928,6.99,1.6900000000000723 +187,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-20,0,7.699999999999919,2.44,5.25999999999992 +188,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-21,0,14,5.38,8.620000000000001 +189,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-22,0,14,3.36,10.64 +190,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-23,0,1.6999999999999407,2.65,0.9500000000000592 +191,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-23,-1,5.499999999999927,9.02,3.5200000000000724 +192,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-1,0,-2.5000000000000444,2.54,5.0400000000000444 +193,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 +194,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-2,-1,5.299999999999928,4.41,0.8899999999999277 +195,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-3,-1,4.199999999999932,4.0,0.1999999999999318 +196,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-4,-1,4.59999999999993,5.77,1.1700000000000692 +197,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-5,-1,5.099999999999929,3.92,1.1799999999999287 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fit,QM+LEC,SAMPL8-16,-2,12.099999999999904,5.1,6.999999999999904 +10,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-16,-1,10.699999999999909,5.1,5.599999999999909 +11,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-16,0,6.699999999999923,5.1,1.5999999999999233 +12,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-17,-1,11.499999999999906,6.58,4.919999999999906 +13,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-17,0,7.299999999999921,6.58,0.7199999999999207 +14,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-18,-1,11.199999999999907,2.72,8.479999999999906 +15,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-18,0,5.199999999999928,2.72,2.479999999999928 +16,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,-1,6.699999999999923,4.93,1.7699999999999232 +17,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,-1,6.699999999999923,6.99,0.2900000000000773 +18,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,0,5.999999999999925,4.93,1.0699999999999257 +19,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,0,5.999999999999925,6.99,0.9900000000000748 +20,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,1,3.3999999999999346,4.93,1.530000000000065 +21,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-19,1,3.3999999999999346,6.99,3.5900000000000656 +22,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,-1,3.599999999999934,2.54,1.0599999999999339 +23,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,-1,3.599999999999934,5.01,1.4100000000000659 +24,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,0,-0.6000000000000512,2.54,3.140000000000051 +25,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,0,-0.6000000000000512,5.01,5.610000000000051 +26,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-20,-1,10.09999999999991,2.44,7.659999999999911 +27,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-20,0,4.69999999999993,2.44,2.25999999999993 +28,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-20,1,0.199999999999946,2.44,2.240000000000054 +29,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-21,-2,12.9999999999999,5.38,7.619999999999901 +30,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-21,-1,8.599999999999916,5.38,3.2199999999999163 +31,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-21,0,7.799999999999919,5.38,2.419999999999919 +32,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-21,1,2.8999999999999364,5.38,2.4800000000000635 +33,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-22,-1,12.499999999999902,3.36,9.139999999999903 +34,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-22,0,5.499999999999927,3.36,2.1399999999999273 +35,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-22,1,-0.9000000000000501,3.36,4.2600000000000495 +36,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-23,-1,8.899999999999915,2.65,6.249999999999915 +37,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-23,-1,8.899999999999915,9.02,0.12000000000008448 +38,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-23,0,4.399999999999931,2.65,1.7499999999999312 +39,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-23,0,4.399999999999931,9.02,4.6200000000000685 +40,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-2,-1,3.899999999999933,4.41,0.5100000000000673 +41,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-3,-2,7.299999999999921,4.0,3.2999999999999208 +42,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-3,-1,3.299999999999935,4.0,0.700000000000065 +43,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-3,0,-1.1000000000000494,4.0,5.100000000000049 +44,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-4,-1,3.4999999999999343,5.77,2.2700000000000653 +45,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-4,0,2.399999999999938,5.77,3.3700000000000614 +46,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-5,-1,3.1999999999999353,3.92,0.7200000000000646 +47,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-5,0,-1.6000000000000476,3.92,5.5200000000000475 +48,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-6,-1,3.3999999999999346,4.17,0.7700000000000653 +49,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-6,0,3.3999999999999346,4.17,0.7700000000000653 +50,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-7,-1,11.899999999999904,6.63,5.2699999999999045 +51,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-7,0,7.899999999999919,6.63,1.2699999999999187 +52,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-8,0,1.7999999999999403,2.78,0.9800000000000595 +53,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-9,-1,12.199999999999903,6.08,6.119999999999903 +54,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-9,0,7.699999999999919,6.08,1.6199999999999193 +55,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999914,7.71,1.489999999999914 +56,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-12,-1,14.299999999999896,6.98,7.3199999999998955 +57,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-2,5.099999999999929,7.27,2.170000000000071 +58,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-1,7.299999999999921,7.27,0.0299999999999212 +59,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,6.999999999999922,2.54,4.459999999999922 +60,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.599999999999916,5.1,3.4999999999999165 +61,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-17,-1,4.199999999999932,6.58,2.3800000000000683 +62,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-18,-1,4.999999999999929,2.72,2.2799999999999288 +63,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,4.93,4.269999999999914 +64,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.199999999999914,6.99,2.209999999999914 +65,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,4.93,1.4699999999999243 +66,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.399999999999924,6.99,0.5900000000000762 +67,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,4.93,6.130000000000049 +68,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.200000000000049,6.99,8.19000000000005 +69,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,2.54,2.0599999999999303 +70,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 +71,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.7999999999999226,2.44,4.359999999999923 +72,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-2,19.399999999999878,5.38,14.019999999999879 +73,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-1,6.299999999999924,5.38,0.9199999999999244 +74,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-22,-1,5.199999999999928,3.36,1.8399999999999284 +75,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,2.65,6.549999999999914 +76,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.199999999999914,9.02,0.17999999999991445 +77,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,2.65,1.4499999999999322 +78,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.099999999999932,9.02,4.920000000000067 +79,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.299999999999907,4.41,6.889999999999906 +80,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.899999999999922,4.0,2.899999999999922 +81,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.399999999999938,5.77,3.3700000000000614 +82,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.399999999999931,3.92,0.47999999999993115 +83,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,0,14.599999999999895,3.92,10.679999999999895 +84,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 +85,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,0,13.1999999999999,4.17,9.0299999999999 +86,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-7,-1,4.999999999999929,6.63,1.630000000000071 +87,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.899999999999929,2.78,2.1199999999999295 +88,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-9,-1,3.899999999999933,6.08,2.180000000000067 +89,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-10,0,5.599999999999927,7.71,2.110000000000073 +90,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-12,-1,19.09999999999988,6.98,12.11999999999988 +91,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-2,11.599999999999905,7.27,4.329999999999906 +92,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-1,11.499999999999906,7.27,4.229999999999906 +93,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-15,0,4.299999999999931,2.54,1.7599999999999314 +94,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-16,0,4.69999999999993,5.1,0.40000000000006963 +95,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,-1,12.299999999999903,6.58,5.719999999999903 +96,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,0,4.499999999999931,6.58,2.0800000000000693 +97,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,-1,9.599999999999913,2.72,6.879999999999912 +98,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,0,4.199999999999932,2.72,1.4799999999999316 +99,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,4.93,6.169999999999908 +100,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.099999999999907,6.99,4.109999999999907 +101,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,4.93,4.2300000000000555 +102,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.6999999999999442,6.99,6.290000000000056 +103,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,1,-0.9000000000000501,4.93,5.83000000000005 +104,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,1,-0.9000000000000501,6.99,7.89000000000005 +105,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,2.54,1.559999999999932 +106,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.099999999999932,5.01,0.9100000000000676 +107,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,0,1.3999999999999417,2.44,1.0400000000000582 +108,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-3,19.899999999999878,5.38,14.519999999999879 +109,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-2,16.29999999999989,5.38,10.919999999999892 +110,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-1,13.699999999999898,5.38,8.319999999999897 +111,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-22,-1,13.899999999999897,3.36,10.539999999999898 +112,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,9.999999999999911,2.65,7.349999999999911 +113,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,9.999999999999911,9.02,0.9799999999999116 +114,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.299999999999935,2.65,0.6499999999999351 +115,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.299999999999935,9.02,5.720000000000065 +116,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-2,-1,6.099999999999925,4.41,1.689999999999925 +117,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-2,8.799999999999915,4.0,4.7999999999999154 +118,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-1,6.699999999999923,4.0,2.699999999999923 +119,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,-1,6.499999999999924,5.77,0.729999999999924 +120,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,0,-5.3290705182007514e-14,5.77,5.770000000000053 +121,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,-1,4.499999999999931,3.92,0.5799999999999308 +122,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,0,-1.200000000000049,3.92,5.120000000000049 +123,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,-1,3.9999999999999325,4.17,0.17000000000006743 +124,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,0,1.9999999999999396,4.17,2.1700000000000603 +125,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,-1,16.39999999999989,6.63,9.76999999999989 +126,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,0,11.299999999999907,6.63,4.669999999999907 +127,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-8,0,4.399999999999931,2.78,1.6199999999999313 +128,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,-1,15.699999999999891,6.08,9.61999999999989 +129,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,0,4.499999999999931,6.08,1.5800000000000693 +130,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-10,0,7.0999999999999215,7.71,0.6100000000000785 +131,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-12,-1,17.699999999999882,6.98,10.719999999999882 +132,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-12,0,4.899999999999929,6.98,2.080000000000071 +133,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-12,1,-5.0000000000000355,6.98,11.980000000000036 +134,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-14,-3,20.799999999999873,7.27,13.529999999999873 +135,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-14,-2,16.29999999999989,7.27,9.029999999999891 +136,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-14,-1,11.499999999999906,7.27,4.229999999999906 +137,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-14,0,5.3999999999999275,7.27,1.870000000000072 +138,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-14,1,-3.80000000000004,7.27,11.07000000000004 +139,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-15,0,1.3999999999999417,2.54,1.1400000000000583 +140,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-16,0,3.9999999999999325,5.1,1.1000000000000671 +141,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-17,-1,14.199999999999896,6.58,7.619999999999896 +142,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-17,0,4.69999999999993,6.58,1.88000000000007 +143,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-18,-1,11.399999999999906,2.72,8.679999999999906 +144,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-18,0,1.6999999999999407,2.72,1.0200000000000595 +145,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-19,-1,6.999999999999922,4.93,2.069999999999922 +146,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-19,-1,6.999999999999922,6.99,0.009999999999921627 +147,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-19,0,4.099999999999932,4.93,0.8300000000000676 +148,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-19,0,4.099999999999932,6.99,2.890000000000068 +149,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-19,1,-2.2000000000000455,4.93,7.130000000000045 +150,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-19,1,-2.2000000000000455,6.99,9.190000000000046 +151,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-1,-1,4.59999999999993,2.54,2.0599999999999303 +152,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-1,-1,4.59999999999993,5.01,0.4100000000000694 +153,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-1,0,-2.5000000000000444,2.54,5.0400000000000444 +154,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-1,0,-2.5000000000000444,5.01,7.510000000000044 +155,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-20,0,1.4999999999999414,2.44,0.9400000000000586 +156,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-21,-3,20.399999999999874,5.38,15.019999999999875 +157,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-21,-2,17.199999999999886,5.38,11.819999999999887 +158,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-21,-1,8.199999999999918,5.38,2.8199999999999177 +159,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-21,0,3.799999999999933,5.38,1.5800000000000667 +160,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-21,1,-5.500000000000034,5.38,10.880000000000035 +161,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-22,-1,14.699999999999894,3.36,11.339999999999895 +162,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-22,0,2.0999999999999392,3.36,1.2600000000000606 +163,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-22,1,-7.700000000000026,3.36,11.060000000000025 +164,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-23,-1,10.09999999999991,2.65,7.4499999999999105 +165,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-23,-1,10.09999999999991,9.02,1.0799999999999113 +166,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-23,0,1.9999999999999396,2.65,0.6500000000000603 +167,PKA_ECRISM,EC-RISM,QM+LEC,SAMPL8-23,0,1.9999999999999396,9.02,7.02000000000006 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a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_ranked/mean_abs_error_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_ranked/mean_abs_error_plot.pdf new file mode 100644 index 0000000..11c970d Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_ranked/mean_abs_error_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_ranked/mean_error_plot.pdf b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_ranked/mean_error_plot.pdf new file mode 100644 index 0000000..e786612 Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_ranked/mean_error_plot.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_ranked/popular_transitions_pKa_data.csv b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_ranked/popular_transitions_pKa_data.csv new file mode 100644 index 0000000..a28af30 --- /dev/null +++ b/physical_properties/pKa/macrostate_analysis/selected_transitions_analysis/supplementary_figures/Run-2/analysis_outputs_ranked/popular_transitions_pKa_data.csv @@ -0,0 +1,145 @@ +,Submission,Method Name,Method Type,Molecule ID,Formal Charge,Predicted pKa,Experimental pKa,Absolute Error +0,pKa-3DS-1,COSMO-RS one pKa fit,QM+LEC,SAMPL8-1,0,-0.6000000000000512,2.54,3.140000000000051 +1,pKa-3DS-1,COSMO-RS one pKa 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fit,LFER,SAMPL8-10,0,8.389999999999501,7.71,0.6799999999995014 -1,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,-1,14.54999999999937,6.98,7.56999999999937 -2,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,0,8.539999999999498,6.98,1.5599999999994978 -3,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-12,1,2.7099999999996225,6.98,4.270000000000378 -4,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,-2,13.62999999999939,7.27,6.35999999999939 -5,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,-1,9.739999999999473,7.27,2.469999999999473 -6,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,0,8.619999999999497,7.27,1.349999999999497 -7,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-14,1,3.489999999999606,7.27,3.7800000000003937 -8,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-15,0,3.989999999999595,2.54,1.4499999999995952 -9,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,-2,12.17999999999942,5.1,7.079999999999421 -10,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,-1,10.76999999999945,5.1,5.669999999999451 -11,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-16,0,6.759999999999536,5.1,1.6599999999995365 -12,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-17,-1,11.529999999999434,6.58,4.949999999999434 -13,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-17,0,7.349999999999524,6.58,0.7699999999995235 -14,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-18,-1,11.26999999999944,2.72,8.54999999999944 -15,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-18,0,5.249999999999568,2.72,2.529999999999568 -16,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,-1,6.739999999999537,4.93,1.8099999999995369 -17,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,-1,6.739999999999537,6.99,0.25000000000046363 -18,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,0,6.079999999999551,4.93,1.149999999999551 -19,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,0,6.079999999999551,6.99,0.9100000000004496 -20,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,1,3.4199999999996074,4.93,1.5100000000003924 -21,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-19,1,3.4199999999996074,6.99,3.570000000000393 -22,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,-1,3.6599999999996022,2.54,1.1199999999996022 -23,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,-1,3.6599999999996022,5.01,1.3500000000003975 -24,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,0,-0.5100000000003089,2.54,3.050000000000309 -25,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-1,0,-0.5100000000003089,5.01,5.520000000000309 -26,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,-1,10.149999999999464,2.44,7.709999999999464 -27,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,-1,10.149999999999464,11.44,1.2900000000005356 -28,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,0,4.70999999999958,2.44,2.26999999999958 -29,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,0,4.70999999999958,11.44,6.73000000000042 -30,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,1,0.2699999999996745,2.44,2.1700000000003254 -31,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-20,1,0.2699999999996745,11.44,11.170000000000325 -32,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,-2,13.069999999999402,5.38,7.689999999999402 -33,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,-1,8.599999999999497,5.38,3.219999999999497 -34,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,0,7.809999999999514,5.38,2.429999999999514 -35,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-21,1,2.9499999999996174,5.38,2.4300000000003825 -36,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,-1,12.529999999999413,3.36,9.169999999999414 -37,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,0,5.509999999999563,3.36,2.149999999999563 -38,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-22,1,-0.8700000000003012,3.36,4.230000000000301 -39,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,-1,8.91999999999949,2.65,6.26999999999949 -40,pKa-3DS-1,COSMO-RS one pKa fit,LFER,SAMPL8-23,-1,8.91999999999949,9.02,0.10000000000050946 -41,pKa-3DS-1,COSMO-RS one pKa 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fit,LFER,SAMPL8-22,-1,12.869999999999406,3.36,9.509999999999406 -130,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-22,0,4.3499999999995875,3.36,0.9899999999995877 -131,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-22,1,-3.3400000000002485,3.36,6.700000000000248 -132,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-23,-1,8.4899999999995,2.65,5.839999999999499 -133,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-23,-1,8.4899999999995,9.02,0.5300000000005003 -134,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-23,0,3.109999999999614,2.65,0.45999999999961405 -135,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-23,0,3.109999999999614,9.02,5.910000000000386 -136,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-2,-1,1.6299999999996455,4.41,2.7800000000003546 -137,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-3,-2,6.609999999999539,4.0,2.6099999999995394 -138,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-3,-1,1.7699999999996425,4.0,2.2300000000003575 -139,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-3,0,-3.550000000000244,4.0,7.550000000000244 -140,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-4,-1,1.88999999999964,5.77,3.8800000000003596 -141,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-4,0,0.7699999999996638,5.77,5.000000000000336 -142,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-5,-1,1.5799999999996466,3.92,2.3400000000003534 -143,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-5,0,-4.21000000000023,3.92,8.13000000000023 -144,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-6,-1,1.8699999999996404,4.17,2.3000000000003595 -145,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-6,0,1.9599999999996385,4.17,2.2100000000003615 -146,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-7,-1,12.17999999999942,6.63,5.549999999999421 -147,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-7,0,7.309999999999524,6.63,0.6799999999995245 -148,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-8,0,1.8599999999996406,2.78,0.9200000000003592 -149,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-9,-1,12.469999999999414,6.08,6.389999999999414 -150,pKa-3DS-2,COSMO-RS base pKa fit,LFER,SAMPL8-9,0,7.02999999999953,6.08,0.9499999999995303 -151,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-10,0,9.439999999999479,7.71,1.729999999999479 -152,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-12,-1,15.04999999999936,6.98,8.069999999999359 -153,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-12,0,9.149999999999485,6.98,2.169999999999485 -154,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-12,1,3.4499999999996067,6.98,3.5300000000003937 -155,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-14,-2,14.139999999999379,7.27,6.869999999999379 -156,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-14,-1,10.32999999999946,7.27,3.0599999999994605 -157,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-14,0,9.239999999999483,7.27,1.9699999999994837 -158,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-14,1,4.199999999999591,7.27,3.070000000000409 -159,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-15,0,5.869999999999555,2.54,3.329999999999555 -160,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-16,-2,12.739999999999409,5.1,7.639999999999409 -161,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-16,-1,11.339999999999439,5.1,6.239999999999439 -162,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-16,0,7.409999999999522,5.1,2.3099999999995227 -163,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-17,-1,12.089999999999423,6.58,5.5099999999994225 -164,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-17,0,7.98999999999951,6.58,1.4099999999995099 -165,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-18,-1,11.829999999999428,2.72,9.109999999999427 -166,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-18,0,5.929999999999554,2.72,3.2099999999995537 -167,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-19,-1,7.389999999999523,4.93,2.459999999999523 -168,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-19,-1,7.389999999999523,6.99,0.3999999999995225 -169,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-19,0,6.739999999999537,4.93,1.8099999999995369 -170,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-19,0,6.739999999999537,6.99,0.25000000000046363 -171,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-19,1,4.139999999999592,4.93,0.7900000000004077 -172,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-19,1,4.139999999999592,6.99,2.850000000000408 -173,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-1,-1,4.369999999999587,2.54,1.829999999999587 -174,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-1,-1,4.369999999999587,5.01,0.6400000000004127 -175,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-1,0,0.2799999999996743,2.54,2.2600000000003257 -176,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-1,0,0.2799999999996743,5.01,4.7300000000003255 -177,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-20,-1,10.739999999999451,2.44,8.299999999999452 -178,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-20,-1,10.739999999999451,11.44,0.7000000000005482 -179,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-20,0,5.399999999999565,2.44,2.959999999999565 -180,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-20,0,5.399999999999565,11.44,6.040000000000434 -181,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-20,1,1.0299999999996583,2.44,1.4100000000003416 -182,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-20,1,1.0299999999996583,11.44,10.410000000000341 -183,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-21,-2,13.59999999999939,5.38,8.219999999999391 -184,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-21,-1,9.219999999999484,5.38,3.839999999999484 -185,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-21,0,8.4399999999995,5.38,3.0599999999995005 -186,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-21,1,3.669999999999602,5.38,1.7100000000003979 -187,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-22,-1,13.069999999999402,3.36,9.709999999999402 -188,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-22,0,6.189999999999548,3.36,2.8299999999995484 -189,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-22,1,-0.08000000000031804,3.36,3.440000000000318 -190,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-23,-1,9.519999999999477,2.65,6.869999999999477 -191,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-23,-1,9.519999999999477,9.02,0.49999999999947775 -192,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-23,0,5.15999999999957,2.65,2.5099999999995704 -193,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-23,0,5.15999999999957,9.02,3.8600000000004293 -194,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-2,-1,3.9699999999995956,4.41,0.4400000000004045 -195,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-3,-2,7.99999999999951,4.0,3.9999999999995097 -196,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-3,-1,4.0699999999995935,4.0,0.0699999999995935 -197,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-3,0,-0.24000000000031463,4.0,4.240000000000315 -198,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-4,-1,4.22999999999959,5.77,1.5400000000004095 -199,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-4,0,3.199999999999612,5.77,2.5700000000003875 -200,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-5,-1,3.9199999999995967,3.92,4.0323300254385686e-13 -201,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-5,0,-0.7700000000003033,3.92,4.690000000000303 -202,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-6,-1,4.199999999999591,4.17,0.0299999999995908 -203,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-6,0,4.179999999999591,4.17,0.009999999999591225 -204,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-7,-1,12.519999999999413,6.63,5.8899999999994135 -205,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-7,0,8.559999999999498,6.63,1.929999999999498 -206,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-8,0,4.149999999999592,2.78,1.369999999999592 -207,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-9,-1,12.749999999999408,6.08,6.669999999999408 -208,pKa-3DS-3,COSMO-RS pKa fit,LFER,SAMPL8-9,0,8.339999999999502,6.08,2.2599999999995024 -209,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-10,0,6.56999999999954,7.71,1.1400000000004598 -210,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-12,-1,14,6.98,7.02 -211,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-14,-3,-9.110000000000126,7.27,16.380000000000123 -212,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-14,-1,15.169999999999357,7.27,7.899999999999357 -213,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-15,0,1.1099999999996566,2.54,1.4300000000003434 -214,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-16,0,3.6899999999996016,5.1,1.410000000000398 -215,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-17,-1,18.079999999999295,6.58,11.499999999999295 -216,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-17,0,5.199999999999569,6.58,1.3800000000004307 -217,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-18,-1,16.869999999999322,2.72,14.149999999999322 -218,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-18,0,1.6199999999996457,2.72,1.1000000000003545 -219,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,-1,11.999999999999424,4.93,7.069999999999425 -220,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,-1,11.999999999999424,6.99,5.009999999999424 -221,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,0,3.149999999999613,4.93,1.7800000000003866 -222,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-19,0,3.149999999999613,6.99,3.840000000000387 -223,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-1,-1,7.609999999999518,2.54,5.069999999999518 -224,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-1,-1,7.609999999999518,5.01,2.5999999999995183 -225,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-20,0,1.229999999999654,2.44,1.210000000000346 -226,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-20,0,1.229999999999654,11.44,10.210000000000345 -227,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-21,-1,17.29999999999931,5.38,11.919999999999312 -228,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-22,-1,17.50999999999931,3.36,14.14999999999931 -229,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,-1,13.58999999999939,2.65,10.93999999999939 -230,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,-1,13.58999999999939,9.02,4.569999999999391 -231,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,0,2.1099999999996353,2.65,0.5400000000003646 -232,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-23,0,2.1099999999996353,9.02,6.910000000000364 -233,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-2,-1,8.189999999999506,4.41,3.7799999999995055 -234,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-3,-1,6.379999999999544,4.0,2.3799999999995443 -235,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-4,-1,11.139999999999443,5.77,5.369999999999443 -236,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-4,0,-7.98000000000015,5.77,13.75000000000015 -237,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-5,-1,7.649999999999517,3.92,3.7299999999995173 -238,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-5,0,-10.010000000000106,3.92,13.930000000000106 -239,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-6,-1,5.889999999999555,4.17,1.7199999999995548 -240,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-6,0,-5.260000000000208,4.17,9.430000000000208 -241,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-7,0,8.819999999999492,6.63,2.1899999999994924 -242,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-8,0,4.609999999999582,2.78,1.8299999999995822 -243,pKa_SabatinoRodriguezPaluch_uESE,RFE-uESE,QM,SAMPL8-9,0,5.919999999999554,6.08,0.160000000000446 -244,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-10,0,9.199999999999484,7.71,1.4899999999994842 -245,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-12,-1,14.379999999999374,6.98,7.399999999999373 -246,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-2,5.119999999999571,7.27,2.1500000000004285 -247,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-14,-1,7.319999999999524,7.27,0.04999999999952465 -248,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-15,0,7.05999999999953,2.54,4.51999999999953 -249,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-16,0,8.669999999999495,5.1,3.569999999999496 -250,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-17,-1,4.289999999999589,6.58,2.2900000000004113 -251,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-18,-1,5.0099999999995735,2.72,2.2899999999995733 -252,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.229999999999484,4.93,4.299999999999484 -253,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,-1,9.229999999999484,6.99,2.2399999999994833 -254,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.479999999999542,4.93,1.5499999999995424 -255,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,0,6.479999999999542,6.99,0.5100000000004581 -256,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.1400000000002954,4.93,6.070000000000295 -257,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-19,1,-1.1400000000002954,6.99,8.130000000000296 -258,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.599999999999582,2.54,2.059999999999582 -259,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-1,-1,4.599999999999582,5.01,0.4100000000004176 -260,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.869999999999534,2.44,4.429999999999534 -261,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-20,0,6.869999999999534,11.44,4.570000000000466 -262,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-2,19.499999999999265,5.38,14.119999999999266 -263,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-21,-1,6.299999999999546,5.38,0.9199999999995461 -264,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-22,-1,5.229999999999569,3.36,1.869999999999569 -265,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.219999999999484,2.65,6.569999999999483 -266,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,-1,9.219999999999484,9.02,0.19999999999948415 -267,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.169999999999591,2.65,1.5199999999995915 -268,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-23,0,4.169999999999591,9.02,4.850000000000408 -269,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-2,-1,11.389999999999437,4.41,6.979999999999437 -270,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-3,-1,6.939999999999532,4.0,2.9399999999995323 -271,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-4,-1,2.4299999999996285,5.77,3.340000000000371 -272,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,-1,4.449999999999585,3.92,0.5299999999995855 -273,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-5,0,14.669999999999368,3.92,10.749999999999368 -274,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,-1,4.039999999999594,4.17,0.1300000000004058 -275,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-6,0,13.219999999999398,4.17,9.049999999999399 -276,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-7,-1,5.089999999999572,6.63,1.5400000000004281 -277,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-8,0,4.919999999999575,2.78,2.1399999999995756 -278,pKa-RobertRaddi_DeepGP,Deep Gaussian Process,QSPR/ML,SAMPL8-9,-1,3.959999999999596,6.08,2.1200000000004042 -279,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-10,0,5.669999999999559,7.71,2.0400000000004406 -280,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-12,-1,19.17999999999927,6.98,12.199999999999271 -281,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-2,11.659999999999432,7.27,4.389999999999432 -282,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-14,-1,11.529999999999434,7.27,4.259999999999435 -283,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-15,0,4.299999999999589,2.54,1.7599999999995886 -284,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-16,0,4.739999999999579,5.1,0.36000000000042043 -285,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,-1,12.379999999999416,6.58,5.799999999999416 -286,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-17,0,4.579999999999583,6.58,2.0000000000004174 -287,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,-1,9.629999999999475,2.72,6.909999999999474 -288,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-18,0,4.23999999999959,2.72,1.5199999999995897 -289,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.149999999999443,4.93,6.219999999999443 -290,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,-1,11.149999999999443,6.99,4.159999999999442 -291,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.7799999999996636,4.93,4.150000000000336 -292,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,0,0.7799999999996636,6.99,6.210000000000337 -293,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,1,-0.8900000000003008,4.93,5.8200000000003005 -294,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-19,1,-0.8900000000003008,6.99,7.880000000000301 -295,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.149999999999592,2.54,1.6099999999995918 -296,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-1,-1,4.149999999999592,5.01,0.860000000000408 -297,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,0,1.4599999999996491,2.44,0.9800000000003508 -298,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-20,0,1.4599999999996491,11.44,9.98000000000035 -299,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-3,19.979999999999254,5.38,14.599999999999255 -300,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-2,16.32999999999933,5.38,10.949999999999331 -301,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-21,-1,13.749999999999387,5.38,8.369999999999386 -302,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-22,-1,13.899999999999384,3.36,10.539999999999385 -303,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,10.019999999999467,2.65,7.369999999999466 -304,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,-1,10.019999999999467,9.02,0.9999999999994671 -305,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.3099999999996097,2.65,0.6599999999996098 -306,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-23,0,3.3099999999996097,9.02,5.71000000000039 -307,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-2,-1,6.09999999999955,4.41,1.68999999999955 -308,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-2,8.88999999999949,4.0,4.889999999999491 -309,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-3,-1,6.779999999999536,4.0,2.7799999999995357 -310,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,-1,6.57999999999954,5.77,0.8099999999995404 -311,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-4,0,0.07999999999967855,5.77,5.690000000000321 -312,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,-1,4.519999999999584,3.92,0.599999999999584 -313,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-5,0,-1.160000000000295,3.92,5.080000000000295 -314,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,-1,4.019999999999595,4.17,0.15000000000040536 -315,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-6,0,2.0399999999996368,4.17,2.130000000000363 -316,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,-1,16.41999999999933,6.63,9.789999999999331 -317,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-7,0,11.389999999999437,6.63,4.759999999999438 -318,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-8,0,4.3999999999995865,2.78,1.6199999999995867 -319,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,-1,15.749999999999345,6.08,9.669999999999344 -320,pKa-ZhiyiWu-1,QM with linear fitting,QM,SAMPL8-9,0,4.559999999999583,6.08,1.520000000000417 -321,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-10,0,6.4599999999995426,7.71,1.2500000000004574 -322,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-12,-1,13.259999999999398,6.98,6.279999999999397 -323,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-14,-2,4.089999999999593,7.27,3.1800000000004065 -324,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-14,-1,4.119999999999592,7.27,3.150000000000407 -325,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-15,0,5.589999999999561,2.54,3.049999999999561 -326,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-16,0,6.279999999999546,5.1,1.1799999999995467 -327,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-17,-1,4.579999999999583,6.58,2.0000000000004174 -328,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-18,-1,4.559999999999583,2.72,1.8399999999995829 -329,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,-1,5.389999999999565,4.93,0.45999999999956565 -330,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,-1,5.389999999999565,6.99,1.6000000000004349 -331,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,0,5.919999999999554,4.93,0.9899999999995543 -332,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,0,5.919999999999554,6.99,1.0700000000004461 -333,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,1,-1.2900000000002922,4.93,6.220000000000292 -334,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-19,1,-1.2900000000002922,6.99,8.280000000000292 -335,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-1,-1,4.669999999999581,2.54,2.1299999999995807 -336,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-1,-1,4.669999999999581,5.01,0.3400000000004191 -337,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-20,0,7.769999999999515,2.44,5.329999999999515 -338,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-20,0,7.769999999999515,11.44,3.670000000000485 -339,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-21,-2,10.009999999999467,5.38,4.629999999999467 -340,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-21,-1,2.449999999999628,5.38,2.930000000000372 -341,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-22,-1,7.829999999999513,3.36,4.469999999999514 -342,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-23,-1,5.529999999999562,2.65,2.8799999999995625 -343,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-23,-1,5.529999999999562,9.02,3.490000000000437 -344,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-23,0,1.7399999999996432,2.65,0.9100000000003567 -345,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-23,0,1.7399999999996432,9.02,7.280000000000356 -346,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-2,-1,4.899999999999576,4.41,0.48999999999957566 -347,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-3,-1,4.749999999999579,4.0,0.749999999999579 -348,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-4,-1,3.379999999999608,5.77,2.3900000000003914 -349,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-5,-1,0.29999999999967386,3.92,3.620000000000326 -350,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-5,0,9.559999999999476,3.92,5.6399999999994765 -351,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-6,-1,-0.010000000000319531,4.17,4.1800000000003195 -352,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-6,0,13.949999999999383,4.17,9.779999999999383 -353,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-7,-1,7.629999999999518,6.63,0.9999999999995177 -354,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-8,0,4.059999999999594,2.78,1.279999999999594 -355,pKa-RobertRaddi_RF,Random Forest,QSPR/ML,SAMPL8-9,-1,7.99999999999951,6.08,1.9199999999995097 -356,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-10,0,7.189999999999527,7.71,0.520000000000473 -357,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-12,-1,17.789999999999303,6.98,10.809999999999302 -358,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-12,0,4.9599999999995745,6.98,2.020000000000426 -359,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-12,1,-4.940000000000214,6.98,11.920000000000215 -360,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-14,-3,20.809999999999235,7.27,13.539999999999235 -361,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-14,-2,16.37999999999933,7.27,9.109999999999332 -362,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-14,-1,11.539999999999434,7.27,4.269999999999435 -363,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-14,0,5.449999999999564,7.27,1.8200000000004355 -364,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-14,1,-3.75000000000024,7.27,11.02000000000024 -365,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-15,0,1.4499999999996493,2.54,1.0900000000003507 -366,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-16,0,3.999999999999595,5.1,1.1000000000004047 -367,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-17,-1,14.229999999999377,6.58,7.649999999999377 -368,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-17,0,4.789999999999578,6.58,1.790000000000422 -369,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-18,-1,11.479999999999436,2.72,8.759999999999435 -370,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-18,0,1.789999999999642,2.72,0.9300000000003581 -371,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-19,-1,7.099999999999529,4.93,2.169999999999529 -372,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-19,-1,7.099999999999529,6.99,0.1099999999995287 -373,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-19,0,4.129999999999592,4.93,0.8000000000004075 -374,PKA_ECRISM,EC_RISM,QM+LEC,SAMPL8-19,0,4.129999999999592,6.99,2.860000000000408 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a/physical_properties/pKa/macrostate_analysis/titration_curve_plots/pKa_SabatinoRodriguezPaluch_uESE_modified:SAMPL8-9.pdf b/physical_properties/pKa/macrostate_analysis/titration_curve_plots/pKa_SabatinoRodriguezPaluch_uESE_modified:SAMPL8-9.pdf new file mode 100644 index 0000000..db79e4f Binary files /dev/null and b/physical_properties/pKa/macrostate_analysis/titration_curve_plots/pKa_SabatinoRodriguezPaluch_uESE_modified:SAMPL8-9.pdf differ diff --git a/physical_properties/pKa/macrostate_analysis/titration_curves.py b/physical_properties/pKa/macrostate_analysis/titration_curves.py index 38a21b5..8c8fcd7 100644 --- a/physical_properties/pKa/macrostate_analysis/titration_curves.py +++ b/physical_properties/pKa/macrostate_analysis/titration_curves.py @@ -20,11 +20,11 @@ # ============================================================================= # CONSTANTS # ============================================================================= -pKa_SUBMISSIONS_DIR_PATH = '../submissions' -EXPERIMENTAL_DATA_FILE_PATH = '../experimental_pKas.csv' +pKa_SUBMISSIONS_DIR_PATH = '/Users/aakankschitnandkeolyar/Desktop/SAMPL8/physical_properties/pKa/submissions' +EXPERIMENTAL_DATA_FILE_PATH = '/Users/aakankschitnandkeolyar/Desktop/SAMPL8/physical_properties/pKa/experimental_pKas.csv' USER_MAP_FILE_PATH = '../SAMPL8-pKa-user-map.csv' -if not os.path.exists("./titration_curve_plots"): - os.makedirs("./titration_curve_plots") +if not os.path.exists("/Users/aakankschitnandkeolyar/Desktop/SAMPL8/physical_properties/pKa/macrostate_analysis/titration_curve_plots/"): + os.makedirs("/Users/aakankschitnandkeolyar/Desktop/SAMPL8/physical_properties/pKa/macrostate_analysis/titration_curve_plots/") # ============================================================================= # Utility Classes # ============================================================================= @@ -336,122 +336,123 @@ def pop_charge_microstates(pH, formal_charge, state_details): # Construct Experimental and Predicted Data Frame # Loops over Experimental and Predicted pKa values to construct a data frame that contains all possible combinations of predicted and experimental pKa's -pKa_dt = pd.DataFrame(columns=['Submission','Method Name','Method Type','Molecule ID','Formal Charge','Predicted pKa','Experimental pKa','Absolute Error']) -for submission in microstates_df: - submission_data = submission.data - # Create a dictionary with the microstate details for each molecule in the submission - molecules = {} - for index, row in submission_data.iterrows(): - SM = index - state = row["ID tag"] - charge = row["total charge"] - rfe = row["pKa mean"] - sem = row["pKa SEM"] - model_uncertainty = row["pKa model uncertainty"] - - if SM in molecules: - molecules[SM].append((state, rfe, charge, sem, model_uncertainty)) - else: - molecules[SM] = [(state, rfe, charge, sem, model_uncertainty)] - - # Loop over molecules, convert to state_details - SM_names = [x for x in molecules.keys()] - SM_names.sort() - # Loop Over all molecules - pKa_dt_temp = pd.DataFrame(columns=['Submission','Method Name','Method Type','Molecule ID','Formal Charge','Predicted pKa','Experimental pKa','Absolute Error']) - for names in SM_names: - mol_details = molecules[names] # Get the state details for each molecule - form_charge = [] - for items in mol_details: - form_charge.append(items[2]) - formal_charge = form_charge - formal_charge = np.unique(formal_charge) - form_charge.append(0) - form_charge = np.unique(form_charge) - charge_dist_df = pd.DataFrame(columns = ["pH","pop_charge","formal_charge"]) - charge_dist_df_microstate = pd.DataFrame(columns = ["pH","pop_charge","formal_charge"]) - for charges in form_charge: - for pH in pH_vals: - n_frac, microstates = pop_charge_microstates(pH,charges,mol_details) - pH_microstates = np.tile(pH,(len(microstates),)) - temp_df = pd.DataFrame({"pH": pH_microstates, - "pop_charge":n_frac, - "formal_charge":microstates}) - if charges == 3: - charge_label = "+3" - elif charges == 2: - charge_label = "+2" - elif charges == 1: - charge_label = "+1" - elif charges == 0: - charge_label = "0" - elif charges == -1: - charge_label = "-1" - elif charges == -2: - charge_label = "-2" - elif charges == -3: - charge_label = "-3" - - charge_dist_df = charge_dist_df.append({"pH":pH,"pop_charge":pop_charge(pH,charges,mol_details),"formal_charge":charges},ignore_index = True) - charge_dist_df_microstate = pd.concat([charge_dist_df_microstate,temp_df], ignore_index=True) - charge_dist_df_microstate["formal_charge"] = charge_dist_df_microstate["formal_charge"].astype("category") - # Slice DataFrame for Plotting Titration Curves - plotting_dt_formal_charge = charge_dist_df.loc[charge_dist_df['pH'].between(0,15,inclusive=True),] # Only formal charges - plotting_dt_microstates = charge_dist_df_microstate.loc[charge_dist_df_microstate['pH'].between(0,15,inclusive=True),] # Microstates - # Graphical Options for Figure - fig_name = submission.file_name+":"+names.split('_')[0] - plt.figure(figsize=(10,6)) - sns.lineplot(data=plotting_dt_formal_charge,x="pH",y="pop_charge",hue="formal_charge") - sns.lineplot(data=plotting_dt_microstates,x="pH",y="pop_charge",hue="formal_charge",linestyle="--",palette="husl") - plt.xticks(np.arange(0,14,1).tolist()) - plt.ylabel("population fraction", fontsize = 14) - plt.xlabel("pH", fontsize=14) - plt.title(fig_name, fontsize = 18) - lgd = plt.legend(loc='upper center', bbox_to_anchor=(0.5, -0.15),fancybox=True, shadow=True, ncol=4,prop={'size': 12}) - plt.savefig("./titration_curve_plots"+"/"+fig_name+".pdf",bbox_extra_artists=(lgd,), bbox_inches='tight') - plt.close('all') - # Experimental Macro pKas - exp_pKas = experimental_data.loc[experimental_data.index==names.split('_')[0],'pKa mean'].values - # Macrostate Calculation and Absolute Error Computation - temp_df2 = pd.DataFrame(columns=['Submission','Method Name','Method Type','Molecule ID','Formal Charge','Predicted pKa','Experimental pKa','Absolute Error']) - for first, second in zip(form_charge[1:], form_charge): - idx = np.argwhere(np.diff(np.sign( - charge_dist_df.loc[charge_dist_df.loc[:, 'formal_charge'] == first, 'pop_charge'].values - - charge_dist_df.loc[charge_dist_df.loc[:, 'formal_charge'] == second, 'pop_charge'].values))).flatten() - pred_pKa = charge_dist_df.loc[charge_dist_df.loc[:, 'formal_charge'] == second, 'pH'].values[idx] - # Formal Charge Assignment - # This is based on the end transition state - if first == 3 and second == 2: - formal_charge_val = 2 - elif first == 2 and second == 1: - formal_charge_val = 1 - elif first == 1 and second == 0: - formal_charge_val = 0 - elif first == 0 and second == -1: - formal_charge_val = -1 - elif first == -1 and second == -2: - formal_charge_val = -2 - elif first == -2 and second == -3: - formal_charge_val = -3 - for exp_pKa in exp_pKas: - abs_error = np.abs(pred_pKa-exp_pKa) - temp_df3 = pd.DataFrame({'Submission': submission.file_name,'Method Name': submission.method_name,'Method Type':submission.category,'Molecule ID':names.split('_')[0], 'Formal Charge':formal_charge_val, 'Predicted pKa': pred_pKa,'Experimental pKa':exp_pKa,'Absolute Error':abs_error}) - temp_df2 = pd.concat([temp_df2, temp_df3],ignore_index=True) - if temp_df2.empty: - for exp_pKa in exp_pKas: - if 14 - exp_pKa > abs(0 - exp_pKa): - pred_pKa = 14 - else: - pred_pKa = 0 - abs_error = np.abs(pred_pKa - exp_pKa) - temp_df4 = pd.DataFrame({'Submission': submission.file_name, 'Method Name': submission.method_name, - 'Method Type': submission.category, 'Molecule ID': names.split('_')[0], - 'Formal Charge': formal_charge_val, 'Predicted pKa': [pred_pKa], - 'Experimental pKa': exp_pKa, 'Absolute Error': abs_error}) - temp_df2 = pd.concat([temp_df2, temp_df4], ignore_index=True) - pKa_dt_temp = pd.concat([pKa_dt_temp, temp_df2],ignore_index=True) - pKa_dt = pd.concat([pKa_dt, pKa_dt_temp],ignore_index=True) - -# Write dataframe to csv file -# Located in the same folder as the titration curves -pKa_dt.to_csv("./titration_curve_plots"+"/"+"macro_pKas_data.csv") \ No newline at end of file +if __name__ == "__main__": + pKa_dt = pd.DataFrame(columns=['Submission','Method Name','Method Type','Molecule ID','Formal Charge','Predicted pKa','Experimental pKa','Absolute Error']) + for submission in microstates_df: + submission_data = submission.data + # Create a dictionary with the microstate details for each molecule in the submission + molecules = {} + for index, row in submission_data.iterrows(): + SM = index + state = row["ID tag"] + charge = row["total charge"] + rfe = row["pKa mean"] + sem = row["pKa SEM"] + model_uncertainty = row["pKa model uncertainty"] + + if SM in molecules: + molecules[SM].append((state, rfe, charge, sem, model_uncertainty)) + else: + molecules[SM] = [(state, rfe, charge, sem, model_uncertainty)] + + # Loop over molecules, convert to state_details + SM_names = [x for x in molecules.keys()] + SM_names.sort() + # Loop Over all molecules + pKa_dt_temp = pd.DataFrame(columns=['Submission','Method Name','Method Type','Molecule ID','Formal Charge','Predicted pKa','Experimental pKa','Absolute Error']) + for names in SM_names: + mol_details = molecules[names] # Get the state details for each molecule + form_charge = [] + for items in mol_details: + form_charge.append(items[2]) + formal_charge = form_charge + formal_charge = np.unique(formal_charge) + form_charge.append(0) + form_charge = np.unique(form_charge) + charge_dist_df = pd.DataFrame(columns = ["pH","pop_charge","formal_charge"]) + charge_dist_df_microstate = pd.DataFrame(columns = ["pH","pop_charge","formal_charge"]) + for charges in form_charge: + for pH in pH_vals: + n_frac, microstates = pop_charge_microstates(pH,charges,mol_details) + pH_microstates = np.tile(pH,(len(microstates),)) + temp_df = pd.DataFrame({"pH": pH_microstates, + "pop_charge":n_frac, + "formal_charge":microstates}) + if charges == 3: + charge_label = "+3" + elif charges == 2: + charge_label = "+2" + elif charges == 1: + charge_label = "+1" + elif charges == 0: + charge_label = "0" + elif charges == -1: + charge_label = "-1" + elif charges == -2: + charge_label = "-2" + elif charges == -3: + charge_label = "-3" + + pd.concat([charge_dist_df, pd.DataFrame([{"pH":pH,"pop_charge":pop_charge(pH,charges,mol_details),"formal_charge":charges}])], ignore_index=True) + charge_dist_df_microstate = pd.concat([charge_dist_df_microstate,temp_df], ignore_index=True) + charge_dist_df_microstate["formal_charge"] = charge_dist_df_microstate["formal_charge"].astype("category") + # Slice DataFrame for Plotting Titration Curves + plotting_dt_formal_charge = charge_dist_df.loc[charge_dist_df['pH'].between(0,15,inclusive="both"),] # Only formal charges + plotting_dt_microstates = charge_dist_df_microstate.loc[charge_dist_df_microstate['pH'].between(0,15,inclusive="both"),] # Microstates + # Graphical Options for Figure + fig_name = submission.file_name+":"+names.split('_')[0] + plt.figure(figsize=(10,6)) + sns.lineplot(data=plotting_dt_formal_charge,x="pH",y="pop_charge",hue="formal_charge") + sns.lineplot(data=plotting_dt_microstates,x="pH",y="pop_charge",hue="formal_charge",linestyle="--",palette="husl") + plt.xticks(np.arange(0,14,1).tolist()) + plt.ylabel("population fraction", fontsize = 14) + plt.xlabel("pH", fontsize=14) + plt.title(fig_name, fontsize = 18) + lgd = plt.legend(loc='upper center', bbox_to_anchor=(0.5, -0.15),fancybox=True, shadow=True, ncol=4,prop={'size': 12}) + plt.savefig("/Users/aakankschitnandkeolyar/Desktop/SAMPL8/physical_properties/pKa/macrostate_analysis/titration_curve_plots"+"/"+fig_name+".pdf",bbox_extra_artists=(lgd,), bbox_inches='tight') + plt.close('all') + # Experimental Macro pKas + exp_pKas = experimental_data.loc[experimental_data.index==names.split('_')[0],'pKa mean'].values + # Macrostate Calculation and Absolute Error Computation + temp_df2 = pd.DataFrame(columns=['Submission','Method Name','Method Type','Molecule ID','Formal Charge','Predicted pKa','Experimental pKa','Absolute Error']) + for first, second in zip(form_charge[1:], form_charge): + idx = np.argwhere(np.diff(np.sign( + charge_dist_df.loc[charge_dist_df.loc[:, 'formal_charge'] == first, 'pop_charge'].values - + charge_dist_df.loc[charge_dist_df.loc[:, 'formal_charge'] == second, 'pop_charge'].values))).flatten() + pred_pKa = charge_dist_df.loc[charge_dist_df.loc[:, 'formal_charge'] == second, 'pH'].values[idx] + # Formal Charge Assignment + # This is based on the end transition state + if first == 3 and second == 2: + formal_charge_val = 2 + elif first == 2 and second == 1: + formal_charge_val = 1 + elif first == 1 and second == 0: + formal_charge_val = 0 + elif first == 0 and second == -1: + formal_charge_val = -1 + elif first == -1 and second == -2: + formal_charge_val = -2 + elif first == -2 and second == -3: + formal_charge_val = -3 + for exp_pKa in exp_pKas: + abs_error = np.abs(pred_pKa-exp_pKa) + temp_df3 = pd.DataFrame({'Submission': submission.file_name,'Method Name': submission.method_name,'Method Type':submission.category,'Molecule ID':names.split('_')[0], 'Formal Charge':formal_charge_val, 'Predicted pKa': pred_pKa,'Experimental pKa':exp_pKa,'Absolute Error':abs_error}) + temp_df2 = pd.concat([temp_df2, temp_df3],ignore_index=True) + if temp_df2.empty: + for exp_pKa in exp_pKas: + if 14 - exp_pKa > abs(0 - exp_pKa): + pred_pKa = 14 + else: + pred_pKa = 0 + abs_error = np.abs(pred_pKa - exp_pKa) + temp_df4 = pd.DataFrame({'Submission': submission.file_name, 'Method Name': submission.method_name, + 'Method Type': submission.category, 'Molecule ID': names.split('_')[0], + 'Formal Charge': formal_charge_val, 'Predicted pKa': [pred_pKa], + 'Experimental pKa': exp_pKa, 'Absolute Error': abs_error}) + temp_df2 = pd.concat([temp_df2, temp_df4], ignore_index=True) + pKa_dt_temp = pd.concat([pKa_dt_temp, temp_df2],ignore_index=True) + pKa_dt = pd.concat([pKa_dt, pKa_dt_temp],ignore_index=True) + + # Write dataframe to csv file + # Located in the same folder as the titration curves + pKa_dt.to_csv("/Users/aakankschitnandkeolyar/Desktop/SAMPL8/physical_properties/pKa/macrostate_analysis/titration_curve_plots"+"/"+"macro_pKas_data.csv") \ No newline at end of file diff --git a/physical_properties/pKa/submissions/PKA_ECRISM.csv b/physical_properties/pKa/submissions/Original_submissions/PKA_ECRISM.csv similarity index 99% rename from physical_properties/pKa/submissions/PKA_ECRISM.csv rename to physical_properties/pKa/submissions/Original_submissions/PKA_ECRISM.csv index 8c257c1..48df181 100644 --- a/physical_properties/pKa/submissions/PKA_ECRISM.csv +++ b/physical_properties/pKa/submissions/Original_submissions/PKA_ECRISM.csv @@ -268,7 +268,7 @@ Participant organization: TU Dortmund University Name: -EC_RISM +EC-RISM Compute time: 27 hours, CPU diff --git a/physical_properties/pKa/submissions/Original_submissions/PKA_ECRISM_modified.csv b/physical_properties/pKa/submissions/Original_submissions/PKA_ECRISM_modified.csv new file mode 100644 index 0000000..43c9099 --- /dev/null +++ b/physical_properties/pKa/submissions/Original_submissions/PKA_ECRISM_modified.csv @@ -0,0 +1,359 @@ +Predictions: +SAMPL8-1_micro000,SAMPL8-1_micro001,-1,28.33,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_micro002,-1,6.92,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_micro003,-1,27.66,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,7.16,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_micro005,-1,7.07,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_micro008,-1,25.69,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_micro006,0,30.73,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_micro007,0,21.88,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_micro009,0,22.88,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_micro010,0,20.37,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_EC-RISM_extra001,1,3.37,0.01,1.04 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,7.31,0.01,1.04 +SAMPL8-2_micro000,SAMPL8-2_micro003,-1,30.55,0.01,1.04 +SAMPL8-2_micro000,SAMPL8-2_micro002,0,19.96,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro007,-2,7.11,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro012,-2,7.53,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro013,-2,-11.46,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro014,-2,-11.69,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro019,-2,11.04,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro021,-2,11.82,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro001,-1,-2.06,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro003,-1,5.37,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro005,-1,-6.96,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro009,-1,-0.79,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,-25.91,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro011,-1,1.98,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro015,-1,13.62,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,-18.78,0.01,1.04 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+SAMPL8-20_micro000,SAMPL8-20_micro008,0,30.72,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro009,0,16.37,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro010,0,22.43,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro012,0,26.54,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro013,0,18.77,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro017,0,-9.73,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro018,0,-4.48,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro019,0,22.36,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro020,0,32.04,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro021,0,16.33,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro022,0,-12.83,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro023,0,28.17,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro024,0,29.02,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro027,0,27.91,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro002,1,-11.43,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro003,1,-11.61,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro005,1,32.01,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro006,1,-11.27,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro007,1,11.43,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro011,1,-8.51,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro014,1,30.52,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro015,1,-8.12,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro016,1,2.46,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro025,1,23.73,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro026,1,-14.97,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro028,1,24.63,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro010,-3,42.38,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro001,-2,21.79,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro002,-2,27.53,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro004,-2,26.26,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro005,-2,14.84,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro012,-2,28.88,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro013,-2,20.79,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro015,-2,15.11,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro017,-2,15.45,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro021,-2,15.02,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro003,-1,3.33,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro006,-1,9.55,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro007,-1,15.32,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro009,-1,3.20,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro011,-1,9.08,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro014,-1,3.51,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro016,-1,3.14,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro018,-1,3.49,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro019,-1,14.61,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro020,-1,5.13,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro022,-1,-9.42,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro024,-1,1.56,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro026,-1,8.28,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro027,-1,10.06,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro008,0,-5.77,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro023,0,-9.99,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro025,0,-10.18,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro028,0,-20.78,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro029,0,-6.68,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra002,1,-25.27,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra004,1,-14.35,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra005,1,-14.23,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra006,1,-25.29,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra008,1,-22.78,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra009,1,-22.81,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra011,1,-25.48,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra001,2,-17.37,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra003,2,-18.13,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra007,2,-13.81,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra010,2,-18.07,0.01,1.04 +SAMPL8-22_micro000,SAMPL8-22_micro001,-1,11.86,0.01,1.04 +SAMPL8-22_micro000,SAMPL8-22_micro002,0,-8.42,0.01,1.04 +SAMPL8-22_micro000,SAMPL8-22_micro003,0,2.67,0.01,1.04 +SAMPL8-22_micro000,SAMPL8-22_EC-RISM_extra002,1,-11.00,0.01,1.04 +SAMPL8-22_micro000,SAMPL8-22_EC-RISM_extra004,1,-9.32,0.01,1.04 +SAMPL8-22_micro000,SAMPL8-22_EC-RISM_extra005,1,-10.96,0.01,1.04 +SAMPL8-22_micro000,SAMPL8-22_EC-RISM_extra001,2,-0.55,0.01,1.04 +SAMPL8-22_micro000,SAMPL8-22_EC-RISM_extra003,2,-0.55,0.01,1.04 +SAMPL8-23_micro000,SAMPL8-23_micro002,-1,14.22,0.01,1.04 +SAMPL8-23_micro000,SAMPL8-23_micro005,-1,-3.03,0.01,1.04 +SAMPL8-23_micro000,SAMPL8-23_micro003,0,-8.46,0.01,1.04 +SAMPL8-23_micro000,SAMPL8-23_micro004,0,16.96,0.01,1.04 +SAMPL8-23_micro000,SAMPL8-23_micro007,0,-16.93,0.01,1.04 +SAMPL8-23_micro000,SAMPL8-23_micro001,1,5.75,0.01,1.04 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-19.77,0.01,1.04 + +Participant name: +Stefan M. Kast, Nicolas Tielker + +Participant organization: +TU Dortmund University + +Name: +EC-RISM + +Compute time: +27 hours, CPU + +Computing and hardware: +All calculations were conducted on the LiDO 3 high performance cluster of TU Dortmund University. Calculations were automatically scheduled and ran on either an Intel Xeon E5-4604v4 or an Intel Xeon E5-2640v4 CPU, depending on node availability. + +Software: +Corina 4.3.0 +Gaussian 09 Rev E.01 +Gaussian 16 Rev C.01 +3D RISM (inhouse development) +EC-RISM (inhouse development) +Python 3.6 +Anaconda2018.12 +Amber 12 +Mathematica 12.2 (Wolfram) + +Category: +QM+LEC + +Method: +Geometries were generated using Maestro 2020-4/Macromodel with the OPLS3/Water force field with mixed torsional/low-mode sampling, 100 steps per RB and 1000 steps max (default parameters). +These conformations were then optimized using Gaussian 16revC01 with IEF-PCM using default settings for water at the B3LYP/6-311+G(d,p)/PCM level of theory. +Additional stereoisomers were treated as if they were additional conformational states of the same microstate so that for each microsate only up to 5 conformations with the lowest PCM energies for each solvent were treated with MP2/6-311+G(d,p)EC-RISM using the PSE2 closure [REF1] and the resulting EC-RISM energies corrected using (c1*mu_{ex}+c2*PMV_{EC-RISM}+c3*q). The correction for water has a fixed parameter c1 = 1 since this additional parameter was found to be of no predictive value in previous challenges, c2 = -0.1025 kcal*mol^-1*A^-3 and c3 = -15.7284 kcal mol^-1 e^-1. [REF2]. These yield G_{mtc} where m refers to the ionization state, t to the tautomer (microstate per ionization state) and c to the respective conformation. The different statistical weights of conformations were taken into account by computing the free energy of the resulting discrete partition function G_{mt}=-RT*ln[sum_c(exp(-G_{mtc}/RT))]. For the deprotonation process of a microstate with k protons, pKa_{raw}=(G_{k}-G_{k-1})/(RT ln(10)) and the macrostate pKa follows from m*pKa_{raw}+b where parameters m and b are calculated within the chosen level of theory by fitting to the reference data set from [REF3]. Here, m = 0.7449 and b = -150.7196. To calculate the relative free energies with respect to each micro000, different formulas must be used, depending on the difference in the protonation state. If there is no difference in the protonation state, i.e. the microstates are tautomers, the relative free energy is calculated via m*(G(micro000)-G(m2)) to achieve thermodynamically consistent cycles. Since micro000 is always a neutral species for a single deprotonation the relative free energy is calculated using m*(G(micro000)-G(m2))+b, and -(m*(G(micro000)-G(m2))+b) for a protonation process. For the doubly protonated species the calculated relative free energy is m*(G(micro000)-G(m2))+2*b, and -(m*(G(micro000)-G(m2))+2*b) etc. for higher or lower protonation states [REF4]. Macrostate pKa values were calculated using the partition function approach of Eq. 5 in [REF5]. +The SEM was estimated as the convergence criterion for a single EC-RISM calculation. The uncertainty was estimated as the RMSE from the pKa training set. + +References: +REF1: N. Tielker, D. Tomazic, J. Heil, T. Kloss, S. Ehrhart, S. Guessregen, K. F. Schmidt, S. M. Kast, J. Comput.-Aided Mol. Des. 30, 1035-1044 (2016). +REF2: N. Tielker, L. Eberlein, S. Guessregen, S. M. Kast, J. Comput.-Aided Mol. Des. 32, 1151-1163 (2018). +REF3: J. J. Klicic, R. A. Friesner, S. Liu, W. C. Guida, J. Phys. Chem. A 106, 1327-1335 (2002). +REF4: T. D. Bergazin, N. Tielker, Y. Zhang, J. Mao, M. R. Gunner, K. Francisco, C. Ballatore, S. M. Kast, D. L. Mobley, J. Comput.-Aided Mol. Des., accepted (2021). +REF5: N. Tielker, L. Eberlein, C. Chodun, S. Guessregen, S. M. Kast, J. Mol. Model. 25, 139 (2019). + +Macro pKa values: +SAMPL8-1,-2.47,0.,1. +SAMPL8-1,4.80,-1.,0. +SAMPL8-2,5.36,-1.,0. +SAMPL8-3,-11.71,0.,1. +SAMPL8-3,4.31,-1.,0. +SAMPL8-3,10.48,-2.,-1. +SAMPL8-4,0.13,0.,1. +SAMPL8-4,4.74,-1.,0. +SAMPL8-5,-2.58,0.,1. +SAMPL8-5,5.08,-1.,0. +SAMPL8-6,2.94,0.,1. +SAMPL8-6,4.78,-1.,0. +SAMPL8-7,4.17,0.,1. +SAMPL8-7,15.11,-1.,0. +SAMPL8-8,-0.33,0.,1. +SAMPL8-9,5.68,0.,1. +SAMPL8-9,14.42,-1.,0. +SAMPL8-10,7.24,0.,1. +SAMPL8-11,8.93,0.,1. +SAMPL8-11,0.18,1.,2. +SAMPL8-12,4.92,0.,1. +SAMPL8-12,17.90,-1.,0. +SAMPL8-12,-4.99,1.,2. +SAMPL8-13,0.11,0.,1. +SAMPL8-13,15.16,-1.,0. +SAMPL8-14,5.37,0.,1. +SAMPL8-14,11.61,-1.,0. +SAMPL8-14,-3.81,1.,2. +SAMPL8-14,16.54,-2.,-1. +SAMPL8-14,20.86,-3.,-2. +SAMPL8-15,1.45,0.,1. +SAMPL8-16,4.03,0.,1. +SAMPL8-17,4.82,0.,1. +SAMPL8-17,14.34,-1.,0. +SAMPL8-18,1.77,0.,1. +SAMPL8-18,11.55,-1.,0. +SAMPL8-19,4.15,0.,1. +SAMPL8-19,7.06,-1.,0. +SAMPL8-19,-2.05,1.,2. +SAMPL8-20,1.57,0.,1. +SAMPL8-21,3.71,0.,1. +SAMPL8-21,8.32,-1.,0. +SAMPL8-21,-5.42,1.,2. +SAMPL8-21,17.48,-2.,-1. +SAMPL8-21,20.47,-3.,-2. +SAMPL8-22,2.10,0.,1. +SAMPL8-22,14.86,-1.,0. +SAMPL8-22,-7.64,1.,2. +SAMPL8-23,2.08,0.,1. +SAMPL8-23,10.19,-1.,0. + +Ranked: +True diff --git a/physical_properties/pKa/submissions/Original_submissions/modify_submission_names.sh b/physical_properties/pKa/submissions/Original_submissions/modify_submission_names.sh new file mode 100755 index 0000000..060e893 --- /dev/null +++ b/physical_properties/pKa/submissions/Original_submissions/modify_submission_names.sh @@ -0,0 +1,31 @@ +#!/bin/bash + +# Directory to process (change as needed or pass as $1) +DIR="." + +# Loop over all files (not directories) in the given directory +for INPUT in "$DIR"/*; do + # Only process regular files + [ -f "$INPUT" ] || continue + + # Get base name and extension + BASENAME="${INPUT##*/}" + EXT="${BASENAME##*.}" + FILENAME="${BASENAME%.*}" + + # Output file: add _modified before extension + OUTPUT="$DIR/${FILENAME}_modified.${EXT}" + + # Extract method name from Name: section, trim, replace spaces with underscores + METHOD_NAME=$(awk '/^Name:/{getline; gsub(/^[ \t"]+|[ \t"]+$/, "", $0); print; exit}' "$INPUT") + METHOD_NAME_UNDERSCORE="${METHOD_NAME// /_}" + + # Escape for sed (slashes, ampersands) + METHOD_NAME_ESCAPED=$(printf '%s' "$METHOD_NAME_UNDERSCORE" | sed 's/[\/&]/\\&/g') + + # Replace all SAMPL8-XX_extraNNN with SAMPL8-XX__extraNNN + sed -E "s/(SAMPL8-[0-9]+)_extra([0-9]+)/\1_${METHOD_NAME_ESCAPED}_extra\2/g" "$INPUT" > "$OUTPUT" + + echo "Processed $INPUT -> $OUTPUT" +done + diff --git a/physical_properties/pKa/submissions/Original_submissions/modify_submission_names_modified.sh b/physical_properties/pKa/submissions/Original_submissions/modify_submission_names_modified.sh new file mode 100644 index 0000000..060e893 --- /dev/null +++ b/physical_properties/pKa/submissions/Original_submissions/modify_submission_names_modified.sh @@ -0,0 +1,31 @@ +#!/bin/bash + +# Directory to process (change as needed or pass as $1) +DIR="." + +# Loop over all files (not directories) in the given directory +for INPUT in "$DIR"/*; do + # Only process regular files + [ -f "$INPUT" ] || continue + + # Get base name and extension + BASENAME="${INPUT##*/}" + EXT="${BASENAME##*.}" + FILENAME="${BASENAME%.*}" + + # Output file: add _modified before extension + OUTPUT="$DIR/${FILENAME}_modified.${EXT}" + + # Extract method name from Name: section, trim, replace spaces with underscores + METHOD_NAME=$(awk '/^Name:/{getline; gsub(/^[ \t"]+|[ \t"]+$/, "", $0); print; exit}' "$INPUT") + METHOD_NAME_UNDERSCORE="${METHOD_NAME// /_}" + + # Escape for sed (slashes, ampersands) + METHOD_NAME_ESCAPED=$(printf '%s' "$METHOD_NAME_UNDERSCORE" | sed 's/[\/&]/\\&/g') + + # Replace all SAMPL8-XX_extraNNN with SAMPL8-XX__extraNNN + sed -E "s/(SAMPL8-[0-9]+)_extra([0-9]+)/\1_${METHOD_NAME_ESCAPED}_extra\2/g" "$INPUT" > "$OUTPUT" + + echo "Processed $INPUT -> $OUTPUT" +done + diff --git a/physical_properties/pKa/submissions/pKa-3DS-1.csv b/physical_properties/pKa/submissions/Original_submissions/pKa-3DS-1.csv similarity index 99% rename from physical_properties/pKa/submissions/pKa-3DS-1.csv rename to physical_properties/pKa/submissions/Original_submissions/pKa-3DS-1.csv index 11988a5..5426e28 100644 --- a/physical_properties/pKa/submissions/pKa-3DS-1.csv +++ b/physical_properties/pKa/submissions/Original_submissions/pKa-3DS-1.csv @@ -296,7 +296,7 @@ TURBOMOLE 7.5: The quantum chemistry suite. University of Karlsruhe and Forschun # Pick only one category label.,,,,,, # The `Category:` keyword is required.,,,,,, Category: -LFER +QM+LEC # METHOD DESCRIPTION SECTION,,,,,, #,,,,,, diff --git a/physical_properties/pKa/submissions/Original_submissions/pKa-3DS-1_modified.csv b/physical_properties/pKa/submissions/Original_submissions/pKa-3DS-1_modified.csv new file mode 100644 index 0000000..2ffc072 --- /dev/null +++ b/physical_properties/pKa/submissions/Original_submissions/pKa-3DS-1_modified.csv @@ -0,0 +1,383 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction),,,,,, +#,,,,,, +# This file will be automatically parsed. It must contain the following four elements:,,,,,, +# predictions, name of method, software listing, and method description.,,, +# These elements must be provided in the order shown with their respective headers.,,,,,, +#,,,,,, +# Any line that begins with a # is considered a comment and will be ignored when parsing.,,,,,, +#,,,,,, +# PREDICTION SECTION,,,,,, +#,,,,,, +# It is mandatory to submit relative free energy (RFE) predictions for all 23 molecules. Incomplete submissions will not be accepted.,,,,,, +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty.,,,,,, +# Note that we here follow the same sign convention and submission format as the SAMPL7 pKa challenge.,,,,,, +#,,,,,, +# The data in each prediction line should be structured as follows:,,,,,, +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, +#,,,,,, +# If you have evaluated additional microstates, include the following:,,,,, +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +#,,,,,, +# The molecule ID of the other microstate needs to be in the format: `SAMPL8-X_extra001` (number can vary),,,,,, +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders,,,,,, +# Please send the `.mol2` file to the email listed on the instructions page.,,,,,, +#,,,,,, +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here.,,,,,, +Predictions: +SAMPL8-1_micro000,SAMPL8-1_COSMO-RS_one_pKa_fit_extra001,1,1.1,0.1,1.4 +SAMPL8-1_micro000,SAMPL8-1_COSMO-RS_one_pKa_fit_extra002,1,1.12,0.1,1.4 +SAMPL8-1_micro000,SAMPL8-1_micro000,0,0.0,0.1,1.4 +SAMPL8-1_micro000,SAMPL8-1_micro007,0,15.42,0.1,1.4 +SAMPL8-1_micro000,SAMPL8-1_micro010,0,14.07,0.1,1.4 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,5.03,0.1,1.4 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-11.52,0.1,0.73 +SAMPL8-10_micro000,SAMPL8-10_micro000,0,0.0,0.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_one_pKa_fit_extra001,2,-2.48,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_one_pKa_fit_extra007,2,-8.9,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_one_pKa_fit_extra008,2,-15.46,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_one_pKa_fit_extra002,1,-3.86,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_one_pKa_fit_extra003,1,-11.7,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_one_pKa_fit_extra004,1,-9.45,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_one_pKa_fit_extra005,1,-3.09,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_one_pKa_fit_extra009,1,-9.43,, +SAMPL8-12_micro000,SAMPL8-12_micro000,0,0.0,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_micro002,0,8.49,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_micro003 ,0,6.11,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_micro001,-1,19.98,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra009,2,-24.98,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra001,1,-20.17,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra002,1,-17.95,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra003,1,-9.57,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra004,1,-12.04,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra010,1,-13.11,, +SAMPL8-14_micro000,SAMPL8-14_micro024,0,-8.34,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra005,0,-4.46,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra006,0,-1.07,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra007,0,8.49,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra008,0,3.48,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro000,0,0.0,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro002,0,-1.6,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro013,0,-2.12,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro017,0,-0.72,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,5.03,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro004,-1,17.03,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro005,-1,12.52,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro010,-1,10.84,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro021,-1,16.17,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro022,-1,12.07,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro027,-1,15.61,0.1,1.4 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The ""Participant name:"" entry is required.",,,,, +Participant name: +"Michael Diedenhofen, Selman Terzi, Frank Eckert" + +#,,,,,, +#,,,,,, +# Please list your organization/affiliation, using only UTF-8 characters as described above.,,,,, +Participant organization: +Dassault Systemes Deutschland GmbH BIOVIA + +#,,,,,, +#,,,,,, +# NAME SECTION +#,,,,,, +# Please provide an informal but informative name of the method used.,,,,,, +# The name of the method should not exceed 40 characters.,,,,,, +# The 'Name:' keyword is required as shown here.,,,,,, +Name: +COSMO-RS one pKa fit + +#,,,,,, +#,,,,,, +# COMPUTE TIME SECTION,,,,,, +#,,,,,, +# Please provide the average compute time across all of the molecules.,,,,,, +# For physical methods, report the GPU and/or CPU compute time in hours.,,,,, +# For empirical methods, report the query time in hours.,,,,, +# Create a new line for each processor type.,,,,,, +# The 'Compute time:' keyword is required as shown here.,,,,,, +Compute time: +1076 hours, CPU + +#,,,,,, +# COMPUTING AND HARDWARE SECTION,,,,,, +#,,,,,, +# Please provide details of the computing resources that were used to train models and make predictions.,,,,,, +# Please specify compute time for training models and querying separately for empirical prediction methods.,,,,,, +# Provide a detailed description of the hardware used to run the simulations.,,,,,, +# The 'Computing and hardware:' keyword is required as shown here.,,,,,, +Computing and hardware: +We have use a linux cluster (Intel(R) Xeon(R) Gold 6248R CPU @ 3.00GHz). The calculations could use up to 20 cores. The number of actually use CPU differ during the steps of the conformer search procedure +The timings given above are wall times estimated from 33 structures and extrapolated to 203 microstates + +# SOFTWARE SECTION,,,,,, +#,,,,,, +# List all major software packages used and their versions.,,,,,, +# Create a new line for each software.,,,,,, +# The 'Software:' keyword is required.,,,,,, +Software: +BIOVIA COSMOquick 2021: A proprietary tool of Dassault Systemes to generate tautomeric states. +BIOVIA COSMOconf 2021: A proprietary tool of Dassault Systemes for conformer generation (uses TURBOMOLE and COSMOtherm) +BIOVIA COSMOtherm 2021: The proprietary software developed and distributed by Dassault Systemes, which uses COSMO-RS. COSMO-RS is a published theory: Klamt A (1995) Conductor-like screening model for real solvents: a new approach to the quantitative calculation of solvation phenomena. J Phys Chem 99:2224-2235. https://doi.org/10.1021/j100007a062 +TURBOMOLE 7.5: The quantum chemistry suite. University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989-2007, TURBOMOLE GmbH, since 2007; available from http://www.turbomole.com: Karlsruhe, Germany,2020 +# METHOD CATEGORY SECTION +#,,,,,, +# State if your prediction method is better classified as an,,,,,, +# experimental database lookup (DL), linear free energy relationship (LFER),,,,, +# quantitative structure-property relationship or machine learning (QSPR/ML),,,,,, +# quantum mechanics without empirical correction (QM) model, quantum mechanics with,,,,, +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular,,,,, +# mechanics (QM+MM), or Other, using the following category labels:,,,, +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`., +#,,,,,, +# Pick only one category label.,,,,,, +# The `Category:` keyword is required.,,,,,, +Category: +QM+LEC + +# METHOD DESCRIPTION SECTION,,,,,, +#,,,,,, +# Methodology and computational details.,,,,,, +# Level of details should be roughly equivalent to that used in a publication.,,,,,, +# Please include the values of key parameters with units.,,,,,, +# Please explain how statistical uncertainties were estimated.,,,,,, +# Use as many lines of text as you need.,,,,,, +#,,,,,, +# We strongly encourage you to submit your predicted macro pKa values in this section in consecutive lines following this format:,,,,,, +# compound name, macro pKa, initial formal charge, formal charge after transition, e.g.:,, +# SAMPL8-1,3.5,0,1,,, +Method: +Workflow +"1) We used COSMOquick to generate possible tautomeric and ionic states. Irrelevant states where discarded due to an internal energy threshold implemented in COSMOquick. In a subsequent manual check we discarded all dissociated structures. After a first DFT optimization we checked the relative energies of the microstates with same charge and reduced the number of states with an energy threshold. We performed DFT optimizations of the SAMPL8 microstates proposals and checked the structures against the already created microstates. Missing, energetically relevant structures were added to the set." +2) COSMOconf was used to create the conformer set of the microstates. +3) The conformer sets of the microstates were used to calculate the pKa values of the reactions between the microstates. We used the COSMO-RS theory with the BP-TZVPD-FINE 21 parametrization. The pKa values were predicted using a LFER approach based on the fee Gibbs energies of the microstates at infinite dilution in water. +"We normally use two LFER fits, one for the pKa (HA +H2O -> H3O+ + A-) and one for the pKa of the conjugated base (BH+ + H2O -> B + H3O+). Here we used the pKa model for SAMPL8-2 and the base pKa model for SAMPL8-10, SAMPL8-11, SAMPL8-15, SAMPL8-8. All other predictions have been done with a harmonized LFER model (fit of one model for the pKa and base pKa data). The RSME values in kcal/mol are 0.7 for the pKa model, 0.73 for the base pKa model, and 1.4 for the harmonized model." +The COSMO-RS algorithm by itself has no statistical error. The overall workflow including the conformational search (or molecule or state) has a statistical noise smaller than 0.1 kcal/mol. + +#,,,,,, +Macro pKa values +SAMPL8-1,-0.61,1,0 +SAMPL8-1,3.69,0,-1 +SAMPL8-2,3.99,0,-1 +SAMPL8-3,-1.04,1,0 +SAMPL8-3,3.39,0,-1 +SAMPL8-3,7.41,-1,-2 +SAMPL8-4,2.6,1,0 +SAMPL8-4,3.44,0,-1 +SAMPL8-5,-1.58,1,0 +SAMPL8-5,3.23,0,-1 +SAMPL8-6,3.76,1,0 +SAMPL8-6,3.25,0,-1 +SAMPL8-7,8,1,0 +SAMPL8-7,12.04,0,-1 +SAMPL8-8,1.88,1,0 +SAMPL8-9,7.77,1,0 +SAMPL8-9,12.28,0,-1 +SAMPL8-10,8.44,1,0 +SAMPL8-11,3.02,2,1 +SAMPL8-11,11.02,1,0 +SAMPL8-12,2.76,2,1 +SAMPL8-12,8.58,1,0 +SAMPL8-12,14.65,0,-1 +SAMPL8-13,2.69,1,0 +SAMPL8-13,12.62,0,-1 +SAMPL8-14,3.53,2,1 +SAMPL8-14,8.68,1,0 +SAMPL8-14,9.8,0,-1 +SAMPL8-14,13.71,-1,-2 +SAMPL8-15,4.02,1,0 +SAMPL8-16,6.81,1,0 +SAMPL8-16,10.84,0,-1 +SAMPL8-16,12.27,-1,-2 +SAMPL8-17,7.44,1,0 +SAMPL8-17,11.57,0,-1 +SAMPL8-18,5.29,1,0 +SAMPL8-18,11.35,0,-1 +SAMPL8-19,3.45,2,1 +SAMPL8-19,6.12,1,0 +SAMPL8-19,6.67,0,-1 +SAMPL8-20,0.41,2,1 +SAMPL8-20,4.64,1,0 +SAMPL8-20,10.19,0,-1 +SAMPL8-21,2.99,2,1 +SAMPL8-21,7.86,1,0 +SAMPL8-21,8.65,0,-1 +SAMPL8-21,13.2,-1,-2 +SAMPL8-22,-0.84,2,1 +SAMPL8-22,5.52,1,0 +SAMPL8-22,12.61,0,-1 +SAMPL8-23,4.51,1,0 +SAMPL8-23,8.97,0,-1 + +#,,,,,, +#,,,,,, +# All submissions must either be ranked or non-ranked.,,,,,, +# Only one ranked submission per participant is allowed.,,,,,, +# Multiple ranked submissions from the same participant will not be judged.,,,,,, +# Non-ranked submissions are accepted so we can verify that they were made before the deadline.,,,,,, +"# The ""Ranked:"" keyword is required", and expects a Boolean value (True/False),,,,, +Ranked: +True diff --git a/physical_properties/pKa/submissions/pKa-3DS-2.csv b/physical_properties/pKa/submissions/Original_submissions/pKa-3DS-2.csv similarity index 99% rename from physical_properties/pKa/submissions/pKa-3DS-2.csv rename to physical_properties/pKa/submissions/Original_submissions/pKa-3DS-2.csv index 7670591..1456fbe 100644 --- a/physical_properties/pKa/submissions/pKa-3DS-2.csv +++ b/physical_properties/pKa/submissions/Original_submissions/pKa-3DS-2.csv @@ -297,7 +297,7 @@ TURBOMOLE 7.5: The quantum chemistry suite. University of Karlsruhe and Forschun # Pick only one category label.,,,,,, # The `Category:` keyword is required.,,,,,, Category: -LFER +QM+LEC # METHOD DESCRIPTION SECTION,,,,,, #,,,,,, diff --git a/physical_properties/pKa/submissions/Original_submissions/pKa-3DS-2_modified.csv b/physical_properties/pKa/submissions/Original_submissions/pKa-3DS-2_modified.csv new file mode 100644 index 0000000..30ecd2b --- /dev/null +++ b/physical_properties/pKa/submissions/Original_submissions/pKa-3DS-2_modified.csv @@ -0,0 +1,385 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction),,,,,, +#,,,,,, +# This file will be automatically parsed. It must contain the following four elements:,,,,,, +# predictions, name of method, software listing, and method description.,,, +# These elements must be provided in the order shown with their respective headers.,,,,,, +#,,,,,, +# Any line that begins with a # is considered a comment and will be ignored when parsing.,,,,,, +#,,,,,, +# PREDICTION SECTION,,,,,, +#,,,,,, +# It is mandatory to submit relative free energy (RFE) predictions for all 23 molecules. Incomplete submissions will not be accepted.,,,,,, +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty.,,,,,, +# Note that we here follow the same sign convention and submission format as the SAMPL7 pKa challenge.,,,,,, +#,,,,,, +# The data in each prediction line should be structured as follows:,,,,,, +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, +#,,,,,, +# If you have evaluated additional microstates, include the following:,,,,, +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +#,,,,,, +# The molecule ID of the other microstate needs to be in the format: `SAMPL8-X_extra001` (number can vary),,,,,, +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders,,,,,, +# Please send the `.mol2` file to the email listed on the instructions page.,,,,,, +#,,,,,, +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here.,,,,,, +Predictions: +SAMPL8-1_micro000,SAMPL8-1_COSMO-RS_base_pKa_fit_extra001,1,4.48,0.1,0.73 +SAMPL8-1_micro000,SAMPL8-1_COSMO-RS_base_pKa_fit_extra002,1,4.51,1.1,0.73 +SAMPL8-1_micro000,SAMPL8-1_micro000,0,0.0,2.1,0.73 +SAMPL8-1_micro000,SAMPL8-1_micro007,0,18.66,3.1,0.73 +SAMPL8-1_micro000,SAMPL8-1_micro010,0,17.03,4.1,0.73 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,2.93,5.1,1.4 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-11.52,6.1,0.73 +SAMPL8-10_micro000,SAMPL8-10_micro000,0,0.0,7.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_base_pKa_fit_extra001,2,3.32,14.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_base_pKa_fit_extra007,2,-4.46,15.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_base_pKa_fit_extra008,2,-12.4,16.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_base_pKa_fit_extra002,1,-1.51,17.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_base_pKa_fit_extra003,1,-11.0,18.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_base_pKa_fit_extra004,1,-8.28,19.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_base_pKa_fit_extra005,1,-0.58,20.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_base_pKa_fit_extra009,1,-8.26,21.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_micro000,0,0.0,22.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_micro002,0,10.28,23.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_micro003 ,0,7.4,24.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_micro001,-1,21.02,25.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra009,2,-23.92,30.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra001,1,-21.26,31.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra002,1,-18.57,32.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra003,1,-8.42,33.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra004,1,-11.41,34.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra010,1,-12.7,35.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_micro024,0,-10.09,36.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra005,0,-5.4,37.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra006,0,-1.29,38.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra007,0,10.27,39.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra008,0,4.21,40.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_micro000,0,0.0,41.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_micro002,0,-1.93,42.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_micro013,0,-2.56,43.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_micro017,0,-0.88,44.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,2.93,45.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro004,-1,17.45,46.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro005,-1,12.0,47.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro010,-1,9.96,48.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro021,-1,16.41,49.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro022,-1,11.45,50.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro027,-1,15.73,51.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro028,-1,11.2,52.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro029,-1,13.01,53.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro032,-1,10.97,54.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro007,-2,28.91,55.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro018,-2,34.82,56.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro020,-2,29.98,57.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro001,-2,24.54,58.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro003,-2,22.46,59.1,1.4 +SAMPL8-15_micro000,SAMPL8-15_micro004,1,-11.73,60.1,0.73 +SAMPL8-15_micro000,SAMPL8-15_micro003,1,-7.07,61.1,0.73 +SAMPL8-15_micro000,SAMPL8-15_micro001,0,-6.24,62.1,0.73 +SAMPL8-15_micro000,SAMPL8-15_micro000,0,0.0,63.1,0.73 +SAMPL8-15_micro000,SAMPL8-15_micro002,0,0.13,64.1,0.73 +SAMPL8-16_micro000,SAMPL8-16_micro004,1,-8.09,65.1,0.73 +SAMPL8-16_micro000,SAMPL8-16_micro008,1,7.67,66.1,0.73 +SAMPL8-16_micro000,SAMPL8-16_micro000,0,0.0,67.1,0.73 +SAMPL8-16_micro000,SAMPL8-16_COSMO-RS_base_pKa_fit_extra002,0,11.85,68.1,0.73 +SAMPL8-16_micro000,SAMPL8-16_micro007,0,13.75,69.1,0.73 +SAMPL8-16_micro000,SAMPL8-16_micro011,0,15.66,70.1,0.73 +SAMPL8-16_micro000,SAMPL8-16_COSMO-RS_base_pKa_fit_extra003,-1,14.74,71.1,1.4 +SAMPL8-16_micro000,SAMPL8-16_COSMO-RS_base_pKa_fit_extra004,-1,18.87,72.1,1.4 +SAMPL8-16_micro000,SAMPL8-16_COSMO-RS_base_pKa_fit_extra005,-2,31.83,73.1,1.4 +SAMPL8-17_micro000,SAMPL8-17_micro002,1,-9.14,74.1,0.73 +SAMPL8-17_micro000,SAMPL8-17_micro003,1,2.81,75.1,0.73 +SAMPL8-17_micro000,SAMPL8-17_micro000,0,0.0,76.1,0.73 +SAMPL8-17_micro000,SAMPL8-17_micro004,0,1.63,77.1,0.73 +SAMPL8-17_micro000,SAMPL8-17_micro001,-1,15.93,78.1,1.4 +SAMPL8-18_micro000,SAMPL8-18_COSMO-RS_base_pKa_fit_extra001,1,-0.81,79.1,0.73 +SAMPL8-18_micro000,SAMPL8-18_micro004,1,-13.07,80.1,0.73 +SAMPL8-18_micro000,SAMPL8-18_micro003,1,-7.65,81.1,0.73 +SAMPL8-18_micro000,SAMPL8-18_micro002,0,-7.5,82.1,0.73 +SAMPL8-18_micro000,SAMPL8-18_micro001,0,-0.01,83.1,0.73 +SAMPL8-18_micro000,SAMPL8-18_micro000,0,0.0,84.1,0.73 +SAMPL8-18_micro000,SAMPL8-18_micro005,-1,8.08,85.1,1.4 +SAMPL8-19_micro000,SAMPL8-19_COSMO-RS_base_pKa_fit_extra001,2,-15.38,86.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_COSMO-RS_base_pKa_fit_extra002,2,-15.0,87.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro002,2,-13.63,88.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro003,2,-8.18,89.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro017,2,-12.57,90.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro005,1,-12.77,91.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro009,1,-12.67,92.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro004,1,-0.1,93.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro022,1,-3.71,94.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro008,1,-8.97,95.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro006,1,-7.5,96.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro019,1,-6.05,97.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro013,0,-5.79,98.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_COSMO-RS_base_pKa_fit_extra003,0,0.56,99.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro024,0,-4.45,100.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro007,0,-5.63,101.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro000,0,0.0,102.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro015,0,-1.94,103.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro020,0,6.79,104.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro025,0,-0.59,105.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro011,-1,1.76,106.1,1.4 +SAMPL8-19_micro000,SAMPL8-19_micro010,-1,10.26,107.1,1.4 +SAMPL8-2_micro000,SAMPL8-2_micro000,0,0.0,108.1,0.73 +SAMPL8-2_micro000,SAMPL8-2_micro002,0,18.4,109.1,0.73 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,2.24,110.1,1.4 +SAMPL8-20_micro000,SAMPL8-20_COSMO-RS_base_pKa_fit_extra001,2,-14.19,111.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro006,1,-16.44,112.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro015,1,-9.11,113.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro011,1,-10.1,114.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro002,1,-15.02,115.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro003,1,-16.13,116.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro026,1,-14.9,117.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro016,1,-2.55,118.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro022,0,-12.16,119.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro018,0,-4.9,120.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro017,0,-10.52,121.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_COSMO-RS_base_pKa_fit_extra002,0,-3.11,122.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro000,0,0.0,123.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro001,0,1.8,124.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_COSMO-RS_base_pKa_fit_extra003,-1,1.48,125.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra001,2,-14.8,126.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra010,2,-28.07,127.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra011,2,-19.06,128.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra002,1,-26.29,129.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra003,1,-23.99,130.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra004,1,-16.83,131.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra005,1,-17.83,132.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra012,1,-16.34,133.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_micro028,0,-16.48,134.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra006,0,-13.17,135.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra007,0,-12.0,136.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra008,0,-2.16,137.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra009,0,-4.34,138.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_micro000,0,0.0,139.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_micro008,0,-4.17,140.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_micro023,0,-8.18,141.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_micro025,0,-8.15,142.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_micro029,0,-4.95,143.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_micro022,-1,-5.35,144.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro016,-1,3.62,145.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro007,-1,14.81,146.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro009,-1,4.18,147.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro018,-1,0.47,148.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro020,-1,3.73,149.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro024,-1,1.94,150.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro026,-1,6.33,151.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro027,-1,8.22,152.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro013,-2,16.73,153.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro004,-2,24.8,154.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro005,-2,13.33,155.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro012,-2,26.14,156.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro015,-2,14.63,157.1,1.4 +SAMPL8-22_micro000,SAMPL8-22_COSMO-RS_base_pKa_fit_extra004,2,-10.62,158.1,0.73 +SAMPL8-22_micro000,SAMPL8-22_COSMO-RS_base_pKa_fit_extra001,1,-15.16,159.1,0.73 +SAMPL8-22_micro000,SAMPL8-22_COSMO-RS_base_pKa_fit_extra002,1,-13.42,160.1,0.73 +SAMPL8-22_micro000,SAMPL8-22_COSMO-RS_base_pKa_fit_extra003,1,-4.66,161.1,0.73 +SAMPL8-22_micro000,SAMPL8-22_micro002,0,-9.21,162.1,0.73 +SAMPL8-22_micro000,SAMPL8-22_micro000,0,0.0,163.1,0.73 +SAMPL8-22_micro000,SAMPL8-22_micro003,0,0.64,164.1,0.73 +SAMPL8-22_micro000,SAMPL8-22_micro001,-1,8.46,165.1,1.4 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-17.25,166.1,0.73 +SAMPL8-23_micro000,SAMPL8-23_micro007,0,-12.97,167.1,0.73 +SAMPL8-23_micro000,SAMPL8-23_micro003,0,-5.73,168.1,0.73 +SAMPL8-23_micro000,SAMPL8-23_micro000,0,0.0,169.1,0.73 +SAMPL8-23_micro000,SAMPL8-23_micro005,-1,-1.31,170.1,1.4 +SAMPL8-23_micro000,SAMPL8-23_micro002,-1,12.11,171.1,1.4 +SAMPL8-3_micro000,SAMPL8-3_COSMO-RS_base_pKa_fit_extra001,1,-27.19,172.1,0.73 +SAMPL8-3_micro000,SAMPL8-3_COSMO-RS_base_pKa_fit_extra003,1,-19.07,173.1,0.73 +SAMPL8-3_micro000,SAMPL8-3_micro000,0,0.0,174.1,0.73 +SAMPL8-3_micro000,SAMPL8-3_micro006,0,-32.06,175.1,0.73 +SAMPL8-3_micro000,SAMPL8-3_COSMO-RS_base_pKa_fit_extra002,0,-18.65,176.1,0.73 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,-23.22,177.1,1.4 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,-29.63,178.1,1.4 +SAMPL8-3_micro000,SAMPL8-3_micro013,-2,-20.55,179.1,1.4 +SAMPL8-4_micro000,SAMPL8-4_micro002,1,-6.54,180.1,0.73 +SAMPL8-4_micro000,SAMPL8-4_micro010,0,-5.09,181.1,0.73 +SAMPL8-4_micro000,SAMPL8-4_COSMO-RS_base_pKa_fit_extra001,0,17.45,182.1,0.73 +SAMPL8-4_micro000,SAMPL8-4_COSMO-RS_base_pKa_fit_extra002,0,15.65,183.1,0.73 +SAMPL8-4_micro000,SAMPL8-4_micro000,0,0.0,184.1,0.73 +SAMPL8-4_micro000,SAMPL8-4_micro001,0,-5.04,185.1,0.73 +SAMPL8-4_micro000,SAMPL8-4_micro005,-1,-2.88,186.1,1.4 +SAMPL8-4_micro000,SAMPL8-4_micro003,-1,1.17,187.1,1.4 +SAMPL8-4_micro000,SAMPL8-4_micro008,-1,8.6,188.1,1.4 +SAMPL8-5_micro000,SAMPL8-5_micro003,1,5.77,189.1,0.73 +SAMPL8-5_micro000,SAMPL8-5_micro006,1,17.05,190.1,0.73 +SAMPL8-5_micro000,SAMPL8-5_micro000,0,0.0,191.1,0.73 +SAMPL8-5_micro000,SAMPL8-5_micro005,0,13.49,192.1,0.73 +SAMPL8-5_micro000,SAMPL8-5_micro001,0,8.58,193.1,0.73 +SAMPL8-5_micro000,SAMPL8-5_micro007,-1,2.17,194.1,1.4 +SAMPL8-6_micro000,SAMPL8-6_micro003,1,-3.35,195.1,0.73 +SAMPL8-6_micro000,SAMPL8-6_micro000,0,0.0,196.1,0.73 +SAMPL8-6_micro000,SAMPL8-6_micro007,0,-0.42,197.1,0.73 +SAMPL8-6_micro000,SAMPL8-6_micro001,-1,1.91,198.1,1.4 +SAMPL8-6_micro000,SAMPL8-6_micro009,-1,25.23,199.1,1.4 +SAMPL8-7_micro000,SAMPL8-7_micro002,1,-10.05,200.1,0.73 +SAMPL8-7_micro000,SAMPL8-7_micro003,1,3.61,201.1,0.73 +SAMPL8-7_micro000,SAMPL8-7_micro000,0,0.0,202.1,0.73 +SAMPL8-7_micro000,SAMPL8-7_micro004,0,2.86,203.1,0.73 +SAMPL8-7_micro000,SAMPL8-7_micro001,-1,16.72,204.1,1.4 +SAMPL8-8_micro000,SAMPL8-8_micro001,1,-2.56,205.1,0.73 +SAMPL8-8_micro000,SAMPL8-8_micro002,1,13.47,206.1,0.73 +SAMPL8-8_micro000,SAMPL8-8_micro000,0,0.0,207.1,0.73 +SAMPL8-9_micro002,SAMPL8-9_micro002,1,-9.67,208.1,0.73 +SAMPL8-9_micro002,SAMPL8-9_micro004,1,3.02,209.1,0.73 +SAMPL8-9_micro002,SAMPL8-9_micro000,0,0.0,210.1,0.73 +SAMPL8-9_micro002,SAMPL8-9_micro003,0,2.66,211.1,0.73 +SAMPL8-9_micro002,SAMPL8-9_micro001,-1,17.12,212.1,1.4 + +#,,,,,, +#,,,,,, +# Please list your name," using only UTF-8 characters as described above. The ""Participant name:"" entry is required.",,,,, +Participant name: +"Michael Diedenhofen, Selman Terzi, Frank Eckert" + +#,,,,,, +#,,,,,, +# Please list your organization/affiliation, using only UTF-8 characters as described above.,,,,, +Participant organization: +Dassault Systemes Deutschland GmbH, BIOVIA + +#,,,,,, +#,,,,,, +# NAME SECTION,,,,,, +#,,,,,, +# Please provide an informal but informative name of the method used.,,,,,, +# The name of the method should not exceed 40 characters.,,,,,, +# The 'Name:' keyword is required as shown here.,,,,,, +Name: +COSMO-RS base pKa fit + +#,,,,,, +#,,,,,, +# COMPUTE TIME SECTION,,,,,, +#,,,,,, +# Please provide the average compute time across all of the molecules.,,,,,, +# For physical methods, report the GPU and/or CPU compute time in hours.,,,,, +# For empirical methods, report the query time in hours.,,,,, +# Create a new line for each processor type.,,,,,, +# The 'Compute time:' keyword is required as shown here.,,,,,, +Compute time: +1076 hours, CPU + +#,,,,,, +# COMPUTING AND HARDWARE SECTION,,,,,, +#,,,,,, +# Please provide details of the computing resources that were used to train models and make predictions.,,,,,, +# Please specify compute time for training models and querying separately for empirical prediction methods.,,,,,, +# Provide a detailed description of the hardware used to run the simulations.,,,,,, +# The 'Computing and hardware:' keyword is required as shown here.,,,,,, +Computing and hardware: +We have use a linux cluster (Intel(R) Xeon(R) Gold 6248R CPU @ 3.00GHz). The calculations could use up to 20 cores. The number of actually use CPU differ during the steps of the conformer search procedure +The timings given above are wall times estimated from 33 structures and extrapolated to 203 microstates + +# SOFTWARE SECTION,,,,,, +#,,,,,, +# List all major software packages used and their versions.,,,,,, +# Create a new line for each software.,,,,,, +# The 'Software:' keyword is required.,,,,,, +Software: +BIOVIA COSMOquick 2021: A proprietary tool of Dassault Systemes to generate tautomeric states. +BIOVIA COSMOconf 2021: A proprietary tool of Dassault Systemes for conformer generation, TURBOMOLE and COSMOtherm. +BIOVIA COSMOtherm 2021: The proprietary software developed and distributed by Dassault Systemes, which uses COSMO-RS. COSMO-RS is a published theory: Klamt A (1995) Conductor-like screening model for real solvents: a new approach to the quantitative calculation of solvation phenomena. J Phys Chem 99:2224-2235. https://doi.org/10.1021/j100007a062 +TURBOMOLE 7.5: The quantum chemistry suite. University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989-2007, TURBOMOLE GmbH, since 2007; available from http://www.turbomole.com: Karlsruhe, Germany,2020, + +# METHOD CATEGORY SECTION,,,,,, +#,,,,,, +# State if your prediction method is better classified as an,,,,,, +# experimental database lookup (DL), linear free energy relationship (LFER),,,,, +# quantitative structure-property relationship or machine learning (QSPR/ML),,,,,, +# quantum mechanics without empirical correction (QM) model, quantum mechanics with,,,,, +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular,,,,, +# mechanics (QM+MM), or Other, using the following category labels:,,,, +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`., +#,,,,,, +# Pick only one category label.,,,,,, +# The `Category:` keyword is required.,,,,,, +Category: +QM+LEC + +# METHOD DESCRIPTION SECTION,,,,,, +#,,,,,, +# Methodology and computational details.,,,,,, +# Level of details should be roughly equivalent to that used in a publication.,,,,,, +# Please include the values of key parameters with units.,,,,,, +# Please explain how statistical uncertainties were estimated.,,,,,, +# Use as many lines of text as you need.,,,,,, +#,,,,,, +# We strongly encourage you to submit your predicted macro pKa values in this section in consecutive lines following this format:,,,,,, +# compound name, macro pKa, initial formal charge, formal charge after transition, e.g.:,, +# SAMPL8-1,3.5,0,1,,, +Method: +Workflow +"1) We used COSMOquick to generate possible tautomeric and ionic states. Irrelevant states where discarded due to an internal energy threshold implemented in COSMOquick. In a subsequent manual check we discarded all dissociated structures. After a first DFT optimization we checked the relative energies of the microstates with same charge and reduced the number of states with an energy threshold. We performed DFT optimizations of the SAMPL8 microstates proposals and checked the structures against the already created microstates. Missing, energetically relevant structures were added to the set." +2) COSMOconf was used to create the conformer set of the microstates. +4) The conformer sets of the microstates were used to calculate the pKa values of the reactions between the microstates. We used the COSMO-RS theory with the BP-TZVPD-FINE 21 parametrization. The pKa values were predicted using a LFER approach based on the fee Gibbs energies of the microstates at infinite dilution in water. +"We normally use two LFER fits, one for the pKa (HA +H2O -> H3O+ + A-) and one for the pKa of the conjugated base (BH+ + H2O -> B + H3O+). Here we used the pKa model for the conjugated base for all reactions. The RSME value of this model for BH+ + H2O -> B + H3O+ reactions is 0.73 kcal/mol." +The COSMO-RS algorithm by itself has no statistical error. The overall workflow including the conformational search (or molecule or state) has a statistical noise smaller than 0.1 kcal/mol. + +#,,,,,, +Macro pKa values +SAMPL8-1,1,0,-3.05 +SAMPL8-1,0,-1,2.15 +SAMPL8-2,0,-1,1.64 +SAMPL8-3,1,0,-3.58 +SAMPL8-3,0,-1,1.78 +SAMPL8-3,-1,-2,6.66 +SAMPL8-4,1,0,0.84 +SAMPL8-4,0,-1,1.84 +SAMPL8-5,1,0,-4.23 +SAMPL8-5,0,-1,1.59 +SAMPL8-6,1,0,2.23 +SAMPL8-6,0,-1,1.62 +SAMPL8-7,1,0,7.36 +SAMPL8-7,0,-1,12.26 +SAMPL8-8,1,0,1.88 +SAMPL8-9,1,0,7.09 +SAMPL8-9,0,-1,12.55 +SAMPL8-10,1,0,8.44 +SAMPL8-11,2,1,3.02 +SAMPL8-11,1,0,11.02 +SAMPL8-12,2,1,1.02 +SAMPL8-12,1,0,8.07 +SAMPL8-12,0,-1,15.41 +SAMPL8-13,1,0,0.93 +SAMPL8-13,0,-1,12.96 +SAMPL8-14,2,1,1.95 +SAMPL8-14,1,0,8.19 +SAMPL8-14,0,-1,9.55 +SAMPL8-14,-1,-2,14.28 +SAMPL8-15,1,0,4.02 +SAMPL8-16,1,0,5.93 +SAMPL8-16,0,-1,10.80 +SAMPL8-16,-1,-2,12.53 +SAMPL8-17,1,0,6.69 +SAMPL8-17,0,-1,11.69 +SAMPL8-18,1,0,4.08 +SAMPL8-18,0,-1,11.42 +SAMPL8-19,2,1,1.86 +SAMPL8-19,1,0,5.09 +SAMPL8-19,0,-1,5.76 +SAMPL8-20,2,1,-1.82 +SAMPL8-20,1,0,3.30 +SAMPL8-20,0,-1,10.01 +SAMPL8-21,2,1,1.30 +SAMPL8-21,1,0,7.19 +SAMPL8-21,0,-1,8.16 +SAMPL8-21,-1,-2,13.66 +SAMPL8-22,2,1,-3.34 +SAMPL8-22,1,0,4.37 +SAMPL8-22,0,-1,12.95 +SAMPL8-23,1,0,3.14 +SAMPL8-23,0,-1,8.55 + +#,,,,,, +#,,,,,, +# All submissions must either be ranked or non-ranked.,,,,,, +# Only one ranked submission per participant is allowed.,,,,,, +# Multiple ranked submissions from the same participant will not be judged.,,,,,, +# Non-ranked submissions are accepted so we can verify that they were made before the deadline.,,,,,, +"# The ""Ranked:"" keyword is required", and expects a Boolean value (True/False),,,,, + +Ranked: +False \ No newline at end of file diff --git a/physical_properties/pKa/submissions/pKa-3DS-3.csv b/physical_properties/pKa/submissions/Original_submissions/pKa-3DS-3.csv similarity index 99% rename from physical_properties/pKa/submissions/pKa-3DS-3.csv rename to physical_properties/pKa/submissions/Original_submissions/pKa-3DS-3.csv index d76e4fb..491301e 100644 --- a/physical_properties/pKa/submissions/pKa-3DS-3.csv +++ b/physical_properties/pKa/submissions/Original_submissions/pKa-3DS-3.csv @@ -295,7 +295,7 @@ TURBOMOLE 7.5: The quantum chemistry suite. University of Karlsruhe and Forschun # Pick only one category label.,,,,,, # The `Category:` keyword is required.,,,,,, Category: -LFER +QM+LEC # METHOD DESCRIPTION SECTION,,,,,, #,,,,,, diff --git a/physical_properties/pKa/submissions/Original_submissions/pKa-3DS-3_modified.csv b/physical_properties/pKa/submissions/Original_submissions/pKa-3DS-3_modified.csv new file mode 100644 index 0000000..b4a38b4 --- /dev/null +++ b/physical_properties/pKa/submissions/Original_submissions/pKa-3DS-3_modified.csv @@ -0,0 +1,382 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction),,,,,, +#,,,,,, +# This file will be automatically parsed. It must contain the following four elements:,,,,,, +# predictions, name of method, software listing, and method description.,,, +# These elements must be provided in the order shown with their respective headers.,,,,,, +#,,,,,, +# Any line that begins with a # is considered a comment and will be ignored when parsing.,,,,,, +#,,,,,, +# PREDICTION SECTION,,,,,, +#,,,,,, +# It is mandatory to submit relative free energy (RFE) predictions for all 23 molecules. Incomplete submissions will not be accepted.,,,,,, +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty.,,,,,, +# Note that we here follow the same sign convention and submission format as the SAMPL7 pKa challenge.,,,,,, +#,,,,,, +# The data in each prediction line should be structured as follows:,,,,,, +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, +#,,,,,, +# If you have evaluated additional microstates, include the following:,,,,, +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +#,,,,,, +# The molecule ID of the other microstate needs to be in the format: `SAMPL8-X_extra001` (number can vary),,,,,, +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders,,,,,, +# Please send the `.mol2` file to the email listed on the instructions page.,,,,,, +#,,,,,, +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here.,,,,,, +Predictions: +SAMPL8-1_micro000,SAMPL8-1_COSMO-RS_pKa_fit_extra001,1,0.01,0.1,1.4 +SAMPL8-1_micro000,SAMPL8-1_COSMO-RS_pKa_fit_extra002,1,0.03,0.1,1.4 +SAMPL8-1_micro000,SAMPL8-1_micro000,0,0.0,0.1,0.7 +SAMPL8-1_micro000,SAMPL8-1_micro007,0,15.13,0.1,0.7 +SAMPL8-1_micro000,SAMPL8-1_micro010,0,13.81,0.1,0.7 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,6.01,0.1,0.7 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-12.96,0.1,1.4 +SAMPL8-10_micro000,SAMPL8-10_micro000,0,0.0,0.1,0.7 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_pKa_fit_extra001,2,-4.57,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_pKa_fit_extra007,2,-10.87,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_pKa_fit_extra008,2,-17.31,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_pKa_fit_extra002,1,-4.85,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_pKa_fit_extra003,1,-12.54,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_pKa_fit_extra004,1,-10.34,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_pKa_fit_extra005,1,-4.09,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_pKa_fit_extra009,1,-10.32,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_micro000,0,0.0,0.1,0.7 +SAMPL8-12_micro000,SAMPL8-12_micro002,0,8.33,0.1,0.7 +SAMPL8-12_micro000,SAMPL8-12_micro003 ,0,6.0,0.1,0.7 +SAMPL8-12_micro000,SAMPL8-12_micro001,-1,20.67,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra009,2,-26.65,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra001,1,-20.86,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra002,1,-18.68,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra003,1,-10.45,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra004,1,-12.88,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra010,1,-13.92,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro024,0,-8.18,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra005,0,-4.37,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra006,0,-1.05,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra007,0,8.33,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra008,0,3.41,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro000,0,0.0,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro002,0,-1.56,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro013,0,-2.08,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro017,0,-0.71,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,6.01,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro004,-1,17.77,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro005,-1,13.35,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro010,-1,11.7,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro021,-1,16.93,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro022,-1,12.91,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro027,-1,16.38,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro028,-1,12.71,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro029,-1,14.18,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro032,-1,12.52,0.1,0.7 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+SAMPL8-8_micro000,SAMPL8-8_micro001,1,-5.7,0.1,1.4 +SAMPL8-8_micro000,SAMPL8-8_micro002,1,7.29,0.1,1.4 +SAMPL8-8_micro000,SAMPL8-8_micro000,0,0.0,0.1,0.7 +SAMPL8-9_micro002,SAMPL8-9_micro002,1,-11.47,0.1,1.4 +SAMPL8-9_micro002,SAMPL8-9_micro004,1,-1.18,0.1,1.4 +SAMPL8-9_micro002,SAMPL8-9_micro000,0,0.0,0.1,0.7 +SAMPL8-9_micro002,SAMPL8-9_micro003,0,2.16,0.1,0.7 +SAMPL8-9_micro002,SAMPL8-9_micro001,-1,17.5,0.1,0.0 + +#,,,,,, +#,,,,,, +# Please list your name," using only UTF-8 characters as described above. The ""Participant name:"" entry is required.",,,,, +Participant name: +"Michael Diedenhofen, Selman Terzi, Frank Eckert" + +#,,,,,, +#,,,,,, +# Please list your organization/affiliation, using only UTF-8 characters as described above.,,,,, +Participant organization: +Dassault Systemes Deutschland GmbH, BIOVIA + +# NAME SECTION,,,,,, +#,,,,,, +# Please provide an informal but informative name of the method used.,,,,,, +# The name of the method should not exceed 40 characters.,,,,,, +# The 'Name:' keyword is required as shown here.,,,,,, +Name: +COSMO-RS pKa fit + +#,,,,,, +#,,,,,, +# COMPUTE TIME SECTION,,,,,, +#,,,,,, +# Please provide the average compute time across all of the molecules.,,,,,, +# For physical methods, report the GPU and/or CPU compute time in hours.,,,,, +# For empirical methods, report the query time in hours.,,,,, +# Create a new line for each processor type.,,,,,, +# The 'Compute time:' keyword is required as shown here.,,,,,, +Compute time: +1076 hours, CPU + +#,,,,,, +# COMPUTING AND HARDWARE SECTION,,,,,, +#,,,,,, +# Please provide details of the computing resources that were used to train models and make predictions.,,,,,, +# Please specify compute time for training models and querying separately for empirical prediction methods.,,,,,, +# Provide a detailed description of the hardware used to run the simulations.,,,,,, +# The 'Computing and hardware:' keyword is required as shown here.,,,,,, +Computing and hardware: +We have use a linux cluster (Intel(R) Xeon(R) Gold 6248R CPU @ 3.00GHz). The calculations could use up to 20 cores. The number of actually use CPU differ during the steps of the conformer search procedure. +The timings given above are wall times estimated from 33 structures and extrapolated to 203 microstates + +# SOFTWARE SECTION,,,,,, +#,,,,,, +# List all major software packages used and their versions.,,,,,, +# Create a new line for each software.,,,,,, +# The 'Software:' keyword is required.,,,,,, +Software: +BIOVIA COSMOquick 2021: A proprietary tool of Dassault Systemes to generate tautomeric states. +BIOVIA COSMOconf 2021: A proprietary tool of Dassault Systemes for conformer generation (uses TURBOMOLE and COSMOtherm) +BIOVIA COSMOtherm 2021: The proprietary software developed and distributed by Dassault Systemes, which uses COSMO-RS. COSMO-RS is a published theory: Klamt A (1995) Conductor-like screening model for real solvents: a new approach to the quantitative calculation of solvation phenomena. J Phys Chem 99:2224-2235. https://doi.org/10.1021/j100007a062 +TURBOMOLE 7.5: The quantum chemistry suite. University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989-2007, TURBOMOLE GmbH, since 2007; available from http://www.turbomole.com: Karlsruhe, Germany,2020, + +# METHOD CATEGORY SECTION,,,,,, +#,,,,,, +# State if your prediction method is better classified as an,,,,,, +# experimental database lookup (DL), linear free energy relationship (LFER),,,,, +# quantitative structure-property relationship or machine learning (QSPR/ML),,,,,, +# quantum mechanics without empirical correction (QM) model, quantum mechanics with,,,,, +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular,,,,, +# mechanics (QM+MM), or Other, using the following category labels:,,,, +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`., +#,,,,,, +# Pick only one category label.,,,,,, +# The `Category:` keyword is required.,,,,,, +Category: +QM+LEC + +# METHOD DESCRIPTION SECTION,,,,,, +#,,,,,, +# Methodology and computational details.,,,,,, +# Level of details should be roughly equivalent to that used in a publication.,,,,,, +# Please include the values of key parameters with units.,,,,,, +# Please explain how statistical uncertainties were estimated.,,,,,, +# Use as many lines of text as you need.,,,,,, +#,,,,,, +# We strongly encourage you to submit your predicted macro pKa values in this section in consecutive lines following this format:,,,,,, +# compound name, macro pKa, initial formal charge, formal charge after transition, e.g.:,, +# SAMPL8-1,3.5,0,1,,, +Method: +Workflow +"1) We used COSMOquick to generate possible tautomeric and ionic states. Irrelevant states where discarded due to an internal energy threshold implemented in COSMOquick. In a subsequent manual check we discarded all dissociated structures. After a first DFT optimization we checked the relative energies of the microstates with same charge and reduced the number of states with an energy threshold. We performed DFT optimizations of the SAMPL8 microstates proposals and checked the structures against the already created microstates. Missing, energetically relevant structures were added to the set." +2) COSMOconf was used to create the conformer set of the microstates. +4) The conformer sets of the microstates were used to calculate the pKa values of the reactions between the microstates. We used the COSMO-RS theory with the BP-TZVPD-FINE 21 parametrization. The pKa values were predicted using a LFER approach based on the fee Gibbs energies of the microstates at infinite dilution in water. +"We normally use two LFER fits, one for the pKa (HA +H2O -> H3O+ + A-) and one for the pKa of the conjugated base (BH+ + H2O -> B + H3O+). Here we used the pKa model for all reactions. The RSME value of this model in kcal/mol for HA +H2O -> H3O+ + A- reactions is 0.7." +The COSMO-RS algorithm by itself has no statistical error. The overall workflow including the conformational search (or molecule or state) has a statistical noise smaller than 0.1 kcal/mol. +#,,,,,, +Macro pKa values +SAMPL8-1,1,0,0.19 +SAMPL8-1,0,-1,4.40 +SAMPL8-2,0,-1,3.99 +SAMPL8-3,1,0,-0.24 +SAMPL8-3,0,-1,4.11 +SAMPL8-3,-1,-2,8.06 +SAMPL8-4,1,0,3.34 +SAMPL8-4,0,-1,4.15 +SAMPL8-5,1,0,-0.77 +SAMPL8-5,0,-1,3.95 +SAMPL8-6,1,0,4.47 +SAMPL8-6,0,-1,3.97 +SAMPL8-7,1,0,8.63 +SAMPL8-7,0,-1,12.60 +SAMPL8-8,1,0,4.18 +SAMPL8-9,1,0,8.41 +SAMPL8-9,0,-1,12.83 +SAMPL8-10,1,0,9.50 +SAMPL8-11,2,1,5.11 +SAMPL8-11,1,0,11.59 +SAMPL8-12,2,1,3.49 +SAMPL8-12,1,0,9.20 +SAMPL8-12,0,-1,15.15 +SAMPL8-13,1,0,3.42 +SAMPL8-13,0,-1,13.17 +SAMPL8-14,2,1,4.24 +SAMPL8-14,1,0,9.29 +SAMPL8-14,0,-1,10.40 +SAMPL8-14,-1,-2,14.24 +SAMPL8-15,1,0,5.92 +SAMPL8-16,1,0,7.46 +SAMPL8-16,0,-1,11.41 +SAMPL8-16,-1,-2,12.82 +SAMPL8-17,1,0,8.08 +SAMPL8-17,0,-1,12.13 +SAMPL8-18,1,0,5.97 +SAMPL8-18,0,-1,11.92 +SAMPL8-19,2,1,4.16 +SAMPL8-19,1,0,6.79 +SAMPL8-19,0,-1,7.32 +SAMPL8-20,2,1,1.18 +SAMPL8-20,1,0,5.33 +SAMPL8-20,0,-1,10.77 +SAMPL8-21,2,1,3.71 +SAMPL8-21,1,0,8.49 +SAMPL8-21,0,-1,9.27 +SAMPL8-21,-1,-2,13.73 +SAMPL8-22,2,1,-0.04 +SAMPL8-22,1,0,6.20 +SAMPL8-22,0,-1,13.16 +SAMPL8-23,1,0,5.20 +SAMPL8-23,0,-1,9.59 + +#,,,,,, +#,,,,,, +# All submissions must either be ranked or non-ranked.,,,,,, +# Only one ranked submission per participant is allowed.,,,,,, +# Multiple ranked submissions from the same participant will not be judged.,,,,,, +# Non-ranked submissions are accepted so we can verify that they were made before the deadline.,,,,,, +"# The ""Ranked:"" keyword is required", and expects a Boolean value (True/False),,,,, + +Ranked: +False diff --git a/physical_properties/pKa/submissions/pKa-RobertRaddi_AdaBoost.csv b/physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_AdaBoost.csv similarity index 100% rename from physical_properties/pKa/submissions/pKa-RobertRaddi_AdaBoost.csv rename to physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_AdaBoost.csv diff --git a/physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_AdaBoost_modified.csv b/physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_AdaBoost_modified.csv new file mode 100644 index 0000000..93ad03d --- /dev/null +++ b/physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_AdaBoost_modified.csv @@ -0,0 +1,285 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction) +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# PREDICTION SECTION +# +# It is mandatory to submit relative free energy (RFE) predictions for all 22 molecules. Incomplete submissions will not be accepted. +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty. +# +# The data in each prediction line should be structured as follows: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty +# +# If you have evaluated additional microstates, include the following: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +# +# The molecule ID of the other microstate needs to be in the format: `SMXX_extra001` (number can vary) +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders, +# Please send the `.mol2` file to the email listed on the instructions page. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: +SAMPL8-1_micro000,SAMPL8-1_micro001,-1,14.01,2.05,2.05 +SAMPL8-1_micro000,SAMPL8-1_micro002,-1,11.74,2.05,2.05 +SAMPL8-1_micro000,SAMPL8-1_micro003,-1,14.01,2.05,2.05 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,7.0,2.05,2.05 +SAMPL8-1_micro000,SAMPL8-1_micro005,-1,12.38,2.05,2.05 +SAMPL8-1_micro000,SAMPL8-1_micro008,-1,14.01,2.05,2.05 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,6.56,2.05,2.05 +SAMPL8-2_micro000,SAMPL8-2_micro003,-1,-0.0,2.05,2.05 +SAMPL8-2_micro000,SAMPL8-2_micro002,0,-9.94,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro001,-1,14.01,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro003,-1,23.05,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro005,-1,12.25,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro009,-1,15.86,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,7.0,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro011,-1,23.05,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro015,-1,27.47,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,14.69,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro017,-1,23.05,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro018,-1,14.01,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro020,-1,10.23,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro002,0,12.69,2.05,2.05 +SAMPL8-4_micro000,SAMPL8-4_micro003,-1,9.4,2.05,2.05 +SAMPL8-4_micro000,SAMPL8-4_micro005,-1,9.02,2.05,2.05 +SAMPL8-4_micro000,SAMPL8-4_micro006,-1,7.34,2.05,2.05 +SAMPL8-4_micro000,SAMPL8-4_micro008,-1,4.94,2.05,2.05 +SAMPL8-5_micro000,SAMPL8-5_micro002,-1,-0.0,2.05,2.05 +SAMPL8-5_micro000,SAMPL8-5_micro007,-1,6.04,2.05,2.05 +SAMPL8-5_micro000,SAMPL8-5_micro003,1,-5.25,2.05,2.05 +SAMPL8-5_micro000,SAMPL8-5_micro006,1,-19.67,2.05,2.05 +SAMPL8-5_micro000,SAMPL8-5_micro001,0,0.0,2.05,2.05 +SAMPL8-6_micro000,SAMPL8-6_micro001,-1,7.0,2.05,2.05 +SAMPL8-6_micro000,SAMPL8-6_micro006,-1,7.62,2.05,2.05 +SAMPL8-6_micro000,SAMPL8-6_micro009,-1,-0.0,2.05,2.05 +SAMPL8-6_micro000,SAMPL8-6_micro002,1,-19.31,2.05,2.05 +SAMPL8-6_micro000,SAMPL8-6_micro003,1,-12.47,2.05,2.05 +SAMPL8-7_micro000,SAMPL8-7_micro001,-1,11.23,2.05,2.05 +SAMPL8-8_micro000,SAMPL8-8_micro001,1,-5.02,2.05,2.05 +SAMPL8-8_micro000,SAMPL8-8_micro002,1,-7.93,2.05,2.05 +SAMPL8-9_micro000,SAMPL8-9_micro001,-1,11.04,2.05,2.05 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-7.34,2.05,2.05 +SAMPL8-12_micro000,SAMPL8-12_micro001,-1,18.5,2.05,2.05 +SAMPL8-12_micro000,SAMPL8-12_micro002,0,0.46,2.05,2.05 +SAMPL8-12_micro000,SAMPL8-12_micro003,0,-0.0,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro004,-1,21.5,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro005,-1,10.83,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,10.0,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro009,-1,4.12,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro010,-1,5.85,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro012,-1,7.92,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro019,-1,10.83,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro021,-1,8.24,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro022,-1,10.36,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro025,-1,12.24,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro027,-1,11.38,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro028,-1,10.23,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro029,-1,9.13,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro032,-1,10.36,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro001,-2,9.71,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro003,-2,18.82,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro002,0,-7.14,2.05,2.05 +SAMPL8-15_micro000,SAMPL8-15_micro003,1,-9.13,2.05,2.05 +SAMPL8-15_micro000,SAMPL8-15_micro004,1,-8.85,2.05,2.05 +SAMPL8-15_micro000,SAMPL8-15_micro001,0,0.0,2.05,2.05 +SAMPL8-15_micro000,SAMPL8-15_micro002,0,-0.0,2.05,2.05 +SAMPL8-16_micro000,SAMPL8-16_micro001,1,-11.04,2.05,2.05 +SAMPL8-16_micro000,SAMPL8-16_micro003,1,-15.78,2.05,2.05 +SAMPL8-16_micro000,SAMPL8-16_micro004,1,-7.98,2.05,2.05 +SAMPL8-16_micro000,SAMPL8-16_micro006,1,-7.49,2.05,2.05 +SAMPL8-16_micro000,SAMPL8-16_micro008,1,-11.08,2.05,2.05 +SAMPL8-16_micro000,SAMPL8-16_micro009,1,-12.51,2.05,2.05 +SAMPL8-16_micro000,SAMPL8-16_micro010,1,-9.27,2.05,2.05 +SAMPL8-16_micro000,SAMPL8-16_micro002,0,-5.86,2.05,2.05 +SAMPL8-17_micro000,SAMPL8-17_micro001,-1,16.4,2.05,2.05 +SAMPL8-17_micro000,SAMPL8-17_micro005,-1,7.19,2.05,2.05 +SAMPL8-18_micro000,SAMPL8-18_micro005,-1,5.47,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro010,-1,7.21,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro011,-1,11.67,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro001,1,-10.83,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro004,1,-6.61,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro005,1,-6.61,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro006,1,-0.0,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro008,1,-0.0,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro009,1,-0.0,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro016,1,-5.54,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro018,1,-0.0,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro019,1,-0.0,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro022,1,-1.98,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro023,1,-1.59,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro002,2,-7.34,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro003,2,-4.16,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro002,1,-4.84,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro003,1,-5.75,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro005,1,4.24,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro006,1,-4.5,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro007,1,0.0,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro011,1,-10.98,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro014,1,5.3,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro015,1,-4.52,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro016,1,-6.28,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro025,1,-0.0,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro026,1,-5.33,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro028,1,-0.0,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro001,0,-0.0,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro003,-1,9.44,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro006,-1,5.86,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro007,-1,6.98,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro009,-1,11.72,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro011,-1,12.35,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro014,-1,7.34,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro016,-1,19.2,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro018,-1,5.4,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro019,-1,12.92,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro020,-1,4.91,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro022,-1,5.17,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro024,-1,4.91,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro026,-1,5.33,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro027,-1,5.25,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro001,-2,17.14,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro002,-2,21.92,2.05,2.05 +SAMPL8-22_micro000,SAMPL8-22_micro001,-1,7.34,2.05,2.05 +SAMPL8-22_micro000,SAMPL8-22_micro002,0,-2.41,2.05,2.05 +SAMPL8-22_micro000,SAMPL8-22_micro003,0,-0.0,2.05,2.05 +SAMPL8-23_micro000,SAMPL8-23_micro002,-1,11.08,2.05,2.05 +SAMPL8-23_micro000,SAMPL8-23_micro005,-1,14.99,2.05,2.05 +SAMPL8-23_micro000,SAMPL8-23_micro001,1,-4.41,2.05,2.05 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-4.77,2.05,2.05 +SAMPL8-23_micro000,SAMPL8-23_micro003,0,5.24,2.05,2.05 +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Robert Raddi + +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +Temple University + +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name of the method should not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +AdaBoost + +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +0.16 hr (compute features, 4-6 CPUs) +0.15 hr (prediction calculations, 4-6 CPUs) +0.31 hr (total, 4-6 CPUs) +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +1.0 hr to train the model (4 CPUs) +3 GHz 6-Core Intel Core i5 + +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +In order of usage (1st listed is used the most) +RDKit 2020.03.4 +pandas 1.0.3 +numpy 1.18.2 +scikit-learn 0.22.1 +openeye-toolkits 2019.10.2 +openforcefield 0.6.0 + +# METHOD CATEGORY SECTION +# +# State if your prediction method is better classified as an +# experimental database lookup (DL), linear free energy relationship (LFER), +# quantitative structure-property relationship or machine learning (QSPR/ML), +# quantum mechanics without empirical correction (QM) model, quantum mechanics with +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular +# mechanics (QM+MM), or Other, using the following category labels: +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`. +# +# Pick only one category label. +# The `Category:` keyword is required. +Category: +QSPR/ML + +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# Use as many lines of text as you need. +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. +Method: +This submission uses a method that predicts microscopic pKa values that are directly related to relative free energies following the work by Gunner et al.\cite{gunner2020standard} in units of kcal/mol. Our method uses our publicly avialable database (http://doi.org/10.5281/zenodo.5027418) with recomputed AM1BCC partial charge features (AM1BCCELF10) from OpenEye. Previously, we used a DeepGP model to predict SAMPL6 & SAMPL7 molecules\cite{raddi2021stacking}. Here, we blindly test the DeepGP model on the SAMPL8 small moleculue set in addition to the following machine learning (ML) models: Random Forest, AdaBoost and XGBoost. Model parameters for AdaBoost and XGBoost follow a recent work from Yang et al.\cite{yang2020holistic}. Model parameters for the DeepGP and the Random Forest models are presented in the work from Raddi et al\cite{raddi2021stacking}. Note that similarity filtering was only used for the DeepGP model due to it's slight performance enhancements. The ten feature calculations were closely followed from Bannan et al.\cite{bannan2018sampl6} with the exception of changing AM1BCC to AM1BCCELF10 partial charges. Our hand curated training set consists of approximately 3000 small molecules entirely from open-source databases. 5-fold model validation for each of these ML methods using our database results in very similar performance. +Statistical uncertainty (SEM) for the relative free energies was calculated during model validation and standard errors for each microtransition was calculated using 10-round bootstrapping. The standard Gaussian process model automatically provides uncertainties that correspond to how closely the molecule of interest overlaps with the molecules in the training set, so no bootstrapping was needed here. Note that the predictions reported have have high uncertainty due to the lack of chemical space in the training set as well as the lack of similarity of the molecules of interest to that of the molecules found in the training set. + +//ref.bib +@article{raddi2021stacking, + title={Stacking Gaussian Processes to Improve pKa Predictions in the SAMPL7 Challenge}, + author={Raddi, Robert and Voelz, Vincent}, + year={2021} +} +@article{yang2020holistic, + title={Holistic Prediction of the pKa in Diverse Solvents Based on a Machine-Learning Approach}, + author={Yang, Qi and Li, Yao and Yang, Jin-Dong and Liu, Yidi and Zhang, Long and Luo, Sanzhong and Cheng, Jin-Pei}, + journal={Angewandte Chemie}, + volume={132}, + number={43}, + pages={19444--19453}, + year={2020}, + publisher={Wiley Online Library} +} +@article{bannan2018sampl6, + title={SAMPL6 challenge results from $pK_a$ predictions based on a general Gaussian process model}, + author={Bannan, Caitlin C and Mobley, David L and Skillman, A Geoffrey}, + journal={Journal of computer-aided molecular design}, + volume={32}, + number={10}, + pages={1165--1177}, + year={2018}, + publisher={Springer} +} +@article{gunner2020standard, + title={Standard state free energies, not pK as, are ideal for describing small molecule protonation and tautomeric states}, + author={Gunner, Marilyn R and Murakami, Taichi and Rustenburg, Ari{\"e}n S and I{\c{s}}{\i}k, Mehtap and Chodera, John D}, + journal={Journal of Computer-Aided Molecular Design}, + pages={1--13}, + year={2020}, + publisher={Springer} +} + + + +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) +Ranked: +False + diff --git a/physical_properties/pKa/submissions/pKa-RobertRaddi_DeepGP.csv b/physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_DeepGP.csv similarity index 100% rename from physical_properties/pKa/submissions/pKa-RobertRaddi_DeepGP.csv rename to physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_DeepGP.csv diff --git a/physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_DeepGP_modified.csv b/physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_DeepGP_modified.csv new file mode 100644 index 0000000..a433f40 --- /dev/null +++ b/physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_DeepGP_modified.csv @@ -0,0 +1,267 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction) +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# PREDICTION SECTION +# +# It is mandatory to submit relative free energy (RFE) predictions for all 22 molecules. Incomplete submissions will not be accepted. +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty. +# +# The data in each prediction line should be structured as follows: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty +# +# If you have evaluated additional microstates, include the following: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +# +# The molecule ID of the other microstate needs to be in the format: `SMXX_extra001` (number can vary) +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders, +# Please send the `.mol2` file to the email listed on the instructions page. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: +SAMPL8-1_micro000,SAMPL8-1_micro001,-1,11.61,4.73,4.73 +SAMPL8-1_micro000,SAMPL8-1_micro002,-1,8.08,3.14,3.14 +SAMPL8-1_micro000,SAMPL8-1_micro003,-1,13.16,4.95,4.95 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,6.54,2.46,2.46 +SAMPL8-1_micro000,SAMPL8-1_micro005,-1,7.16,2.83,2.83 +SAMPL8-1_micro000,SAMPL8-1_micro008,-1,13.22,4.97,4.97 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,6.53,2.43,2.43 +SAMPL8-2_micro000,SAMPL8-2_micro002,0,-9.11,2.73,2.73 +SAMPL8-3_micro000,SAMPL8-3_micro001,-1,20.25,5.86,5.86 +SAMPL8-3_micro000,SAMPL8-3_micro003,-1,28.68,8.8,8.8 +SAMPL8-3_micro000,SAMPL8-3_micro005,-1,10.87,2.9,2.9 +SAMPL8-3_micro000,SAMPL8-3_micro009,-1,16.88,5.96,5.96 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,9.98,2.94,2.94 +SAMPL8-3_micro000,SAMPL8-3_micro011,-1,26.76,8.85,8.85 +SAMPL8-3_micro000,SAMPL8-3_micro015,-1,24.59,3.84,3.84 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,21.27,5.79,5.79 +SAMPL8-3_micro000,SAMPL8-3_micro017,-1,28.02,8.82,8.82 +SAMPL8-3_micro000,SAMPL8-3_micro018,-1,20.53,5.84,5.84 +SAMPL8-3_micro000,SAMPL8-3_micro020,-1,10.04,2.94,2.94 +SAMPL8-3_micro000,SAMPL8-3_micro002,0,8.31,3.04,3.04 +SAMPL8-4_micro000,SAMPL8-4_micro003,-1,11.76,1.77,1.77 +SAMPL8-4_micro000,SAMPL8-4_micro005,-1,3.99,2.4,2.4 +SAMPL8-4_micro000,SAMPL8-4_micro006,-1,11.71,2.01,2.01 +SAMPL8-4_micro000,SAMPL8-4_micro008,-1,3.59,2.2,2.2 +SAMPL8-5_micro000,SAMPL8-5_micro007,-1,6.12,2.35,2.35 +SAMPL8-5_micro000,SAMPL8-5_micro003,1,-6.61,2.65,2.65 +SAMPL8-5_micro000,SAMPL8-5_micro006,1,-20.15,5.82,5.82 +SAMPL8-6_micro000,SAMPL8-6_micro001,-1,5.55,2.35,2.35 +SAMPL8-6_micro000,SAMPL8-6_micro006,-1,13.28,2.24,2.24 +SAMPL8-6_micro000,SAMPL8-6_micro002,1,-18.15,4.99,4.99 +SAMPL8-6_micro000,SAMPL8-6_micro003,1,-9.54,2.94,2.94 +SAMPL8-7_micro000,SAMPL8-7_micro001,-1,7.0,2.28,2.28 +SAMPL8-8_micro000,SAMPL8-8_micro001,1,-5.28,1.85,1.85 +SAMPL8-8_micro000,SAMPL8-8_micro002,1,-6.71,2.8,2.8 +SAMPL8-9_micro000,SAMPL8-9_micro001,-1,5.44,2.11,2.11 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-12.64,1.75,1.75 +SAMPL8-12_micro000,SAMPL8-12_micro001,-1,17.32,6.12,6.12 +SAMPL8-12_micro000,SAMPL8-12_micro002,0,-2.41,8.94,8.94 +SAMPL8-14_micro000,SAMPL8-14_micro004,-1,38.73,9.76,9.76 +SAMPL8-14_micro000,SAMPL8-14_micro005,-1,24.81,6.17,6.17 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,12.23,2.23,2.23 +SAMPL8-14_micro000,SAMPL8-14_micro009,-1,11.39,2.83,2.83 +SAMPL8-14_micro000,SAMPL8-14_micro010,-1,10.24,3.38,3.38 +SAMPL8-14_micro000,SAMPL8-14_micro012,-1,26.37,6.41,6.41 +SAMPL8-14_micro000,SAMPL8-14_micro019,-1,28.39,6.09,6.09 +SAMPL8-14_micro000,SAMPL8-14_micro021,-1,26.95,6.27,6.27 +SAMPL8-14_micro000,SAMPL8-14_micro022,-1,12.14,2.32,2.32 +SAMPL8-14_micro000,SAMPL8-14_micro025,-1,21.3,6.91,6.91 +SAMPL8-14_micro000,SAMPL8-14_micro027,-1,12.26,2.21,2.21 +SAMPL8-14_micro000,SAMPL8-14_micro028,-1,12.3,2.2,2.2 +SAMPL8-14_micro000,SAMPL8-14_micro029,-1,12.34,2.11,2.11 +SAMPL8-14_micro000,SAMPL8-14_micro032,-1,12.22,2.24,2.24 +SAMPL8-14_micro000,SAMPL8-14_micro001,-2,21.44,4.2,4.2 +SAMPL8-14_micro000,SAMPL8-14_micro003,-2,17.1,5.55,5.55 +SAMPL8-14_micro000,SAMPL8-14_micro002,0,11.61,13.42,13.42 +SAMPL8-15_micro000,SAMPL8-15_micro003,1,-9.69,2.22,2.22 +SAMPL8-15_micro000,SAMPL8-15_micro004,1,-6.4,2.44,2.44 +SAMPL8-16_micro000,SAMPL8-16_micro001,1,-12.33,2.76,2.76 +SAMPL8-16_micro000,SAMPL8-16_micro003,1,-21.56,5.28,5.28 +SAMPL8-16_micro000,SAMPL8-16_micro004,1,-4.88,2.55,2.55 +SAMPL8-16_micro000,SAMPL8-16_micro006,1,-11.61,2.73,2.73 +SAMPL8-16_micro000,SAMPL8-16_micro008,1,-12.13,2.76,2.76 +SAMPL8-16_micro000,SAMPL8-16_micro009,1,-20.46,5.29,5.29 +SAMPL8-16_micro000,SAMPL8-16_micro010,1,-5.3,2.68,2.68 +SAMPL8-16_micro000,SAMPL8-16_micro002,0,-9.74,2.53,2.53 +SAMPL8-17_micro000,SAMPL8-17_micro001,-1,15.27,4.07,4.07 +SAMPL8-17_micro000,SAMPL8-17_micro005,-1,5.89,1.77,1.77 +SAMPL8-18_micro000,SAMPL8-18_micro005,-1,6.89,2.32,2.32 +SAMPL8-19_micro000,SAMPL8-19_micro010,-1,12.79,3.0,3.0 +SAMPL8-19_micro000,SAMPL8-19_micro011,-1,13.69,3.57,3.57 +SAMPL8-19_micro000,SAMPL8-19_micro001,1,-7.19,1.79,1.79 +SAMPL8-19_micro000,SAMPL8-19_micro004,1,-6.77,1.78,1.78 +SAMPL8-19_micro000,SAMPL8-19_micro005,1,-3.0,2.52,2.52 +SAMPL8-19_micro000,SAMPL8-19_micro016,1,-8.85,2.04,2.04 +SAMPL8-19_micro000,SAMPL8-19_micro022,1,0.08,2.0,2.0 +SAMPL8-19_micro000,SAMPL8-19_micro023,1,-0.34,2.06,2.06 +SAMPL8-19_micro000,SAMPL8-19_micro002,2,-7.34,2.83,2.83 +SAMPL8-19_micro000,SAMPL8-19_micro003,2,-2.27,2.02,2.02 +SAMPL8-20_micro000,SAMPL8-20_micro002,1,-4.45,2.59,2.59 +SAMPL8-20_micro000,SAMPL8-20_micro003,1,-4.51,2.29,2.29 +SAMPL8-20_micro000,SAMPL8-20_micro005,1,5.08,2.08,2.08 +SAMPL8-20_micro000,SAMPL8-20_micro006,1,-5.62,1.94,1.94 +SAMPL8-20_micro000,SAMPL8-20_micro011,1,-8.14,2.57,2.57 +SAMPL8-20_micro000,SAMPL8-20_micro014,1,9.97,2.11,2.11 +SAMPL8-20_micro000,SAMPL8-20_micro015,1,3.92,3.14,3.14 +SAMPL8-20_micro000,SAMPL8-20_micro016,1,-5.7,1.94,1.94 +SAMPL8-20_micro000,SAMPL8-20_micro026,1,-9.36,2.88,2.88 +SAMPL8-21_micro000,SAMPL8-21_micro003,-1,22.82,6.85,6.85 +SAMPL8-21_micro000,SAMPL8-21_micro006,-1,9.8,3.11,3.11 +SAMPL8-21_micro000,SAMPL8-21_micro007,-1,9.12,2.76,2.76 +SAMPL8-21_micro000,SAMPL8-21_micro009,-1,19.4,6.52,6.52 +SAMPL8-21_micro000,SAMPL8-21_micro011,-1,15.02,6.25,6.25 +SAMPL8-21_micro000,SAMPL8-21_micro014,-1,9.23,2.86,2.86 +SAMPL8-21_micro000,SAMPL8-21_micro016,-1,19.03,6.26,6.26 +SAMPL8-21_micro000,SAMPL8-21_micro018,-1,12.59,2.29,2.29 +SAMPL8-21_micro000,SAMPL8-21_micro019,-1,15.97,6.79,6.79 +SAMPL8-21_micro000,SAMPL8-21_micro020,-1,12.73,2.09,2.09 +SAMPL8-21_micro000,SAMPL8-21_micro022,-1,12.59,2.06,2.06 +SAMPL8-21_micro000,SAMPL8-21_micro024,-1,11.85,2.2,2.2 +SAMPL8-21_micro000,SAMPL8-21_micro026,-1,12.51,2.3,2.3 +SAMPL8-21_micro000,SAMPL8-21_micro027,-1,13.1,2.14,2.14 +SAMPL8-21_micro000,SAMPL8-21_micro001,-2,35.43,7.9,7.9 +SAMPL8-21_micro000,SAMPL8-21_micro002,-2,48.96,10.56,10.56 +SAMPL8-22_micro000,SAMPL8-22_micro001,-1,4.99,2.14,2.14 +SAMPL8-22_micro000,SAMPL8-22_micro002,0,-2.18,3.26,3.26 +SAMPL8-23_micro000,SAMPL8-23_micro002,-1,12.66,2.01,2.01 +SAMPL8-23_micro000,SAMPL8-23_micro005,-1,25.01,4.79,4.79 +SAMPL8-23_micro000,SAMPL8-23_micro001,1,-3.17,2.56,2.56 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-5.72,3.9,3.9 +SAMPL8-23_micro000,SAMPL8-23_micro003,0,5.31,3.27,3.27 +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Robert Raddi + +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +Temple University + +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name of the method should not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +Deep Gaussian Process + +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +0.16 hr (compute features, 4-6 CPUs) +0.15 hr (prediction calculations, 4-6 CPUs) +0.31 hr (total, 4-6 CPUs) +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +1.0 hr to train the model (4 CPUs) +3 GHz 6-Core Intel Core i5 + +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +In order of usage (1st listed is used the most) +RDKit 2020.03.4 +pandas 1.0.3 +numpy 1.18.2 +scikit-learn 0.22.1 +openeye-toolkits 2019.10.2 +openforcefield 0.6.0 + +# METHOD CATEGORY SECTION +# +# State if your prediction method is better classified as an +# experimental database lookup (DL), linear free energy relationship (LFER), +# quantitative structure-property relationship or machine learning (QSPR/ML), +# quantum mechanics without empirical correction (QM) model, quantum mechanics with +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular +# mechanics (QM+MM), or Other, using the following category labels: +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`. +# +# Pick only one category label. +# The `Category:` keyword is required. +Category: +QSPR/ML + +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# Use as many lines of text as you need. +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. +Method: +This submission uses a method that predicts microscopic pKa values that are directly related to relative free energies following the work by Gunner et al.\cite{gunner2020standard} in units of kcal/mol. Our method uses our publicly avialable database (http://doi.org/10.5281/zenodo.5027418) with recomputed AM1BCC partial charge features (AM1BCCELF10) from OpenEye. Previously, we used a DeepGP model to predict SAMPL6 & SAMPL7 molecules\cite{raddi2021stacking}. Here, we blindly test the DeepGP model on the SAMPL8 small moleculue set in addition to the following machine learning (ML) models: Random Forest, AdaBoost and XGBoost. Model parameters for AdaBoost and XGBoost follow a recent work from Yang et al.\cite{yang2020holistic}. Model parameters for the DeepGP and the Random Forest models are presented in the work from Raddi et al\cite{raddi2021stacking}. Note that similarity filtering was only used for the DeepGP model due to it's slight performance enhancements. The ten feature calculations were closely followed from Bannan et al.\cite{bannan2018sampl6} with the exception of changing AM1BCC to AM1BCCELF10 partial charges. Our hand curated training set consists of approximately 3000 small molecules entirely from open-source databases. 5-fold model validation for each of these ML methods using our database results in very similar performance. +Statistical uncertainty (SEM) for the relative free energies was calculated during model validation and standard errors for each microtransition was calculated using 10-round bootstrapping. The standard Gaussian process model automatically provides uncertainties that correspond to how closely the molecule of interest overlaps with the molecules in the training set, so no bootstrapping was needed here. Note that the predictions reported have have high uncertainty due to the lack of chemical space in the training set as well as the lack of similarity of the molecules of interest to that of the molecules found in the training set. + +//ref.bib +@article{raddi2021stacking, + title={Stacking Gaussian Processes to Improve pKa Predictions in the SAMPL7 Challenge}, + author={Raddi, Robert and Voelz, Vincent}, + year={2021} +} +@article{yang2020holistic, + title={Holistic Prediction of the pKa in Diverse Solvents Based on a Machine-Learning Approach}, + author={Yang, Qi and Li, Yao and Yang, Jin-Dong and Liu, Yidi and Zhang, Long and Luo, Sanzhong and Cheng, Jin-Pei}, + journal={Angewandte Chemie}, + volume={132}, + number={43}, + pages={19444--19453}, + year={2020}, + publisher={Wiley Online Library} +} +@article{bannan2018sampl6, + title={SAMPL6 challenge results from $pK_a$ predictions based on a general Gaussian process model}, + author={Bannan, Caitlin C and Mobley, David L and Skillman, A Geoffrey}, + journal={Journal of computer-aided molecular design}, + volume={32}, + number={10}, + pages={1165--1177}, + year={2018}, + publisher={Springer} +} +@article{gunner2020standard, + title={Standard state free energies, not pK as, are ideal for describing small molecule protonation and tautomeric states}, + author={Gunner, Marilyn R and Murakami, Taichi and Rustenburg, Ari{\"e}n S and I{\c{s}}{\i}k, Mehtap and Chodera, John D}, + journal={Journal of Computer-Aided Molecular Design}, + pages={1--13}, + year={2020}, + publisher={Springer} +} + + +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) +Ranked: +True + diff --git a/physical_properties/pKa/submissions/pKa-RobertRaddi_RF.csv b/physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_RF.csv similarity index 100% rename from physical_properties/pKa/submissions/pKa-RobertRaddi_RF.csv rename to physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_RF.csv diff --git a/physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_RF_modified.csv b/physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_RF_modified.csv new file mode 100644 index 0000000..b91fb90 --- /dev/null +++ b/physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_RF_modified.csv @@ -0,0 +1,285 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction) +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# PREDICTION SECTION +# +# It is mandatory to submit relative free energy (RFE) predictions for all 22 molecules. Incomplete submissions will not be accepted. +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty. +# +# The data in each prediction line should be structured as follows: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty +# +# If you have evaluated additional microstates, include the following: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +# +# The molecule ID of the other microstate needs to be in the format: `SMXX_extra001` (number can vary) +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders, +# Please send the `.mol2` file to the email listed on the instructions page. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: +SAMPL8-1_micro000,SAMPL8-1_micro001,-1,16.54,2.02,0.57 +SAMPL8-1_micro000,SAMPL8-1_micro002,-1,7.53,2.02,0.28 +SAMPL8-1_micro000,SAMPL8-1_micro003,-1,15.76,2.02,0.61 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,6.62,2.02,0.3 +SAMPL8-1_micro000,SAMPL8-1_micro005,-1,7.62,2.02,0.4 +SAMPL8-1_micro000,SAMPL8-1_micro008,-1,18.65,2.02,0.57 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,6.65,2.02,0.21 +SAMPL8-2_micro000,SAMPL8-2_micro003,-1,-0.0,2.02,0.01 +SAMPL8-2_micro000,SAMPL8-2_micro002,0,-6.73,2.02,0.29 +SAMPL8-3_micro000,SAMPL8-3_micro001,-1,12.46,2.02,0.53 +SAMPL8-3_micro000,SAMPL8-3_micro003,-1,29.12,2.02,1.35 +SAMPL8-3_micro000,SAMPL8-3_micro005,-1,9.47,2.02,0.43 +SAMPL8-3_micro000,SAMPL8-3_micro009,-1,18.58,2.02,0.79 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,6.6,2.02,0.32 +SAMPL8-3_micro000,SAMPL8-3_micro011,-1,28.1,2.02,1.0 +SAMPL8-3_micro000,SAMPL8-3_micro015,-1,25.36,2.02,0.29 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,12.28,2.02,0.55 +SAMPL8-3_micro000,SAMPL8-3_micro017,-1,28.02,2.02,1.24 +SAMPL8-3_micro000,SAMPL8-3_micro018,-1,12.74,2.02,0.61 +SAMPL8-3_micro000,SAMPL8-3_micro020,-1,7.8,2.02,0.45 +SAMPL8-3_micro000,SAMPL8-3_micro002,0,10.22,2.02,0.36 +SAMPL8-4_micro000,SAMPL8-4_micro003,-1,6.68,2.02,0.43 +SAMPL8-4_micro000,SAMPL8-4_micro005,-1,7.63,2.02,0.53 +SAMPL8-4_micro000,SAMPL8-4_micro006,-1,6.62,2.02,0.43 +SAMPL8-4_micro000,SAMPL8-4_micro008,-1,4.7,2.02,0.46 +SAMPL8-5_micro000,SAMPL8-5_micro002,-1,-0.0,2.02,0.01 +SAMPL8-5_micro000,SAMPL8-5_micro007,-1,6.24,2.02,0.1 +SAMPL8-5_micro000,SAMPL8-5_micro003,1,-4.1,2.02,0.28 +SAMPL8-5_micro000,SAMPL8-5_micro006,1,-13.54,2.02,0.56 +SAMPL8-5_micro000,SAMPL8-5_micro001,0,0.0,2.02,0.01 +SAMPL8-6_micro000,SAMPL8-6_micro001,-1,6.31,2.02,0.29 +SAMPL8-6_micro000,SAMPL8-6_micro006,-1,8.33,2.02,0.31 +SAMPL8-6_micro000,SAMPL8-6_micro009,-1,-0.0,2.02,0.01 +SAMPL8-6_micro000,SAMPL8-6_micro002,1,-19.15,2.02,0.58 +SAMPL8-6_micro000,SAMPL8-6_micro003,1,-10.53,2.02,0.41 +SAMPL8-7_micro000,SAMPL8-7_micro001,-1,10.48,2.02,0.35 +SAMPL8-8_micro000,SAMPL8-8_micro001,1,-4.42,2.02,0.35 +SAMPL8-8_micro000,SAMPL8-8_micro002,1,-5.49,2.02,0.29 +SAMPL8-9_micro000,SAMPL8-9_micro001,-1,10.99,2.02,0.29 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-8.88,2.02,0.27 +SAMPL8-12_micro000,SAMPL8-12_micro001,-1,17.6,2.02,0.41 +SAMPL8-12_micro000,SAMPL8-12_micro002,0,0.14,2.02,0.83 +SAMPL8-12_micro000,SAMPL8-12_micro003,0,-0.0,2.02,0.01 +SAMPL8-14_micro000,SAMPL8-14_micro004,-1,31.69,2.02,0.58 +SAMPL8-14_micro000,SAMPL8-14_micro005,-1,13.82,2.02,0.69 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,8.01,2.02,0.25 +SAMPL8-14_micro000,SAMPL8-14_micro009,-1,5.74,2.02,0.34 +SAMPL8-14_micro000,SAMPL8-14_micro010,-1,7.83,2.02,0.41 +SAMPL8-14_micro000,SAMPL8-14_micro012,-1,10.02,2.02,0.63 +SAMPL8-14_micro000,SAMPL8-14_micro019,-1,10.86,2.02,0.6 +SAMPL8-14_micro000,SAMPL8-14_micro021,-1,10.34,2.02,0.5 +SAMPL8-14_micro000,SAMPL8-14_micro022,-1,8.3,2.02,0.4 +SAMPL8-14_micro000,SAMPL8-14_micro025,-1,15.99,2.02,0.77 +SAMPL8-14_micro000,SAMPL8-14_micro027,-1,8.47,2.02,0.37 +SAMPL8-14_micro000,SAMPL8-14_micro028,-1,8.29,2.02,0.3 +SAMPL8-14_micro000,SAMPL8-14_micro029,-1,8.01,2.02,0.33 +SAMPL8-14_micro000,SAMPL8-14_micro032,-1,8.23,2.02,0.45 +SAMPL8-14_micro000,SAMPL8-14_micro001,-2,11.29,2.02,0.55 +SAMPL8-14_micro000,SAMPL8-14_micro003,-2,18.06,2.02,0.83 +SAMPL8-14_micro000,SAMPL8-14_micro002,0,3.58,2.02,1.06 +SAMPL8-15_micro000,SAMPL8-15_micro003,1,-7.86,2.02,0.37 +SAMPL8-15_micro000,SAMPL8-15_micro004,1,-7.99,2.02,0.3 +SAMPL8-15_micro000,SAMPL8-15_micro001,0,0.0,2.02,0.01 +SAMPL8-15_micro000,SAMPL8-15_micro002,0,-0.0,2.02,0.01 +SAMPL8-16_micro000,SAMPL8-16_micro001,1,-10.18,2.02,0.32 +SAMPL8-16_micro000,SAMPL8-16_micro003,1,-17.65,2.02,0.7 +SAMPL8-16_micro000,SAMPL8-16_micro004,1,-7.19,2.02,0.25 +SAMPL8-16_micro000,SAMPL8-16_micro006,1,-6.78,2.02,0.33 +SAMPL8-16_micro000,SAMPL8-16_micro008,1,-10.47,2.02,0.36 +SAMPL8-16_micro000,SAMPL8-16_micro009,1,-17.69,2.02,0.81 +SAMPL8-16_micro000,SAMPL8-16_micro010,1,-6.93,2.02,0.39 +SAMPL8-16_micro000,SAMPL8-16_micro002,0,-9.46,2.02,0.38 +SAMPL8-17_micro000,SAMPL8-17_micro001,-1,15.0,2.02,0.85 +SAMPL8-17_micro000,SAMPL8-17_micro005,-1,6.29,2.02,0.31 +SAMPL8-18_micro000,SAMPL8-18_micro005,-1,6.26,2.02,0.63 +SAMPL8-19_micro000,SAMPL8-19_micro010,-1,7.4,2.02,0.4 +SAMPL8-19_micro000,SAMPL8-19_micro011,-1,12.4,2.02,0.17 +SAMPL8-19_micro000,SAMPL8-19_micro001,1,-7.65,2.02,0.4 +SAMPL8-19_micro000,SAMPL8-19_micro004,1,-7.73,2.02,0.17 +SAMPL8-19_micro000,SAMPL8-19_micro005,1,-5.61,2.02,0.34 +SAMPL8-19_micro000,SAMPL8-19_micro006,1,-0.0,2.02,0.01 +SAMPL8-19_micro000,SAMPL8-19_micro008,1,-0.0,2.02,0.01 +SAMPL8-19_micro000,SAMPL8-19_micro009,1,-0.0,2.02,0.01 +SAMPL8-19_micro000,SAMPL8-19_micro016,1,-6.18,2.02,0.26 +SAMPL8-19_micro000,SAMPL8-19_micro018,1,-0.0,2.02,0.01 +SAMPL8-19_micro000,SAMPL8-19_micro019,1,-0.0,2.02,0.01 +SAMPL8-19_micro000,SAMPL8-19_micro022,1,-3.44,2.02,0.53 +SAMPL8-19_micro000,SAMPL8-19_micro023,1,-1.55,2.02,0.29 +SAMPL8-19_micro000,SAMPL8-19_micro002,2,-6.35,2.02,0.26 +SAMPL8-19_micro000,SAMPL8-19_micro003,2,-4.36,2.02,0.42 +SAMPL8-20_micro000,SAMPL8-20_micro002,1,-5.03,2.02,0.16 +SAMPL8-20_micro000,SAMPL8-20_micro003,1,-11.06,2.02,0.4 +SAMPL8-20_micro000,SAMPL8-20_micro005,1,4.06,2.02,0.57 +SAMPL8-20_micro000,SAMPL8-20_micro006,1,-4.79,2.02,0.2 +SAMPL8-20_micro000,SAMPL8-20_micro007,1,0.0,2.02,0.01 +SAMPL8-20_micro000,SAMPL8-20_micro011,1,-8.68,2.02,0.36 +SAMPL8-20_micro000,SAMPL8-20_micro014,1,4.16,2.02,0.47 +SAMPL8-20_micro000,SAMPL8-20_micro015,1,-8.88,2.02,0.47 +SAMPL8-20_micro000,SAMPL8-20_micro016,1,-6.16,2.02,0.34 +SAMPL8-20_micro000,SAMPL8-20_micro025,1,-0.0,2.02,0.01 +SAMPL8-20_micro000,SAMPL8-20_micro026,1,-7.22,2.02,0.45 +SAMPL8-20_micro000,SAMPL8-20_micro028,1,-0.0,2.02,0.01 +SAMPL8-20_micro000,SAMPL8-20_micro001,0,-0.0,2.02,0.01 +SAMPL8-21_micro000,SAMPL8-21_micro003,-1,11.85,2.02,0.72 +SAMPL8-21_micro000,SAMPL8-21_micro006,-1,6.65,2.02,0.16 +SAMPL8-21_micro000,SAMPL8-21_micro007,-1,6.92,2.02,0.4 +SAMPL8-21_micro000,SAMPL8-21_micro009,-1,13.37,2.02,0.71 +SAMPL8-21_micro000,SAMPL8-21_micro011,-1,12.56,2.02,0.57 +SAMPL8-21_micro000,SAMPL8-21_micro014,-1,6.77,2.02,0.35 +SAMPL8-21_micro000,SAMPL8-21_micro016,-1,19.59,2.02,0.81 +SAMPL8-21_micro000,SAMPL8-21_micro018,-1,4.22,2.02,0.31 +SAMPL8-21_micro000,SAMPL8-21_micro019,-1,13.61,2.02,0.72 +SAMPL8-21_micro000,SAMPL8-21_micro020,-1,4.92,2.02,0.41 +SAMPL8-21_micro000,SAMPL8-21_micro022,-1,4.02,2.02,0.43 +SAMPL8-21_micro000,SAMPL8-21_micro024,-1,4.66,2.02,0.35 +SAMPL8-21_micro000,SAMPL8-21_micro026,-1,4.51,2.02,0.37 +SAMPL8-21_micro000,SAMPL8-21_micro027,-1,4.92,2.02,0.51 +SAMPL8-21_micro000,SAMPL8-21_micro001,-2,17.12,2.02,1.12 +SAMPL8-21_micro000,SAMPL8-21_micro002,-2,25.77,2.02,1.26 +SAMPL8-22_micro000,SAMPL8-22_micro001,-1,7.95,2.02,0.5 +SAMPL8-22_micro000,SAMPL8-22_micro002,0,-2.8,2.02,0.58 +SAMPL8-22_micro000,SAMPL8-22_micro003,0,-0.0,2.02,0.01 +SAMPL8-23_micro000,SAMPL8-23_micro002,-1,7.6,2.02,0.39 +SAMPL8-23_micro000,SAMPL8-23_micro005,-1,15.23,2.02,1.04 +SAMPL8-23_micro000,SAMPL8-23_micro001,1,-1.21,2.02,0.74 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-2.3,2.02,0.63 +SAMPL8-23_micro000,SAMPL8-23_micro003,0,5.43,2.02,0.35 +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Robert Raddi + +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +Temple University + +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name of the method should not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +Random Forest + +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +0.16 hr (compute features, 4-6 CPUs) +0.15 hr (prediction calculations, 4-6 CPUs) +0.31 hr (total, 4-6 CPUs) +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +1.0 hr to train the model (4 CPUs) +3 GHz 6-Core Intel Core i5 + +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +In order of usage (1st listed is used the most) +RDKit 2020.03.4 +pandas 1.0.3 +numpy 1.18.2 +scikit-learn 0.22.1 +openeye-toolkits 2019.10.2 +openforcefield 0.6.0 + +# METHOD CATEGORY SECTION +# +# State if your prediction method is better classified as an +# experimental database lookup (DL), linear free energy relationship (LFER), +# quantitative structure-property relationship or machine learning (QSPR/ML), +# quantum mechanics without empirical correction (QM) model, quantum mechanics with +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular +# mechanics (QM+MM), or Other, using the following category labels: +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`. +# +# Pick only one category label. +# The `Category:` keyword is required. +Category: +QSPR/ML + +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# Use as many lines of text as you need. +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. +Method: +This submission uses a method that predicts microscopic pKa values that are directly related to relative free energies following the work by Gunner et al.\cite{gunner2020standard} in units of kcal/mol. Our method uses our publicly avialable database (http://doi.org/10.5281/zenodo.5027418) with recomputed AM1BCC partial charge features (AM1BCCELF10) from OpenEye. Previously, we used a DeepGP model to predict SAMPL6 & SAMPL7 molecules\cite{raddi2021stacking}. Here, we blindly test the DeepGP model on the SAMPL8 small moleculue set in addition to the following machine learning (ML) models: Random Forest, AdaBoost and XGBoost. Model parameters for AdaBoost and XGBoost follow a recent work from Yang et al.\cite{yang2020holistic}. Model parameters for the DeepGP and the Random Forest models are presented in the work from Raddi et al\cite{raddi2021stacking}. Note that similarity filtering was only used for the DeepGP model due to it's slight performance enhancements. The ten feature calculations were closely followed from Bannan et al.\cite{bannan2018sampl6} with the exception of changing AM1BCC to AM1BCCELF10 partial charges. Our hand curated training set consists of approximately 3000 small molecules entirely from open-source databases. 5-fold model validation for each of these ML methods using our database results in very similar performance. +Statistical uncertainty (SEM) for the relative free energies was calculated during model validation and standard errors for each microtransition was calculated using 10-round bootstrapping. The standard Gaussian process model automatically provides uncertainties that correspond to how closely the molecule of interest overlaps with the molecules in the training set, so no bootstrapping was needed here. Note that the predictions reported have have high uncertainty due to the lack of chemical space in the training set as well as the lack of similarity of the molecules of interest to that of the molecules found in the training set. + +//ref.bib +@article{raddi2021stacking, + title={Stacking Gaussian Processes to Improve pKa Predictions in the SAMPL7 Challenge}, + author={Raddi, Robert and Voelz, Vincent}, + year={2021} +} +@article{yang2020holistic, + title={Holistic Prediction of the pKa in Diverse Solvents Based on a Machine-Learning Approach}, + author={Yang, Qi and Li, Yao and Yang, Jin-Dong and Liu, Yidi and Zhang, Long and Luo, Sanzhong and Cheng, Jin-Pei}, + journal={Angewandte Chemie}, + volume={132}, + number={43}, + pages={19444--19453}, + year={2020}, + publisher={Wiley Online Library} +} +@article{bannan2018sampl6, + title={SAMPL6 challenge results from $pK_a$ predictions based on a general Gaussian process model}, + author={Bannan, Caitlin C and Mobley, David L and Skillman, A Geoffrey}, + journal={Journal of computer-aided molecular design}, + volume={32}, + number={10}, + pages={1165--1177}, + year={2018}, + publisher={Springer} +} +@article{gunner2020standard, + title={Standard state free energies, not pK as, are ideal for describing small molecule protonation and tautomeric states}, + author={Gunner, Marilyn R and Murakami, Taichi and Rustenburg, Ari{\"e}n S and I{\c{s}}{\i}k, Mehtap and Chodera, John D}, + journal={Journal of Computer-Aided Molecular Design}, + pages={1--13}, + year={2020}, + publisher={Springer} +} + + + +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) +Ranked: +False + diff --git a/physical_properties/pKa/submissions/pKa-RobertRaddi_XGBoost.csv b/physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_XGBoost.csv similarity index 100% rename from physical_properties/pKa/submissions/pKa-RobertRaddi_XGBoost.csv rename to physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_XGBoost.csv diff --git a/physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_XGBoost_modified.csv b/physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_XGBoost_modified.csv new file mode 100644 index 0000000..b83d36c --- /dev/null +++ b/physical_properties/pKa/submissions/Original_submissions/pKa-RobertRaddi_XGBoost_modified.csv @@ -0,0 +1,285 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction) +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# PREDICTION SECTION +# +# It is mandatory to submit relative free energy (RFE) predictions for all 22 molecules. Incomplete submissions will not be accepted. +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty. +# +# The data in each prediction line should be structured as follows: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty +# +# If you have evaluated additional microstates, include the following: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +# +# The molecule ID of the other microstate needs to be in the format: `SMXX_extra001` (number can vary) +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders, +# Please send the `.mol2` file to the email listed on the instructions page. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: +SAMPL8-1_micro000,SAMPL8-1_micro001,-1,13.45,1.98,1.98 +SAMPL8-1_micro000,SAMPL8-1_micro002,-1,8.96,1.98,1.98 +SAMPL8-1_micro000,SAMPL8-1_micro003,-1,12.2,1.98,1.98 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,6.79,1.98,1.98 +SAMPL8-1_micro000,SAMPL8-1_micro005,-1,7.87,1.98,1.98 +SAMPL8-1_micro000,SAMPL8-1_micro008,-1,14.17,1.98,1.98 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,6.75,1.98,1.98 +SAMPL8-2_micro000,SAMPL8-2_micro003,-1,-0.0,1.98,1.98 +SAMPL8-2_micro000,SAMPL8-2_micro002,0,-6.64,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro001,-1,12.4,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro003,-1,22.52,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro005,-1,6.51,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro009,-1,15.6,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,7.81,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro011,-1,23.36,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro015,-1,25.37,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,13.55,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro017,-1,22.35,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro018,-1,12.79,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro020,-1,8.32,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro002,0,8.09,1.98,1.98 +SAMPL8-4_micro000,SAMPL8-4_micro003,-1,9.89,1.98,1.98 +SAMPL8-4_micro000,SAMPL8-4_micro005,-1,7.18,1.98,1.98 +SAMPL8-4_micro000,SAMPL8-4_micro006,-1,10.04,1.98,1.98 +SAMPL8-4_micro000,SAMPL8-4_micro008,-1,5.01,1.98,1.98 +SAMPL8-5_micro000,SAMPL8-5_micro002,-1,-0.0,1.98,1.98 +SAMPL8-5_micro000,SAMPL8-5_micro007,-1,6.88,1.98,1.98 +SAMPL8-5_micro000,SAMPL8-5_micro003,1,-2.98,1.98,1.98 +SAMPL8-5_micro000,SAMPL8-5_micro006,1,-12.13,1.98,1.98 +SAMPL8-5_micro000,SAMPL8-5_micro001,0,0.0,1.98,1.98 +SAMPL8-6_micro000,SAMPL8-6_micro001,-1,5.99,1.98,1.98 +SAMPL8-6_micro000,SAMPL8-6_micro006,-1,8.87,1.98,1.98 +SAMPL8-6_micro000,SAMPL8-6_micro009,-1,-0.0,1.98,1.98 +SAMPL8-6_micro000,SAMPL8-6_micro002,1,-21.74,1.98,1.98 +SAMPL8-6_micro000,SAMPL8-6_micro003,1,-9.4,1.98,1.98 +SAMPL8-7_micro000,SAMPL8-7_micro001,-1,10.5,1.98,1.98 +SAMPL8-8_micro000,SAMPL8-8_micro001,1,-6.38,1.98,1.98 +SAMPL8-8_micro000,SAMPL8-8_micro002,1,-5.3,1.98,1.98 +SAMPL8-9_micro000,SAMPL8-9_micro001,-1,11.43,1.98,1.98 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-10.79,1.98,1.98 +SAMPL8-12_micro000,SAMPL8-12_micro001,-1,19.85,1.98,1.98 +SAMPL8-12_micro000,SAMPL8-12_micro002,0,2.25,1.98,1.98 +SAMPL8-12_micro000,SAMPL8-12_micro003,0,-0.0,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro004,-1,27.84,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro005,-1,17.16,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,6.82,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro009,-1,5.4,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro010,-1,6.49,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro012,-1,9.15,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro019,-1,10.53,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro021,-1,10.37,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro022,-1,6.22,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro025,-1,12.97,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro027,-1,8.43,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro028,-1,7.73,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro029,-1,6.12,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro032,-1,7.04,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro001,-2,11.21,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro003,-2,21.04,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro002,0,-3.16,1.98,1.98 +SAMPL8-15_micro000,SAMPL8-15_micro003,1,-8.01,1.98,1.98 +SAMPL8-15_micro000,SAMPL8-15_micro004,1,-9.04,1.98,1.98 +SAMPL8-15_micro000,SAMPL8-15_micro001,0,0.0,1.98,1.98 +SAMPL8-15_micro000,SAMPL8-15_micro002,0,-0.0,1.98,1.98 +SAMPL8-16_micro000,SAMPL8-16_micro001,1,-8.16,1.98,1.98 +SAMPL8-16_micro000,SAMPL8-16_micro003,1,-14.41,1.98,1.98 +SAMPL8-16_micro000,SAMPL8-16_micro004,1,-6.64,1.98,1.98 +SAMPL8-16_micro000,SAMPL8-16_micro006,1,-5.24,1.98,1.98 +SAMPL8-16_micro000,SAMPL8-16_micro008,1,-8.69,1.98,1.98 +SAMPL8-16_micro000,SAMPL8-16_micro009,1,-16.21,1.98,1.98 +SAMPL8-16_micro000,SAMPL8-16_micro010,1,-8.06,1.98,1.98 +SAMPL8-16_micro000,SAMPL8-16_micro002,0,-6.58,1.98,1.98 +SAMPL8-17_micro000,SAMPL8-17_micro001,-1,14.39,1.98,1.98 +SAMPL8-17_micro000,SAMPL8-17_micro005,-1,7.45,1.98,1.98 +SAMPL8-18_micro000,SAMPL8-18_micro005,-1,5.78,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro010,-1,8.86,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro011,-1,13.01,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro001,1,-6.39,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro004,1,-6.95,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro005,1,-6.0,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro006,1,-0.0,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro008,1,-0.0,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro009,1,-0.0,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro016,1,-4.83,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro018,1,-0.0,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro019,1,-0.0,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro022,1,-5.7,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro023,1,-2.95,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro002,2,-7.34,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro003,2,-3.97,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro002,1,-5.16,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro003,1,-8.88,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro005,1,5.35,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro006,1,-4.89,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro007,1,0.0,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro011,1,-10.36,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro014,1,5.4,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro015,1,-8.26,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro016,1,-6.77,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro025,1,-0.0,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro026,1,-8.31,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro028,1,-0.0,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro001,0,-0.0,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro003,-1,16.22,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro006,-1,7.19,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro007,-1,5.38,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro009,-1,14.88,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro011,-1,12.8,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro014,-1,6.51,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro016,-1,20.11,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro018,-1,5.88,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro019,-1,13.1,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro020,-1,6.57,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro022,-1,4.97,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro024,-1,6.74,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro026,-1,6.07,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro027,-1,6.37,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro001,-2,14.82,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro002,-2,22.5,1.98,1.98 +SAMPL8-22_micro000,SAMPL8-22_micro001,-1,7.67,1.98,1.98 +SAMPL8-22_micro000,SAMPL8-22_micro002,0,-3.19,1.98,1.98 +SAMPL8-22_micro000,SAMPL8-22_micro003,0,-0.0,1.98,1.98 +SAMPL8-23_micro000,SAMPL8-23_micro002,-1,7.18,1.98,1.98 +SAMPL8-23_micro000,SAMPL8-23_micro005,-1,17.2,1.98,1.98 +SAMPL8-23_micro000,SAMPL8-23_micro001,1,-2.01,1.98,1.98 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-0.91,1.98,1.98 +SAMPL8-23_micro000,SAMPL8-23_micro003,0,5.21,1.98,1.98 +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Robert Raddi + +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +Temple University + +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name of the method should not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +XGBoost + +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +0.16 hr (compute features, 4-6 CPUs) +0.15 hr (prediction calculations, 4-6 CPUs) +0.31 hr (total, 4-6 CPUs) +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +1.0 hr to train the model (4 CPUs) +3 GHz 6-Core Intel Core i5 + +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +In order of usage (1st listed is used the most) +RDKit 2020.03.4 +pandas 1.0.3 +numpy 1.18.2 +scikit-learn 0.22.1 +openeye-toolkits 2019.10.2 +openforcefield 0.6.0 + +# METHOD CATEGORY SECTION +# +# State if your prediction method is better classified as an +# experimental database lookup (DL), linear free energy relationship (LFER), +# quantitative structure-property relationship or machine learning (QSPR/ML), +# quantum mechanics without empirical correction (QM) model, quantum mechanics with +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular +# mechanics (QM+MM), or Other, using the following category labels: +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`. +# +# Pick only one category label. +# The `Category:` keyword is required. +Category: +QSPR/ML + +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# Use as many lines of text as you need. +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. +Method: +This submission uses a method that predicts microscopic pKa values that are directly related to relative free energies following the work by Gunner et al.\cite{gunner2020standard} in units of kcal/mol. Our method uses our publicly avialable database (http://doi.org/10.5281/zenodo.5027418) with recomputed AM1BCC partial charge features (AM1BCCELF10) from OpenEye. Previously, we used a DeepGP model to predict SAMPL6 & SAMPL7 molecules\cite{raddi2021stacking}. Here, we blindly test the DeepGP model on the SAMPL8 small moleculue set in addition to the following machine learning (ML) models: Random Forest, AdaBoost and XGBoost. Model parameters for AdaBoost and XGBoost follow a recent work from Yang et al.\cite{yang2020holistic}. Model parameters for the DeepGP and the Random Forest models are presented in the work from Raddi et al\cite{raddi2021stacking}. Note that similarity filtering was only used for the DeepGP model due to it's slight performance enhancements. The ten feature calculations were closely followed from Bannan et al.\cite{bannan2018sampl6} with the exception of changing AM1BCC to AM1BCCELF10 partial charges. Our hand curated training set consists of approximately 3000 small molecules entirely from open-source databases. 5-fold model validation for each of these ML methods using our database results in very similar performance. +Statistical uncertainty (SEM) for the relative free energies was calculated during model validation and standard errors for each microtransition was calculated using 10-round bootstrapping. The standard Gaussian process model automatically provides uncertainties that correspond to how closely the molecule of interest overlaps with the molecules in the training set, so no bootstrapping was needed here. Note that the predictions reported have have high uncertainty due to the lack of chemical space in the training set as well as the lack of similarity of the molecules of interest to that of the molecules found in the training set. + +//ref.bib +@article{raddi2021stacking, + title={Stacking Gaussian Processes to Improve pKa Predictions in the SAMPL7 Challenge}, + author={Raddi, Robert and Voelz, Vincent}, + year={2021} +} +@article{yang2020holistic, + title={Holistic Prediction of the pKa in Diverse Solvents Based on a Machine-Learning Approach}, + author={Yang, Qi and Li, Yao and Yang, Jin-Dong and Liu, Yidi and Zhang, Long and Luo, Sanzhong and Cheng, Jin-Pei}, + journal={Angewandte Chemie}, + volume={132}, + number={43}, + pages={19444--19453}, + year={2020}, + publisher={Wiley Online Library} +} +@article{bannan2018sampl6, + title={SAMPL6 challenge results from $pK_a$ predictions based on a general Gaussian process model}, + author={Bannan, Caitlin C and Mobley, David L and Skillman, A Geoffrey}, + journal={Journal of computer-aided molecular design}, + volume={32}, + number={10}, + pages={1165--1177}, + year={2018}, + publisher={Springer} +} +@article{gunner2020standard, + title={Standard state free energies, not pK as, are ideal for describing small molecule protonation and tautomeric states}, + author={Gunner, Marilyn R and Murakami, Taichi and Rustenburg, Ari{\"e}n S and I{\c{s}}{\i}k, Mehtap and Chodera, John D}, + journal={Journal of Computer-Aided Molecular Design}, + pages={1--13}, + year={2020}, + publisher={Springer} +} + + + +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) +Ranked: +False + diff --git a/physical_properties/pKa/submissions/pKa-ZhiyiWu-1.csv b/physical_properties/pKa/submissions/Original_submissions/pKa-ZhiyiWu-1.csv similarity index 100% rename from physical_properties/pKa/submissions/pKa-ZhiyiWu-1.csv rename to physical_properties/pKa/submissions/Original_submissions/pKa-ZhiyiWu-1.csv diff --git a/physical_properties/pKa/submissions/Original_submissions/pKa-ZhiyiWu-1_modified.csv b/physical_properties/pKa/submissions/Original_submissions/pKa-ZhiyiWu-1_modified.csv new file mode 100644 index 0000000..b05e3c7 --- /dev/null +++ b/physical_properties/pKa/submissions/Original_submissions/pKa-ZhiyiWu-1_modified.csv @@ -0,0 +1,375 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction) +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# PREDICTION SECTION +# +# It is mandatory to submit relative free energy (RFE) predictions for all 22 molecules. Incomplete submissions will not be accepted. +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty. +# Note that we here follow the same sign convention and submission format as the SAMPL7 pKa challenge. +# +# The data in each prediction line should be structured as follows: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty +# +# If you have evaluated additional microstates, include the following: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +# +# The molecule ID of the other microstate needs to be in the format: `SAMPL8-X_extra001` (number can vary) +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders, +# Please send the `.mol2` file to the email listed on the instructions page. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: +SAMPL8-1_micro000,SAMPL8-1_micro001,-1,23.04,1.00,1.00 +SAMPL8-1_micro000,SAMPL8-1_micro002,-1,16.82,1.00,1.00 +SAMPL8-1_micro000,SAMPL8-1_micro003,-1,24.10,1.00,1.00 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,6.25,1.00,1.00 +SAMPL8-1_micro000,SAMPL8-1_micro005,-1,6.01,1.00,1.00 +SAMPL8-1_micro000,SAMPL8-1_micro006,0,19.72,1.00,1.00 +SAMPL8-1_micro000,SAMPL8-1_micro007,0,13.06,1.00,1.00 +SAMPL8-1_micro000,SAMPL8-1_micro008,-1,22.79,1.00,1.00 +SAMPL8-1_micro000,SAMPL8-1_micro009,0,16.23,1.00,1.00 +SAMPL8-1_micro000,SAMPL8-1_micro010,0,11.71,1.00,1.00 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,8.38,1.00,1.00 +SAMPL8-2_micro000,SAMPL8-2_micro002,0,12.24,1.00,1.00 +SAMPL8-2_micro000,SAMPL8-2_micro003,-1,25.16,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro001,-1,6.70,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro002,0,-1.94,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro003,-1,1.29,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro004,0,-7.02,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro005,-1,-0.16,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro006,0,-23.19,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro007,-2,14.47,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro008,0,-2.14,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro009,-1,-3.40,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,-13.41,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro011,-1,4.85,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro012,-2,13.18,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro013,-2,-1.25,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro014,-2,-1.25,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro015,-1,17.31,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,-7.45,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro017,-1,11.90,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro018,-1,4.88,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro019,-2,18.24,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro020,-1,-13.51,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro021,-2,17.30,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro001,0,3.01,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro002,1,-1.39,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro003,-1,8.14,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro004,0,0.02,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro005,-1,8.19,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro006,-1,8.34,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro007,1,-1.41,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro008,-1,10.19,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro009,-1,8.09,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro010,0,-1.62,1.00,1.00 +SAMPL8-5_micro000,SAMPL8-5_micro001,0,0.31,1.00,1.00 +SAMPL8-5_micro000,SAMPL8-5_micro002,-1,18.53,1.00,1.00 +SAMPL8-5_micro000,SAMPL8-5_micro003,1,1.31,1.00,1.00 +SAMPL8-5_micro000,SAMPL8-5_micro004,0,20.90,1.00,1.00 +SAMPL8-5_micro000,SAMPL8-5_micro005,0,9.52,1.00,1.00 +SAMPL8-5_micro000,SAMPL8-5_micro006,1,12.15,1.00,1.00 +SAMPL8-5_micro000,SAMPL8-5_micro007,-1,5.93,1.00,1.00 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+SAMPL8-23_micro000,SAMPL8-23_micro005,-1,4.20,1.00,1.00 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-14.11,1.00,1.00 +SAMPL8-23_micro000,SAMPL8-23_micro007,0,-9.56,1.00,1.00 + + + +# +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Zhiyi Wu; Philip Biggin + +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +University of Oxford + +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name of the method should not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +QM with linear fitting + +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +7000 hours, CPU + +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used to run the simulations. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +All the simulations were performed on 48 core Cascade Lake (Intel Xeon Platinum +8268 CPU @ 2.90GHz) with 392GB RAM on a single node. + +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +Gaussian/16.A.03 +ORCA/4.2.1 +ORCA/5.0.0 +Multiwfn/3.8 +MDAnalysis/develop +uESE/xESE +crest/2.11 +xTB/6.4.1 +obabel/3.1.1 +RDKit/Q1 2021 +shermo/2.2 + + +# METHOD CATEGORY SECTION +# +# State if your prediction method is better classified as an +# experimental database lookup (DL), linear free energy relationship (LFER), +# quantitative structure-property relationship or machine learning (QSPR/ML), +# quantum mechanics without empirical correction (QM) model, quantum mechanics with +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular +# mechanics (QM+MM), or Other, using the following category labels: +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`. +# +# Pick only one category label. +# The `Category:` keyword is required. +Category: +QM + +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# Use as many lines of text as you need. +# +# We strongly encourage you to submit your predicted macro pKa values in this section in consecutive lines following this format: +# compound name, macro pKa, initial formal charge, formal charge after transition, e.g.: +# SAMPL8-1, 3.5, 0, +1 +# This will allow us to check that our analysis of your free energies leads to the same endpoint as your analysis. +# +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. + +Method: +The 3D molecule is generated with obabel and is minimised with xTB at GFN2-xTB +level using alpb implicit water model. Crest is used to generate additional +conformers at the same theoretical level and implicit solvent model. The conformers +are then geometry optimised and vibration analysis are done at B3LYP-D3(BJ)/def2-TZVP +with water as implicit solvent model with Gaussian. The conformer that are +within 6 kcal/mol of the lowest energy conformer are retained. +The conformer that are within 0.1 A RMSD are discarded. +The final energy of these conformer is the sum of +electron energy computed at PWPB95-D3(BJ)/def2-QZVPP with ORCA +thermal correction computed at B3LYP-D3(BJ)/def2-TZVP with Gaussian +solvation free energy computed with uESE/xESE + +The ensemble free energy of all the conformers are then computed with shermo ( +Grimme's entropy interpolation and Truhlar ZPE scaling factor). + + +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) + +Ranked: +True diff --git a/physical_properties/pKa/submissions/pKa_Chemaxon.csv b/physical_properties/pKa/submissions/Original_submissions/pKa_Chemaxon.csv similarity index 100% rename from physical_properties/pKa/submissions/pKa_Chemaxon.csv rename to physical_properties/pKa/submissions/Original_submissions/pKa_Chemaxon.csv diff --git a/physical_properties/pKa/submissions/Original_submissions/pKa_Chemaxon_modified.csv b/physical_properties/pKa/submissions/Original_submissions/pKa_Chemaxon_modified.csv new file mode 100644 index 0000000..1539585 --- /dev/null +++ b/physical_properties/pKa/submissions/Original_submissions/pKa_Chemaxon_modified.csv @@ -0,0 +1,166 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction) +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# PREDICTION SECTION +# +# It is mandatory to submit relative free energy (RFE) predictions for all 22 molecules. Incomplete submissions will not be accepted. +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty. +# Note that we here follow the same sign convention and submission format as the SAMPL7 pKa challenge. +# +# The data in each prediction line should be structured as follows: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty +# +# If you have evaluated additional microstates, include the following: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +# +# The molecule ID of the other microstate needs to be in the format: `SAMPL8-X_extra001` (number can vary) +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders, +# Please send the `.mol2` file to the email listed on the instructions page. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: + +SAMPL8-1_micro000,SAMPL8-1_micro001,-1,3.88,0,0 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,3.49,0,0 +SAMPL8-3_micro000,SAMPL8-3_micro001,-1,4.25,0,0 +SAMPL8-3_micro000,SAMPL8-3_micro007,-2,14.08,0,0 +SAMPL8-3_micro000,SAMPL8-3_Chemaxon_extra001,-3,12.56,0,0 +SAMPL8-4_micro000,SAMPL8-4_micro002,1,-1.02,0,0 +SAMPL8-4_micro000,SAMPL8-4_micro003,-1,3.75,0,0 +SAMPL8-4_micro000,SAMPL8-4_Chemaxon_extra001,-2,18.5,0,0 +SAMPL8-5_micro000,SAMPL8-5_micro007,-1,4.00,0,0 +SAMPL8-6_micro000,SAMPL8-6_micro001,-1,3.50,0,0 +SAMPL8-6_micro000,SAMPL8-6_micro003,1,-2.83,0,0 +SAMPL8-7_micro000,SAMPL8-7_Chemaxon_extra001,1,-7.55,0,0 +SAMPL8-7_micro000,SAMPL8-7_Chemaxon_extra002,-1,14.16,0,0 +SAMPL8-8_micro000,SAMPL8-8_Chemaxon_extra001,1,-2.72,0,0 +SAMPL8-9_micro000,SAMPL8-9_Chemaxon_extra001,1,-7.55,0,0 +SAMPL8-9_micro000,SAMPL8-9_Chemaxon_extra002,-1,14.31,0,0 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-7.11,0,0 +SAMPL8-12_micro000,SAMPL8-12_micro002,1,-6.59,0,0 +SAMPL8-12_micro000,SAMPL8-12_micro003,1,-6.89,0,0 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,11.06,0,0 +SAMPL8-14_micro000,SAMPL8-14_dortmund002,1,-7.16,0,0 +SAMPL8-14_micro000,SAMPL8-14_dortmund001,1,-7.26,0,0 +SAMPL8-15_micro000,SAMPL8-15_micro004,1,-1.53,0,0 +SAMPL8-16_micro000,SAMPL8-16_micro004,1,-5.05,0,0 +SAMPL8-16_micro000,SAMPL8-16_Chemaxon_extra001,-1,11.47,0,0 +SAMPL8-16_micro000,SAMPL8-16_Chemaxon_extra002,-1,25.83,0,0 +SAMPL8-17_micro000,SAMPL8-17_micro002,1,-7.59,0,0 +SAMPL8-17_micro000,SAMPL8-17_micro005,-1,15.05,0,0 +SAMPL8-18_micro000,SAMPL8-18_micro004,1,-1.51,0,0 +SAMPL8-19_micro000,SAMPL8-19_Chemaxon_extra001,-1,9.54,0,0 +SAMPL8-19_micro000,SAMPL8-19_micro009,1,-4.77,0,0 +SAMPL8-19_micro000,SAMPL8-19_Chemaxon_extra002,1,-6.49,0,0 +SAMPL8-20_micro000,SAMPL8-20_micro011,1,-1.33,0,0 +SAMPL8-20_micro000,SAMPL8-20_micro018,-1,13.72,0,0 +SAMPL8-21_micro000,SAMPL8-21_micro027,-1,9.44,0,0 +SAMPL8-21_micro000,SAMPL8-21_Chemaxon_extra001,1,-6.85,0,0 +SAMPL8-21_micro000,SAMPL8-21_dortmund001,2,-8.07,0,0 +SAMPL8-22_micro000,SAMPL8-22_dortmund002,1,-2.94,0,0 +SAMPL8-23_micro000,SAMPL8-23_micro001,1,-3.46,0,0 +SAMPL8-23_micro000,SAMPL8-23_micro002,-1,9.15,0,0 + + + +# +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Dhiman Ray + +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +University of California Irvine + +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name of the method should not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +Chemaxon + +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +None + +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used to run the simulations. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +None + +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +Chemaxon + +# METHOD CATEGORY SECTION +# +# State if your prediction method is better classified as an +# experimental database lookup (DL), linear free energy relationship (LFER), +# quantitative structure-property relationship or machine learning (QSPR/ML), +# quantum mechanics without empirical correction (QM) model, quantum mechanics with +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular +# mechanics (QM+MM), or Other, using the following category labels: +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`. +# +# Pick only one category label. +# The `Category:` keyword is required. +Category: +Other + +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# Use as many lines of text as you need. +# +# We strongly encourage you to submit your predicted macro pKa values in this section in consecutive lines following this format: +# compound name, macro pKa, initial formal charge, formal charge after transition, e.g.: +# SAMPL8-1, 3.5, 0, +1 +# This will allow us to check that our analysis of your free energies leads to the same endpoint as your analysis. +# +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. + +Method: +Reference calculations obtained using ChemAxon softwear + + +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) + +Ranked: +True diff --git a/physical_properties/pKa/submissions/pKa_SabatinoRodriguezPaluch_uESE.csv b/physical_properties/pKa/submissions/Original_submissions/pKa_SabatinoRodriguezPaluch_uESE.csv similarity index 100% rename from physical_properties/pKa/submissions/pKa_SabatinoRodriguezPaluch_uESE.csv rename to physical_properties/pKa/submissions/Original_submissions/pKa_SabatinoRodriguezPaluch_uESE.csv diff --git a/physical_properties/pKa/submissions/pKa_SabatinoRodriguezPaluch_uESE_extra.csv b/physical_properties/pKa/submissions/Original_submissions/pKa_SabatinoRodriguezPaluch_uESE_extra.csv similarity index 100% rename from physical_properties/pKa/submissions/pKa_SabatinoRodriguezPaluch_uESE_extra.csv rename to physical_properties/pKa/submissions/Original_submissions/pKa_SabatinoRodriguezPaluch_uESE_extra.csv diff --git a/physical_properties/pKa/submissions/Original_submissions/pKa_SabatinoRodriguezPaluch_uESE_extra_modified.csv b/physical_properties/pKa/submissions/Original_submissions/pKa_SabatinoRodriguezPaluch_uESE_extra_modified.csv new file mode 100644 index 0000000..1bc63ef --- /dev/null +++ b/physical_properties/pKa/submissions/Original_submissions/pKa_SabatinoRodriguezPaluch_uESE_extra_modified.csv @@ -0,0 +1,429 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction) +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# PREDICTION SECTION +# +# It is mandatory to submit relative free energy (RFE) predictions for all 23 molecules. Incomplete submissions will not be accepted. +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty. +# Note that we here follow the same sign convention and submission format as the SAMPL7 pKa challenge. +# +# The data in each prediction line should be structured as follows: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty +# +# If you have evaluated additional microstates, include the following: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +# +# The molecule ID of the other microstate needs to be in the format: `SAMPL8-X_extra001` (number can vary) +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders, +# Please send the `.mol2` file to the email listed on the instructions page. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: +SAMPL8-1_micro000,SAMPL8-1_micro001,-1,44.96,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro002,-1,31.07,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro003,-1,40.94,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,10.86,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro005,-1,10.87,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro006,0,45.04,0.10,1.40 +SAMPL8-1_micro000,SAMPL8-1_micro007,0,29.74,0.10,1.40 +SAMPL8-1_micro000,SAMPL8-1_micro008,-1,40.06,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro009,0,33.75,0.10,1.40 +SAMPL8-1_micro000,SAMPL8-1_micro010,0,31.74,0.10,1.40 +SAMPL8-1_micro000,SAMPL8-1_RFE-uESE-extra_extra001,1,15.16,0.10,2.90 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,11.25,0.10,3.00 +SAMPL8-2_micro000,SAMPL8-2_micro002,0,26.87,0.10,1.40 +SAMPL8-2_micro000,SAMPL8-2_micro003,-1,37.87,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro001,-1,-1.36,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro002,0,-13.75,0.10,1.40 +SAMPL8-3_micro000,SAMPL8-3_micro003,-1,1.03,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro004,0,-14.19,0.10,1.40 +SAMPL8-3_micro000,SAMPL8-3_micro005,-1,-15.42,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro006,0,-49.40,0.10,1.40 +SAMPL8-3_micro000,SAMPL8-3_micro007,-2,28.73,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro008,0,-12.06,0.10,1.40 +SAMPL8-3_micro000,SAMPL8-3_micro009,-1,-3.57,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,-40.63,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro011,-1,4.97,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro012,-2,48.91,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro013,-2,58.77,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro014,-2,41.40,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro015,-1,17.35,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,-30.76,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro017,-1,5.39,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro018,-1,-2.62,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro019,-2,42.96,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro020,-1,-36.60,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro021,-2,47.42,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_RFE-uESE-extra_extra001,1,-26.31,0.10,2.90 +SAMPL8-4_micro000,SAMPL8-4_micro001,0,9.21,0.10,1.40 +SAMPL8-4_micro000,SAMPL8-4_micro002,1,1.72,0.10,2.90 +SAMPL8-4_micro000,SAMPL8-4_micro003,-1,6.69,0.10,3.00 +SAMPL8-4_micro000,SAMPL8-4_micro004,0,0.00,0.10,1.40 +SAMPL8-4_micro000,SAMPL8-4_micro005,-1,6.17,0.10,3.00 +SAMPL8-4_micro000,SAMPL8-4_micro006,-1,6.38,0.10,3.00 +SAMPL8-4_micro000,SAMPL8-4_micro007,1,1.42,0.10,2.90 +SAMPL8-4_micro000,SAMPL8-4_micro008,-1,10.14,0.10,3.00 +SAMPL8-4_micro000,SAMPL8-4_micro009,-1,6.16,0.10,3.00 +SAMPL8-4_micro000,SAMPL8-4_micro010,0,-9.81,0.10,1.40 +SAMPL8-5_micro000,SAMPL8-5_micro001,0,20.67,0.10,1.40 +SAMPL8-5_micro000,SAMPL8-5_micro002,-1,32.28,0.10,3.00 +SAMPL8-5_micro000,SAMPL8-5_micro003,1,13.74,0.10,2.90 +SAMPL8-5_micro000,SAMPL8-5_micro004,0,40.59,0.10,1.40 +SAMPL8-5_micro000,SAMPL8-5_micro005,0,22.16,0.10,1.40 +SAMPL8-5_micro000,SAMPL8-5_micro006,1,33.80,0.10,2.90 +SAMPL8-5_micro000,SAMPL8-5_micro007,-1,10.51,0.10,3.00 +SAMPL8-6_micro000,SAMPL8-6_micro001,-1,8.09,0.10,3.00 +SAMPL8-6_micro000,SAMPL8-6_micro002,1,41.73,0.10,2.90 +SAMPL8-6_micro000,SAMPL8-6_micro003,1,7.22,0.10,2.90 +SAMPL8-6_micro000,SAMPL8-6_micro004,0,41.17,0.10,1.40 +SAMPL8-6_micro000,SAMPL8-6_micro005,0,29.53,0.10,1.40 +SAMPL8-6_micro000,SAMPL8-6_micro006,-1,45.64,0.10,3.00 +SAMPL8-6_micro000,SAMPL8-6_micro007,0,20.63,0.10,1.40 +SAMPL8-6_micro000,SAMPL8-6_micro008,0,23.12,0.10,1.40 +SAMPL8-6_micro000,SAMPL8-6_micro009,-1,31.06,0.10,3.00 +SAMPL8-7_micro000,SAMPL8-7_micro001,-1,31.11,0.10,3.00 +SAMPL8-7_micro000,SAMPL8-7_micro002,1,-12.12,0.10,2.90 +SAMPL8-7_micro000,SAMPL8-7_micro003,1,10.42,0.10,2.90 +SAMPL8-7_micro000,SAMPL8-7_micro004,0,7.19,0.10,1.40 +SAMPL8-8_micro000,SAMPL8-8_micro001,1,-6.33,0.10,2.90 +SAMPL8-8_micro000,SAMPL8-8_micro002,1,10.83,0.10,2.90 +SAMPL8-9_micro000,SAMPL8-9_micro001,-1,31.63,0.10,3.00 +SAMPL8-9_micro000,SAMPL8-9_micro002,1,-8.14,0.10,2.90 +SAMPL8-9_micro000,SAMPL8-9_micro003,0,7.42,0.10,1.40 +SAMPL8-9_micro000,SAMPL8-9_micro004,1,10.00,0.10,2.90 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-9.03,0.10,2.90 +SAMPL8-12_micro000,SAMPL8-12_micro001,-1,43.81,0.10,3.00 +SAMPL8-12_micro000,SAMPL8-12_micro002,0,22.45,0.10,1.40 +SAMPL8-12_micro000,SAMPL8-12_micro003,0,18.11,0.10,1.40 +SAMPL8-12_micro000,SAMPL8-12_RFE-uESE-extra_extra001,2,52.58,0.10,2.90 +SAMPL8-12_micro000,SAMPL8-12_RFE-uESE-extra_extra002,1,-8.02,0.10,2.90 +SAMPL8-12_micro000,SAMPL8-12_RFE-uESE-extra_extra003,2,61.45,0.10,2.90 +SAMPL8-12_micro000,SAMPL8-12_RFE-uESE-extra_extra004,1,-8.28,0.10,2.90 +SAMPL8-12_micro000,SAMPL8-12_RFE-uESE-extra_extra005,2,52.63,0.10,2.90 +SAMPL8-12_micro000,SAMPL8-12_RFE-uESE-extra_extra006,1,-2.09,0.10,2.90 +SAMPL8-14_micro000,SAMPL8-14_micro001,-2,92.53,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro002,0,-10.93,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro003,-2,93.03,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro004,-1,32.10,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro005,-1,19.33,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro006,0,-0.87,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro007,-2,96.52,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,-1.80,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro09,-1,28.00,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro010,-1,13.28,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro011,-2,95.29,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro012,-1,19.18,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro013,0,-6.00,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro014,-3,78.18,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro015,-2,95.92,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro016,0,-0.12,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro017,0,-4.80,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro018,-2,119.33,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro019,-1,15.37,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro020,-2,103.45,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro021,-1,21.78,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro022,-1,13.77,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro023,0,-10.90,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro024,0,-22.63,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro025,-1,21.93,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro026,-2,103.38,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro027,-1,18.28,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro028,-1,14.07,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro029,-1,19.15,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro030,0,-4.80,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro031,-2,90.72,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro032,-1,15.96,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro033,0,-6.00,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro034,0,-0.96,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_RFE-uESE-extra_extra001,2,23.43,0.10,2.90 +SAMPL8-14_micro000,SAMPL8-14_RFE-uESE-extra_extra002,1,-33.93,0.10,2.90 +SAMPL8-14_micro000,SAMPL8-14_RFE-uESE-extra_extra003,2,23.00,0.10,2.90 +SAMPL8-14_micro000,SAMPL8-14_RFE-uESE-extra_extra004,1,-27.60,0.10,2.90 +SAMPL8-14_micro000,SAMPL8-14_RFE-uESE-extra_extra005,2,23.45,0.10,2.90 +SAMPL8-14_micro000,SAMPL8-14_RFE-uESE-extra_extra006,1,-18.39,0.10,2.90 +SAMPL8-14_micro000,SAMPL8-14_RFE-uESE-extra_extra007,1,-17.89,0.10,2.90 +SAMPL8-14_micro000,SAMPL8-14_RFE-uESE-extra_extra008,2,23.44,0.10,2.90 +SAMPL8-14_micro000,SAMPL8-14_RFE-uESE-extra_extra009,1,-28.36,0.10,2.90 +SAMPL8-14_micro000,SAMPL8-14_RFE-uESE-extra_extra010,2,31.95,0.10,2.90 +SAMPL8-14_micro000,SAMPL8-14_RFE-uESE-extra_extra011,1,-35.00,0.10,2.90 +SAMPL8-14_micro000,SAMPL8-14_RFE-uESE-extra_extra012,1,-34.95,0.10,2.90 +SAMPL8-15_micro000,SAMPL8-15_micro001,0,-9.30,0.10,1.40 +SAMPL8-15_micro000,SAMPL8-15_micro002,0,-1.50,0.10,1.40 +SAMPL8-15_micro000,SAMPL8-15_micro003,1,-6.15,0.10,2.90 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+SAMPL8-21_micro000,SAMPL8-21_micro028,0,-27.68,0.10,1.40 +SAMPL8-21_micro000,SAMPL8-21_micro029,0,-6.32,0.10,1.40 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra001,2,24.42,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra002,1,-33.95,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra003,2,23.92,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra004,1,-18.52,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra005,1,-18.45,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra006,1,-33.93,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra007,2,32.59,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra008,1,-29.00,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra009,1,-32.95,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra010,2,23.74,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra011,1,-33.93,0.10,2.90 +SAMPL8-22_micro000,SAMPL8-22_micro001,-1,16.72,0.10,3.00 +SAMPL8-22_micro000,SAMPL8-22_micro002,0,-7.32,0.10,1.40 +SAMPL8-22_micro000,SAMPL8-22_micro003,0,1.89,0.10,1.40 +SAMPL8-22_micro000,SAMPL8-22_RFE-uESE-extra_extra001,2,41.34,0.10,2.90 +SAMPL8-22_micro000,SAMPL8-22_RFE-uESE-extra_extra002,1,-19.99,0.10,2.90 +SAMPL8-22_micro000,SAMPL8-22_RFE-uESE-extra_extra003,2,41.36,0.10,2.90 +SAMPL8-22_micro000,SAMPL8-22_RFE-uESE-extra_extra004,1,-15.69,0.10,2.90 +SAMPL8-22_micro000,SAMPL8-22_RFE-uESE-extra_extra005,1,-20.04,0.10,2.90 +SAMPL8-23_micro000,SAMPL8-23_micro001,1,15.50,0.10,2.90 +SAMPL8-23_micro000,SAMPL8-23_micro002,-1,16.88,0.10,3.00 +SAMPL8-23_micro000,SAMPL8-23_micro003,0,2.15,0.10,1.40 +SAMPL8-23_micro000,SAMPL8-23_micro004,0,36.98,0.10,1.40 +SAMPL8-23_micro000,SAMPL8-23_micro005,-1,1.59,0.10,3.00 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-19.98,0.10,2.90 +SAMPL8-23_micro000,SAMPL8-23_micro007,0,-17.07,0.10,1.40 + +# +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Spencer J. Sabatino +Sergio Antonio Rodriguez +Andrew S. Paluch + +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +Miami University +University of Santiago del Estero, Argentina +Miami University + +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name of the method should not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +RFE-uESE-extra + +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +60 hours, CPU + +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used to run the simulations. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +All simulations were performed on the Pitzer Cluster at the Ohio Supercomputer Center +(https://www.osc.edu/resources/technical_support/supercomputers/pitzer). +The reported compute time is taken as the walltime times the number of processors (core hours). +Pitzer has a mix of processors. We did not specify the processor type upon submission, so a mix was used. +The original Pitzer cluster was installed in late 2018 and +is a Dell-built, Intel Xeon Skylake processor-based supercomputer with 260 nodes. +In September 2020, OSC installed an additional 398 Intel Xeon Cascade Lake processor-based +nodes as part of a Pitzer Expansion cluster. + +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +Gaussian 16 + +# METHOD CATEGORY SECTION +# +# State if your prediction method is better classified as an +# experimental database lookup (DL), linear free energy relationship (LFER), +# quantitative structure-property relationship or machine learning (QSPR/ML), +# quantum mechanics without empirical correction (QM) model, quantum mechanics with +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular +# mechanics (QM+MM), or Other, using the following category labels: +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`. +# +# Pick only one category label. +# The `Category:` keyword is required. +Category: +QM + +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# Use as many lines of text as you need. +# +# We strongly encourage you to submit your predicted macro pKa values in this section in consecutive lines following this format: +# compound name, macro pKa, initial formal charge, formal charge after transition, e.g.: +# SAMPL8-1, 3.5, 0, +1 +# This will allow us to check that our analysis of your free energies leads to the same endpoint as your analysis. +# +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. + +Method: +Starting with the initial structures provided by the SAMPL8 organizers, geometries were first optimized with the PM7 method. +The geometries were then further optimized at the B3LYP/def2-TZVP level of theory/basis set, followed by frequency calculation. +A single point energy calculation was then performed to computed CM5 charges. The final structure and CM5 charges were used to predict +hydration free energies using the uESE method (DOI: 10.1002/jcc.26531) using code provided by the authors of the uESE manuscript. +The gas phase total free energy of each microstate was computed from the frequency calculation. +The relative free energies in water were computed from this information based on the proton dissociation reaction. +All of the electronic structure calculations were perfomed with Gaussian 16. + +This submission includes the extra microstates provided by the challenge organizers. + +Macro pKa values +SAMPL8-1,7.97,0,-1 +SAMPL8-2,8.25,0,-1 +SAMPL8-3,0.76,0,-1 +SAMPL8-3,6.43,0,0 +SAMPL8-4,4.52,0,-1 +SAMPL8-5,7.71,0,-1 +SAMPL8-6,5.93,0,-1 +SAMPL8-7,8.89,0,1 +SAMPL8-8,4.64,0,1 +SAMPL8-9,5.97,0,1 +SAMPL8-11,10.63,0,1 +SAMPL8-11,0.81,0,1 +SAMPL8-12,6.07,0,1 +SAMPL8-13,3.63,0,1 +SAMPL8-14,10.32,0,-1 +SAMPL8-15,7.94,0,1 +SAMPL8-16,3.72,0,1 +SAMPL8-17,5.24,0,1 +SAMPL8-18,3.77,0,1 +SAMPL8-18,8.07,0,1 +SAMPL8-19,5.73,0,1 +SAMPL8-20,12.62,0,1 +SAMPL8-21,12.37,0,-1 +SAMPL8-22,12.26,0,-1 +SAMPL8-23,12.38,0,-1 + +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) + +Ranked: +True diff --git a/physical_properties/pKa/submissions/Original_submissions/pKa_SabatinoRodriguezPaluch_uESE_modified.csv b/physical_properties/pKa/submissions/Original_submissions/pKa_SabatinoRodriguezPaluch_uESE_modified.csv new file mode 100644 index 0000000..186daad --- /dev/null +++ b/physical_properties/pKa/submissions/Original_submissions/pKa_SabatinoRodriguezPaluch_uESE_modified.csv @@ -0,0 +1,364 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction) +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# PREDICTION SECTION +# +# It is mandatory to submit relative free energy (RFE) predictions for all 23 molecules. Incomplete submissions will not be accepted. +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty. +# Note that we here follow the same sign convention and submission format as the SAMPL7 pKa challenge. +# +# The data in each prediction line should be structured as follows: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty +# +# If you have evaluated additional microstates, include the following: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +# +# The molecule ID of the other microstate needs to be in the format: `SAMPL8-X_extra001` (number can vary) +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders, +# Please send the `.mol2` file to the email listed on the instructions page. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: +SAMPL8-1_micro000,SAMPL8-1_micro001,-1,44.96,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro002,-1,31.07,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro003,-1,40.94,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,10.86,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro005,-1,10.87,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro006,0,45.04,0.10,1.40 +SAMPL8-1_micro000,SAMPL8-1_micro007,0,29.74,0.10,1.40 +SAMPL8-1_micro000,SAMPL8-1_micro008,-1,40.06,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro009,0,33.75,0.10,1.40 +SAMPL8-1_micro000,SAMPL8-1_micro010,0,31.74,0.10,1.40 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,11.25,0.10,3.00 +SAMPL8-2_micro000,SAMPL8-2_micro002,0,26.87,0.10,1.40 +SAMPL8-2_micro000,SAMPL8-2_micro003,-1,37.87,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro001,-1,-1.36,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro002,0,-13.75,0.10,1.40 +SAMPL8-3_micro000,SAMPL8-3_micro003,-1,1.03,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro004,0,-14.19,0.10,1.40 +SAMPL8-3_micro000,SAMPL8-3_micro005,-1,-15.42,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro006,0,-49.4,0.10,1.40 +SAMPL8-3_micro000,SAMPL8-3_micro007,-2,28.73,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro008,0,-12.06,0.10,1.40 +SAMPL8-3_micro000,SAMPL8-3_micro009,-1,-3.57,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,-40.63,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro011,-1,4.97,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro012,-2,48.91,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro013,-2,58.77,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro014,-2,41.4,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro015,-1,17.35,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,-30.76,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro017,-1,5.39,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro018,-1,-2.62,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro019,-2,42.96,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro020,-1,-36.6,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro021,-2,47.42,0.10,3.00 +SAMPL8-4_micro000,SAMPL8-4_micro001,0,9.21,0.10,1.40 +SAMPL8-4_micro000,SAMPL8-4_micro002,1,1.72,0.10,2.90 +SAMPL8-4_micro000,SAMPL8-4_micro003,-1,6.69,0.10,3.00 +SAMPL8-4_micro000,SAMPL8-4_micro004,0,0,0.10,1.40 +SAMPL8-4_micro000,SAMPL8-4_micro005,-1,6.17,0.10,3.00 +SAMPL8-4_micro000,SAMPL8-4_micro006,-1,6.38,0.10,3.00 +SAMPL8-4_micro000,SAMPL8-4_micro007,1,1.42,0.10,2.90 +SAMPL8-4_micro000,SAMPL8-4_micro008,-1,10.14,0.10,3.00 +SAMPL8-4_micro000,SAMPL8-4_micro009,-1,6.16,0.10,3.00 +SAMPL8-4_micro000,SAMPL8-4_micro010,0,-9.81,0.10,1.40 +SAMPL8-5_micro000,SAMPL8-5_micro001,0,20.67,0.10,1.40 +SAMPL8-5_micro000,SAMPL8-5_micro002,-1,32.28,0.10,3.00 +SAMPL8-5_micro000,SAMPL8-5_micro003,1,13.74,0.10,2.90 +SAMPL8-5_micro000,SAMPL8-5_micro004,0,40.59,0.10,1.40 +SAMPL8-5_micro000,SAMPL8-5_micro005,0,22.16,0.10,1.40 +SAMPL8-5_micro000,SAMPL8-5_micro006,1,33.8,0.10,2.90 +SAMPL8-5_micro000,SAMPL8-5_micro007,-1,10.51,0.10,3.00 +SAMPL8-6_micro000,SAMPL8-6_micro001,-1,8.09,0.10,3.00 +SAMPL8-6_micro000,SAMPL8-6_micro002,1,41.73,0.10,2.90 +SAMPL8-6_micro000,SAMPL8-6_micro003,1,7.22,0.10,2.90 +SAMPL8-6_micro000,SAMPL8-6_micro004,0,41.17,0.10,1.40 +SAMPL8-6_micro000,SAMPL8-6_micro005,0,29.53,0.10,1.40 +SAMPL8-6_micro000,SAMPL8-6_micro006,-1,45.64,0.10,3.00 +SAMPL8-6_micro000,SAMPL8-6_micro007,0,20.63,0.10,1.40 +SAMPL8-6_micro000,SAMPL8-6_micro008,0,23.12,0.10,1.40 +SAMPL8-6_micro000,SAMPL8-6_micro009,-1,31.06,0.10,3.00 +SAMPL8-7_micro000,SAMPL8-7_micro001,-1,31.11,0.10,3.00 +SAMPL8-7_micro000,SAMPL8-7_micro002,1,-12.12,0.10,2.90 +SAMPL8-7_micro000,SAMPL8-7_micro003,1,10.42,0.10,2.90 +SAMPL8-7_micro000,SAMPL8-7_micro004,0,7.19,0.10,1.40 +SAMPL8-8_micro000,SAMPL8-8_micro001,1,-6.33,0.10,2.90 +SAMPL8-8_micro000,SAMPL8-8_micro002,1,10.83,0.10,2.90 +SAMPL8-9_micro000,SAMPL8-9_micro001,-1,31.63,0.10,3.00 +SAMPL8-9_micro000,SAMPL8-9_micro002,1,-8.14,0.10,2.90 +SAMPL8-9_micro000,SAMPL8-9_micro003,0,7.42,0.10,1.40 +SAMPL8-9_micro000,SAMPL8-9_micro004,1,10,0.10,2.90 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-9.03,0.10,2.90 +SAMPL8-12_micro000,SAMPL8-12_micro001,-1,43.81,0.10,3.00 +SAMPL8-12_micro000,SAMPL8-12_micro002,0,22.45,0.10,1.40 +SAMPL8-12_micro000,SAMPL8-12_micro003,0,18.11,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro001,-2,92.53,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro002,0,-10.93,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro003,-2,93.03,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro004,-1,32.1,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro005,-1,19.33,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro006,0,-0.87,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro007,-2,96.52,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,-1.8,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro09,-1,28,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro010,-1,13.28,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro011,-2,95.29,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro012,-1,19.18,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro013,0,-6,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro014,-3,78.18,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro015,-2,95.92,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro016,0,-0.12,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro017,0,-4.8,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro018,-2,119.33,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro019,-1,15.37,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro020,-2,103.45,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro021,-1,21.78,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro022,-1,13.77,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro023,0,-10.9,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro024,0,-22.63,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro025,-1,21.93,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro026,-2,103.38,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro027,-1,18.28,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro028,-1,14.07,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro029,-1,19.15,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro030,0,-4.8,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro031,-2,90.72,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro032,-1,15.96,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro033,0,-6,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro034,0,-0.96,0.10,1.40 +SAMPL8-15_micro000,SAMPL8-15_micro001,0,-9.3,0.10,1.40 +SAMPL8-15_micro000,SAMPL8-15_micro002,0,-1.5,0.10,1.40 +SAMPL8-15_micro000,SAMPL8-15_micro003,1,-6.15,0.10,2.90 +SAMPL8-15_micro000,SAMPL8-15_micro004,1,-10.83,0.10,2.90 +SAMPL8-16_micro000,SAMPL8-16_micro001,1,46.98,0.10,2.90 +SAMPL8-16_micro000,SAMPL8-16_micro002,0,37.63,0.10,1.40 +SAMPL8-16_micro000,SAMPL8-16_micro003,1,32.61,0.10,2.90 +SAMPL8-16_micro000,SAMPL8-16_micro004,1,-5.07,0.10,2.90 +SAMPL8-16_micro000,SAMPL8-16_micro005,0,37.67,0.10,1.40 +SAMPL8-16_micro000,SAMPL8-16_micro006,1,41.42,0.10,2.90 +SAMPL8-16_micro000,SAMPL8-16_micro007,0,16.51,0.10,1.40 +SAMPL8-16_micro000,SAMPL8-16_micro008,1,11.41,0.10,2.90 +SAMPL8-16_micro000,SAMPL8-16_micro009,1,45.33,0.10,2.90 +SAMPL8-16_micro000,SAMPL8-16_micro010,1,20.2,0.10,2.90 +SAMPL8-16_micro000,SAMPL8-16_micro011,0,20.04,0.10,1.40 +SAMPL8-17_micro000,SAMPL8-17_micro001,-1,30.66,0.10,3.00 +SAMPL8-17_micro000,SAMPL8-17_micro002,1,-7.14,0.10,2.90 +SAMPL8-17_micro000,SAMPL8-17_micro003,1,9.48,0.10,2.90 +SAMPL8-17_micro000,SAMPL8-17_micro004,0,6.68,0.10,1.40 +SAMPL8-17_micro000,SAMPL8-17_micro005,-1,24.83,0.10,3.00 +SAMPL8-18_micro000,SAMPL8-18_micro001,0,0.85,0.10,1.40 +SAMPL8-18_micro000,SAMPL8-18_micro002,0,-8.77,0.10,1.40 +SAMPL8-18_micro000,SAMPL8-18_micro003,1,-5.14,0.10,2.90 +SAMPL8-18_micro000,SAMPL8-18_micro004,1,-11,0.10,2.90 +SAMPL8-18_micro000,SAMPL8-18_micro005,-1,14.39,0.10,3.00 +SAMPL8-19_micro000,SAMPL8-19_micro001,1,-7.43,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro002,2,50.36,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro003,2,59.54,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro004,1,1.98,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro005,1,-17.62,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro006,1,-13.69,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro007,0,-13.34,0.10,1.40 +SAMPL8-19_micro000,SAMPL8-19_micro008,1,-16.06,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro009,1,-14.65,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro010,-1,19.43,0.10,3.00 +SAMPL8-19_micro000,SAMPL8-19_micro011,-1,3.14,0.10,3.00 +SAMPL8-19_micro000,SAMPL8-19_micro012,2,76.06,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro013,0,-9.58,0.10,1.40 +SAMPL8-19_micro000,SAMPL8-19_micro014,0,36.7,0.10,1.40 +SAMPL8-19_micro000,SAMPL8-19_micro015,0,-9.32,0.10,1.40 +SAMPL8-19_micro000,SAMPL8-19_micro016,1,-7.81,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro017,2,62.69,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro018,1,-13.62,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro019,1,-12.57,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro020,0,5.15,0.10,1.40 +SAMPL8-19_micro000,SAMPL8-19_micro021,2,87.41,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro022,1,-3.57,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro023,1,21.78,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro024,0,10.21,0.10,1.40 +SAMPL8-19_micro000,SAMPL8-19_micro025,0,4.64,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro001,0,4.44,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro002,1,-16.76,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro003,1,-17.21,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro004,0,17.82,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro005,1,41.96,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro006,1,-19.44,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro007,1,13.13,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro008,0,43.83,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro009,0,15.1,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro010,0,29.5,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro011,1,-0.73,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro012,0,33.63,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro013,0,23.39,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro014,1,38.65,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro015,1,-2.4,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro016,1,19.76,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro017,0,-10.64,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro018,0,-2.25,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro019,0,31.17,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro020,0,47.57,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro021,0,23.95,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro022,0,-17.77,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro023,0,36.76,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro024,0,36.54,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro025,1,27.32,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro026,1,-12.61,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro027,0,40.21,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro028,1,39.16,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_micro001,-2,103.6,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro002,-2,111.91,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro003,-1,8.2,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro004,-2,106.42,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro005,-2,94.9,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro006,-1,16.87,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro007,-1,30.27,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro008,0,-1.7,0.10,1.40 +SAMPL8-21_micro000,SAMPL8-21_micro009,-1,12.19,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro010,-3,72.81,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro011,-1,17.03,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro012,-2,114.74,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro013,-2,104.09,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro014,-1,12.17,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro015,-2,106.2,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro016,-1,9.41,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro017,-2,98.71,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro018,-1,12.6,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro019,-1,30.43,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro020,-1,20.23,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro021,-2,95.78,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro022,-1,-3.93,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro023,0,-12.47,0.10,1.40 +SAMPL8-21_micro000,SAMPL8-21_micro024,-1,15.64,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro025,0,-8.76,0.10,1.40 +SAMPL8-21_micro000,SAMPL8-21_micro026,-1,24.29,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro027,-1,26.47,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro028,0,-27.68,0.10,1.40 +SAMPL8-21_micro000,SAMPL8-21_micro029,0,-6.32,0.10,1.40 +SAMPL8-22_micro000,SAMPL8-22_micro001,-1,16.72,0.10,3.00 +SAMPL8-22_micro000,SAMPL8-22_micro002,0,-7.32,0.10,1.40 +SAMPL8-22_micro000,SAMPL8-22_micro003,0,1.89,0.10,1.40 +SAMPL8-23_micro000,SAMPL8-23_micro001,1,15.5,0.10,2.90 +SAMPL8-23_micro000,SAMPL8-23_micro002,-1,16.88,0.10,3.00 +SAMPL8-23_micro000,SAMPL8-23_micro003,0,2.15,0.10,1.40 +SAMPL8-23_micro000,SAMPL8-23_micro004,0,36.98,0.10,1.40 +SAMPL8-23_micro000,SAMPL8-23_micro005,-1,1.59,0.10,3.00 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-19.98,0.10,2.90 +SAMPL8-23_micro000,SAMPL8-23_micro007,0,-17.07,0.10,1.40 + +# +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Spencer J. Sabatino +Sergio Antonio Rodriguez +Andrew S. Paluch + +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +Miami University +University of Santiago del Estero, Argentina +Miami University + +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name of the method should not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +RFE-uESE + +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +60 hours, CPU + +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used to run the simulations. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +All simulations were performed on the Pitzer Cluster at the Ohio Supercomputer Center +(https://www.osc.edu/resources/technical_support/supercomputers/pitzer). +The reported compute time is taken as the walltime times the number of processors (core hours). +Pitzer has a mix of processors. We did not specify the processor type upon submission, so a mix was used. +The original Pitzer cluster was installed in late 2018 and +is a Dell-built, Intel Xeon Skylake processor-based supercomputer with 260 nodes. +In September 2020, OSC installed an additional 398 Intel Xeon Cascade Lake processor-based +nodes as part of a Pitzer Expansion cluster. + +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +Gaussian 16 + +# METHOD CATEGORY SECTION +# +# State if your prediction method is better classified as an +# experimental database lookup (DL), linear free energy relationship (LFER), +# quantitative structure-property relationship or machine learning (QSPR/ML), +# quantum mechanics without empirical correction (QM) model, quantum mechanics with +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular +# mechanics (QM+MM), or Other, using the following category labels: +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`. +# +# Pick only one category label. +# The `Category:` keyword is required. +Category: +QM + +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# Use as many lines of text as you need. +# +# We strongly encourage you to submit your predicted macro pKa values in this section in consecutive lines following this format: +# compound name, macro pKa, initial formal charge, formal charge after transition, e.g.: +# SAMPL8-1, 3.5, 0, +1 +# This will allow us to check that our analysis of your free energies leads to the same endpoint as your analysis. +# +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. + +Method: +Starting with the initial structures provided by the SAMPL8 organizers, geometries were first optimized with the PM7 method. +The geometries were then further optimized at the B3LYP/def2-TZVP level of theory/basis set, followed by frequency calculation. +A single point energy calculation was then performed to computed CM5 charges. The final structure and CM5 charges were used to predict +hydration free energies using the uESE method (DOI: 10.1002/jcc.26531) using code provided by the authors of the uESE manuscript. +The gas phase total free energy of each microstate was computed from the frequency calculation. +The relative free energies in water were computed from this information based on the proton dissociation reaction. +All of the electronic structure calculations were perfomed with Gaussian 16. + +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) + +Ranked: +False diff --git a/physical_properties/pKa/submissions/PKA_ECRISM_modified.csv b/physical_properties/pKa/submissions/PKA_ECRISM_modified.csv new file mode 100644 index 0000000..43c9099 --- /dev/null +++ b/physical_properties/pKa/submissions/PKA_ECRISM_modified.csv @@ -0,0 +1,359 @@ +Predictions: +SAMPL8-1_micro000,SAMPL8-1_micro001,-1,28.33,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_micro002,-1,6.92,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_micro003,-1,27.66,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,7.16,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_micro005,-1,7.07,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_micro008,-1,25.69,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_micro006,0,30.73,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_micro007,0,21.88,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_micro009,0,22.88,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_micro010,0,20.37,0.01,1.04 +SAMPL8-1_micro000,SAMPL8-1_EC-RISM_extra001,1,3.37,0.01,1.04 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,7.31,0.01,1.04 +SAMPL8-2_micro000,SAMPL8-2_micro003,-1,30.55,0.01,1.04 +SAMPL8-2_micro000,SAMPL8-2_micro002,0,19.96,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro007,-2,7.11,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro012,-2,7.53,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro013,-2,-11.46,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro014,-2,-11.69,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro019,-2,11.04,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro021,-2,11.82,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro001,-1,-2.06,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro003,-1,5.37,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro005,-1,-6.96,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro009,-1,-0.79,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,-25.91,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro011,-1,1.98,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro015,-1,13.62,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,-18.78,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro017,-1,6.90,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro018,-1,-5.02,0.01,1.04 +SAMPL8-3_micro000,SAMPL8-3_micro020,-1,-25.88,0.01,1.04 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+SAMPL8-5_micro000,SAMPL8-5_micro004,0,26.89,0.01,1.04 +SAMPL8-5_micro000,SAMPL8-5_micro005,0,14.64,0.01,1.04 +SAMPL8-5_micro000,SAMPL8-5_micro003,1,3.17,0.01,1.04 +SAMPL8-5_micro000,SAMPL8-5_micro006,1,19.80,0.01,1.04 +SAMPL8-6_micro000,SAMPL8-6_micro001,-1,6.46,0.01,1.04 +SAMPL8-6_micro000,SAMPL8-6_micro006,-1,30.13,0.01,1.04 +SAMPL8-6_micro000,SAMPL8-6_micro009,-1,37.22,0.01,1.04 +SAMPL8-6_micro000,SAMPL8-6_micro004,0,32.95,0.01,1.04 +SAMPL8-6_micro000,SAMPL8-6_micro005,0,28.91,0.01,1.04 +SAMPL8-6_micro000,SAMPL8-6_micro007,0,0.84,0.01,1.04 +SAMPL8-6_micro000,SAMPL8-6_micro008,0,13.94,0.01,1.04 +SAMPL8-6_micro000,SAMPL8-6_micro002,1,32.13,0.01,1.04 +SAMPL8-6_micro000,SAMPL8-6_micro003,1,-4.07,0.01,1.04 +SAMPL8-7_micro000,SAMPL8-7_micro001,-1,20.62,0.01,1.04 +SAMPL8-7_micro000,SAMPL8-7_micro004,0,5.90,0.01,1.04 +SAMPL8-7_micro000,SAMPL8-7_micro002,1,-5.70,0.01,1.04 +SAMPL8-7_micro000,SAMPL8-7_micro003,1,2.67,0.01,1.04 +SAMPL8-8_micro000,SAMPL8-8_micro001,1,0.45,0.01,1.04 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+SAMPL8-19_micro000,SAMPL8-19_micro008,1,-18.18,0.01,1.04 +SAMPL8-19_micro000,SAMPL8-19_micro009,1,-17.57,0.01,1.04 +SAMPL8-19_micro000,SAMPL8-19_micro016,1,13.31,0.01,1.04 +SAMPL8-19_micro000,SAMPL8-19_micro018,1,-7.21,0.01,1.04 +SAMPL8-19_micro000,SAMPL8-19_micro019,1,-13.04,0.01,1.04 +SAMPL8-19_micro000,SAMPL8-19_micro022,1,-2.17,0.01,1.04 +SAMPL8-19_micro000,SAMPL8-19_micro023,1,14.85,0.01,1.04 +SAMPL8-19_micro000,SAMPL8-19_micro002,2,-11.61,0.01,1.04 +SAMPL8-19_micro000,SAMPL8-19_micro003,2,-8.41,0.01,1.04 +SAMPL8-19_micro000,SAMPL8-19_micro012,2,14.70,0.01,1.04 +SAMPL8-19_micro000,SAMPL8-19_micro017,2,-16.01,0.01,1.04 +SAMPL8-19_micro000,SAMPL8-19_micro021,2,15.05,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro001,0,5.31,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro004,0,14.13,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro008,0,30.72,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro009,0,16.37,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro010,0,22.43,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro012,0,26.54,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro013,0,18.77,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro017,0,-9.73,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro018,0,-4.48,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro019,0,22.36,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro020,0,32.04,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro021,0,16.33,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro022,0,-12.83,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro023,0,28.17,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro024,0,29.02,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro027,0,27.91,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro002,1,-11.43,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro003,1,-11.61,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro005,1,32.01,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro006,1,-11.27,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro007,1,11.43,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro011,1,-8.51,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro014,1,30.52,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro015,1,-8.12,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro016,1,2.46,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro025,1,23.73,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro026,1,-14.97,0.01,1.04 +SAMPL8-20_micro000,SAMPL8-20_micro028,1,24.63,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro010,-3,42.38,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro001,-2,21.79,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro002,-2,27.53,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro004,-2,26.26,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro005,-2,14.84,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro012,-2,28.88,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro013,-2,20.79,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro015,-2,15.11,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro017,-2,15.45,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro021,-2,15.02,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro003,-1,3.33,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro006,-1,9.55,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro007,-1,15.32,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro009,-1,3.20,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro011,-1,9.08,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro014,-1,3.51,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro016,-1,3.14,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro018,-1,3.49,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro019,-1,14.61,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro020,-1,5.13,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro022,-1,-9.42,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro024,-1,1.56,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro026,-1,8.28,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro027,-1,10.06,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro008,0,-5.77,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro023,0,-9.99,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro025,0,-10.18,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro028,0,-20.78,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_micro029,0,-6.68,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra002,1,-25.27,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra004,1,-14.35,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra005,1,-14.23,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra006,1,-25.29,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra008,1,-22.78,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra009,1,-22.81,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra011,1,-25.48,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra001,2,-17.37,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra003,2,-18.13,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra007,2,-13.81,0.01,1.04 +SAMPL8-21_micro000,SAMPL8-21_EC-RISM_extra010,2,-18.07,0.01,1.04 +SAMPL8-22_micro000,SAMPL8-22_micro001,-1,11.86,0.01,1.04 +SAMPL8-22_micro000,SAMPL8-22_micro002,0,-8.42,0.01,1.04 +SAMPL8-22_micro000,SAMPL8-22_micro003,0,2.67,0.01,1.04 +SAMPL8-22_micro000,SAMPL8-22_EC-RISM_extra002,1,-11.00,0.01,1.04 +SAMPL8-22_micro000,SAMPL8-22_EC-RISM_extra004,1,-9.32,0.01,1.04 +SAMPL8-22_micro000,SAMPL8-22_EC-RISM_extra005,1,-10.96,0.01,1.04 +SAMPL8-22_micro000,SAMPL8-22_EC-RISM_extra001,2,-0.55,0.01,1.04 +SAMPL8-22_micro000,SAMPL8-22_EC-RISM_extra003,2,-0.55,0.01,1.04 +SAMPL8-23_micro000,SAMPL8-23_micro002,-1,14.22,0.01,1.04 +SAMPL8-23_micro000,SAMPL8-23_micro005,-1,-3.03,0.01,1.04 +SAMPL8-23_micro000,SAMPL8-23_micro003,0,-8.46,0.01,1.04 +SAMPL8-23_micro000,SAMPL8-23_micro004,0,16.96,0.01,1.04 +SAMPL8-23_micro000,SAMPL8-23_micro007,0,-16.93,0.01,1.04 +SAMPL8-23_micro000,SAMPL8-23_micro001,1,5.75,0.01,1.04 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-19.77,0.01,1.04 + +Participant name: +Stefan M. Kast, Nicolas Tielker + +Participant organization: +TU Dortmund University + +Name: +EC-RISM + +Compute time: +27 hours, CPU + +Computing and hardware: +All calculations were conducted on the LiDO 3 high performance cluster of TU Dortmund University. Calculations were automatically scheduled and ran on either an Intel Xeon E5-4604v4 or an Intel Xeon E5-2640v4 CPU, depending on node availability. + +Software: +Corina 4.3.0 +Gaussian 09 Rev E.01 +Gaussian 16 Rev C.01 +3D RISM (inhouse development) +EC-RISM (inhouse development) +Python 3.6 +Anaconda2018.12 +Amber 12 +Mathematica 12.2 (Wolfram) + +Category: +QM+LEC + +Method: +Geometries were generated using Maestro 2020-4/Macromodel with the OPLS3/Water force field with mixed torsional/low-mode sampling, 100 steps per RB and 1000 steps max (default parameters). +These conformations were then optimized using Gaussian 16revC01 with IEF-PCM using default settings for water at the B3LYP/6-311+G(d,p)/PCM level of theory. +Additional stereoisomers were treated as if they were additional conformational states of the same microstate so that for each microsate only up to 5 conformations with the lowest PCM energies for each solvent were treated with MP2/6-311+G(d,p)EC-RISM using the PSE2 closure [REF1] and the resulting EC-RISM energies corrected using (c1*mu_{ex}+c2*PMV_{EC-RISM}+c3*q). The correction for water has a fixed parameter c1 = 1 since this additional parameter was found to be of no predictive value in previous challenges, c2 = -0.1025 kcal*mol^-1*A^-3 and c3 = -15.7284 kcal mol^-1 e^-1. [REF2]. These yield G_{mtc} where m refers to the ionization state, t to the tautomer (microstate per ionization state) and c to the respective conformation. The different statistical weights of conformations were taken into account by computing the free energy of the resulting discrete partition function G_{mt}=-RT*ln[sum_c(exp(-G_{mtc}/RT))]. For the deprotonation process of a microstate with k protons, pKa_{raw}=(G_{k}-G_{k-1})/(RT ln(10)) and the macrostate pKa follows from m*pKa_{raw}+b where parameters m and b are calculated within the chosen level of theory by fitting to the reference data set from [REF3]. Here, m = 0.7449 and b = -150.7196. To calculate the relative free energies with respect to each micro000, different formulas must be used, depending on the difference in the protonation state. If there is no difference in the protonation state, i.e. the microstates are tautomers, the relative free energy is calculated via m*(G(micro000)-G(m2)) to achieve thermodynamically consistent cycles. Since micro000 is always a neutral species for a single deprotonation the relative free energy is calculated using m*(G(micro000)-G(m2))+b, and -(m*(G(micro000)-G(m2))+b) for a protonation process. For the doubly protonated species the calculated relative free energy is m*(G(micro000)-G(m2))+2*b, and -(m*(G(micro000)-G(m2))+2*b) etc. for higher or lower protonation states [REF4]. Macrostate pKa values were calculated using the partition function approach of Eq. 5 in [REF5]. +The SEM was estimated as the convergence criterion for a single EC-RISM calculation. The uncertainty was estimated as the RMSE from the pKa training set. + +References: +REF1: N. Tielker, D. Tomazic, J. Heil, T. Kloss, S. Ehrhart, S. Guessregen, K. F. Schmidt, S. M. Kast, J. Comput.-Aided Mol. Des. 30, 1035-1044 (2016). +REF2: N. Tielker, L. Eberlein, S. Guessregen, S. M. Kast, J. Comput.-Aided Mol. Des. 32, 1151-1163 (2018). +REF3: J. J. Klicic, R. A. Friesner, S. Liu, W. C. Guida, J. Phys. Chem. A 106, 1327-1335 (2002). +REF4: T. D. Bergazin, N. Tielker, Y. Zhang, J. Mao, M. R. Gunner, K. Francisco, C. Ballatore, S. M. Kast, D. L. Mobley, J. Comput.-Aided Mol. Des., accepted (2021). +REF5: N. Tielker, L. Eberlein, C. Chodun, S. Guessregen, S. M. Kast, J. Mol. Model. 25, 139 (2019). + +Macro pKa values: +SAMPL8-1,-2.47,0.,1. +SAMPL8-1,4.80,-1.,0. +SAMPL8-2,5.36,-1.,0. +SAMPL8-3,-11.71,0.,1. +SAMPL8-3,4.31,-1.,0. +SAMPL8-3,10.48,-2.,-1. +SAMPL8-4,0.13,0.,1. +SAMPL8-4,4.74,-1.,0. +SAMPL8-5,-2.58,0.,1. +SAMPL8-5,5.08,-1.,0. +SAMPL8-6,2.94,0.,1. +SAMPL8-6,4.78,-1.,0. +SAMPL8-7,4.17,0.,1. +SAMPL8-7,15.11,-1.,0. +SAMPL8-8,-0.33,0.,1. +SAMPL8-9,5.68,0.,1. +SAMPL8-9,14.42,-1.,0. +SAMPL8-10,7.24,0.,1. +SAMPL8-11,8.93,0.,1. +SAMPL8-11,0.18,1.,2. +SAMPL8-12,4.92,0.,1. +SAMPL8-12,17.90,-1.,0. +SAMPL8-12,-4.99,1.,2. +SAMPL8-13,0.11,0.,1. +SAMPL8-13,15.16,-1.,0. +SAMPL8-14,5.37,0.,1. +SAMPL8-14,11.61,-1.,0. +SAMPL8-14,-3.81,1.,2. +SAMPL8-14,16.54,-2.,-1. +SAMPL8-14,20.86,-3.,-2. +SAMPL8-15,1.45,0.,1. +SAMPL8-16,4.03,0.,1. +SAMPL8-17,4.82,0.,1. +SAMPL8-17,14.34,-1.,0. +SAMPL8-18,1.77,0.,1. +SAMPL8-18,11.55,-1.,0. +SAMPL8-19,4.15,0.,1. +SAMPL8-19,7.06,-1.,0. +SAMPL8-19,-2.05,1.,2. +SAMPL8-20,1.57,0.,1. +SAMPL8-21,3.71,0.,1. +SAMPL8-21,8.32,-1.,0. +SAMPL8-21,-5.42,1.,2. +SAMPL8-21,17.48,-2.,-1. +SAMPL8-21,20.47,-3.,-2. +SAMPL8-22,2.10,0.,1. +SAMPL8-22,14.86,-1.,0. +SAMPL8-22,-7.64,1.,2. +SAMPL8-23,2.08,0.,1. +SAMPL8-23,10.19,-1.,0. + +Ranked: +True diff --git a/physical_properties/pKa/submissions/README.md b/physical_properties/pKa/submissions/README.md index 236f4a2..b625903 100644 --- a/physical_properties/pKa/submissions/README.md +++ b/physical_properties/pKa/submissions/README.md @@ -6,4 +6,6 @@ ### File Modification - There were issues in reading the following files `pKa-3DS-1.csv`,`pKa-3DS-2.csv`, `pKa-3DS-3.csv`,`PKA_ECRISM.csv` and `pKa_Chemaxon.csv` given that the SMILE strings were in the same line as the predictions. Hence, these files were modified by removing the smile strings before analysis. - The `pKa_Chemaxon.csv` file was modified by removing comments with SMILE strings. -- Since there were no experimental values for the following compounds - SAMPL8-11 and SAMPL8-13 the predictions were also deleted from each one of the submssions to use the automated analysis scripts. \ No newline at end of file +- Since there were no experimental values for the following compounds - SAMPL8-11 and SAMPL8-13 the predictions were also deleted from each one of the submssions to use the automated analysis scripts. +-Changed Method category for `pKa-3DS.csv` files from LFER to QM+LEC. +-Changed Name of method for the pKa-ECRISM from EC_RISM to EC-RISM \ No newline at end of file diff --git a/physical_properties/pKa/submissions/pKa-3DS-1_modified.csv b/physical_properties/pKa/submissions/pKa-3DS-1_modified.csv new file mode 100644 index 0000000..2ffc072 --- /dev/null +++ b/physical_properties/pKa/submissions/pKa-3DS-1_modified.csv @@ -0,0 +1,383 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction),,,,,, +#,,,,,, +# This file will be automatically parsed. It must contain the following four elements:,,,,,, +# predictions, name of method, software listing, and method description.,,, +# These elements must be provided in the order shown with their respective headers.,,,,,, +#,,,,,, +# Any line that begins with a # is considered a comment and will be ignored when parsing.,,,,,, +#,,,,,, +# PREDICTION SECTION,,,,,, +#,,,,,, +# It is mandatory to submit relative free energy (RFE) predictions for all 23 molecules. Incomplete submissions will not be accepted.,,,,,, +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty.,,,,,, +# Note that we here follow the same sign convention and submission format as the SAMPL7 pKa challenge.,,,,,, +#,,,,,, +# The data in each prediction line should be structured as follows:,,,,,, +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, +#,,,,,, +# If you have evaluated additional microstates, include the following:,,,,, +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +#,,,,,, +# The molecule ID of the other microstate needs to be in the format: `SAMPL8-X_extra001` (number can vary),,,,,, +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders,,,,,, +# Please send the `.mol2` file to the email listed on the instructions page.,,,,,, +#,,,,,, +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here.,,,,,, +Predictions: +SAMPL8-1_micro000,SAMPL8-1_COSMO-RS_one_pKa_fit_extra001,1,1.1,0.1,1.4 +SAMPL8-1_micro000,SAMPL8-1_COSMO-RS_one_pKa_fit_extra002,1,1.12,0.1,1.4 +SAMPL8-1_micro000,SAMPL8-1_micro000,0,0.0,0.1,1.4 +SAMPL8-1_micro000,SAMPL8-1_micro007,0,15.42,0.1,1.4 +SAMPL8-1_micro000,SAMPL8-1_micro010,0,14.07,0.1,1.4 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,5.03,0.1,1.4 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-11.52,0.1,0.73 +SAMPL8-10_micro000,SAMPL8-10_micro000,0,0.0,0.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_one_pKa_fit_extra001,2,-2.48,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_one_pKa_fit_extra007,2,-8.9,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_one_pKa_fit_extra008,2,-15.46,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_one_pKa_fit_extra002,1,-3.86,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_one_pKa_fit_extra003,1,-11.7,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_one_pKa_fit_extra004,1,-9.45,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_one_pKa_fit_extra005,1,-3.09,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_one_pKa_fit_extra009,1,-9.43,, +SAMPL8-12_micro000,SAMPL8-12_micro000,0,0.0,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_micro002,0,8.49,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_micro003 ,0,6.11,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_micro001,-1,19.98,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra009,2,-24.98,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra001,1,-20.17,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra002,1,-17.95,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra003,1,-9.57,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra004,1,-12.04,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra010,1,-13.11,, +SAMPL8-14_micro000,SAMPL8-14_micro024,0,-8.34,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra005,0,-4.46,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra006,0,-1.07,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra007,0,8.49,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_one_pKa_fit_extra008,0,3.48,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro000,0,0.0,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro002,0,-1.6,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro013,0,-2.12,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro017,0,-0.72,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,5.03,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro004,-1,17.03,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro005,-1,12.52,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro010,-1,10.84,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro021,-1,16.17,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro022,-1,12.07,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro027,-1,15.61,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro028,-1,11.87,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro029,-1,13.36,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro032,-1,11.67,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro007,-2,29.11,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro018,-2,33.99,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro020,-2,29.99,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro001,-2,25.5,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro003,-2,23.78,0.1,1.4 +SAMPL8-15_micro000,SAMPL8-15_micro004,1,-11.73,0.1,0.73 +SAMPL8-15_micro000,SAMPL8-15_micro003,1,-7.07,0.1,0.73 +SAMPL8-15_micro000,SAMPL8-15_micro001,0,-6.24,0.1,0.73 +SAMPL8-15_micro000,SAMPL8-15_micro000,0,0.0,0.1,0.73 +SAMPL8-15_micro000,SAMPL8-15_micro002,0,0.13,0.1,0.73 +SAMPL8-16_micro000,SAMPL8-16_micro004,1,-9.29,0.1,1.4 +SAMPL8-16_micro000,SAMPL8-16_micro008,1,3.73,0.1,1.4 +SAMPL8-16_micro000,SAMPL8-16_micro000,0,0.0,0.1,1.4 +SAMPL8-16_micro000,SAMPL8-16_COSMO-RS_one_pKa_fit_extra002,0,9.79,0.1,1.4 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+SAMPL8-6_micro000,SAMPL8-6_micro001,-1,4.18,0.1,1.4 +SAMPL8-6_micro000,SAMPL8-6_micro009,-1,23.45,0.1,1.4 +SAMPL8-7_micro000,SAMPL8-7_micro002,1,-10.91,0.1,1.4 +SAMPL8-7_micro000,SAMPL8-7_micro003,1,0.37,0.1,1.4 +SAMPL8-7_micro000,SAMPL8-7_micro000,0,0.0,0.1,1.4 +SAMPL8-7_micro000,SAMPL8-7_micro004,0,2.36,0.1,1.4 +SAMPL8-7_micro000,SAMPL8-7_micro001,-1,16.43,0.1,1.4 +SAMPL8-8_micro000,SAMPL8-8_micro001,1,-2.56,0.1,0.73 +SAMPL8-8_micro000,SAMPL8-8_micro002,1,13.47,0.1,0.73 +SAMPL8-8_micro000,SAMPL8-8_micro000,0,0.0,0.1,0.73 +SAMPL8-9_micro002,SAMPL8-9_micro002,1,-10.6,0.1,1.4 +SAMPL8-9_micro002,SAMPL8-9_micro004,1,-0.11,0.1,1.4 +SAMPL8-9_micro002,SAMPL8-9_micro000,0,0.0,0.1,1.4 +SAMPL8-9_micro002,SAMPL8-9_micro003,0,2.2,0.1,1.4 +SAMPL8-9_micro002,SAMPL8-9_micro001,-1,16.75,0.1,1.4 + +#,,,,,, +#,,,,,, +# Please list your name," using only UTF-8 characters as described above. The ""Participant name:"" entry is required.",,,,, +Participant name: +"Michael Diedenhofen, Selman Terzi, Frank Eckert" + +#,,,,,, +#,,,,,, +# Please list your organization/affiliation, using only UTF-8 characters as described above.,,,,, +Participant organization: +Dassault Systemes Deutschland GmbH BIOVIA + +#,,,,,, +#,,,,,, +# NAME SECTION +#,,,,,, +# Please provide an informal but informative name of the method used.,,,,,, +# The name of the method should not exceed 40 characters.,,,,,, +# The 'Name:' keyword is required as shown here.,,,,,, +Name: +COSMO-RS one pKa fit + +#,,,,,, +#,,,,,, +# COMPUTE TIME SECTION,,,,,, +#,,,,,, +# Please provide the average compute time across all of the molecules.,,,,,, +# For physical methods, report the GPU and/or CPU compute time in hours.,,,,, +# For empirical methods, report the query time in hours.,,,,, +# Create a new line for each processor type.,,,,,, +# The 'Compute time:' keyword is required as shown here.,,,,,, +Compute time: +1076 hours, CPU + +#,,,,,, +# COMPUTING AND HARDWARE SECTION,,,,,, +#,,,,,, +# Please provide details of the computing resources that were used to train models and make predictions.,,,,,, +# Please specify compute time for training models and querying separately for empirical prediction methods.,,,,,, +# Provide a detailed description of the hardware used to run the simulations.,,,,,, +# The 'Computing and hardware:' keyword is required as shown here.,,,,,, +Computing and hardware: +We have use a linux cluster (Intel(R) Xeon(R) Gold 6248R CPU @ 3.00GHz). The calculations could use up to 20 cores. The number of actually use CPU differ during the steps of the conformer search procedure +The timings given above are wall times estimated from 33 structures and extrapolated to 203 microstates + +# SOFTWARE SECTION,,,,,, +#,,,,,, +# List all major software packages used and their versions.,,,,,, +# Create a new line for each software.,,,,,, +# The 'Software:' keyword is required.,,,,,, +Software: +BIOVIA COSMOquick 2021: A proprietary tool of Dassault Systemes to generate tautomeric states. +BIOVIA COSMOconf 2021: A proprietary tool of Dassault Systemes for conformer generation (uses TURBOMOLE and COSMOtherm) +BIOVIA COSMOtherm 2021: The proprietary software developed and distributed by Dassault Systemes, which uses COSMO-RS. COSMO-RS is a published theory: Klamt A (1995) Conductor-like screening model for real solvents: a new approach to the quantitative calculation of solvation phenomena. J Phys Chem 99:2224-2235. https://doi.org/10.1021/j100007a062 +TURBOMOLE 7.5: The quantum chemistry suite. University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989-2007, TURBOMOLE GmbH, since 2007; available from http://www.turbomole.com: Karlsruhe, Germany,2020 +# METHOD CATEGORY SECTION +#,,,,,, +# State if your prediction method is better classified as an,,,,,, +# experimental database lookup (DL), linear free energy relationship (LFER),,,,, +# quantitative structure-property relationship or machine learning (QSPR/ML),,,,,, +# quantum mechanics without empirical correction (QM) model, quantum mechanics with,,,,, +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular,,,,, +# mechanics (QM+MM), or Other, using the following category labels:,,,, +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`., +#,,,,,, +# Pick only one category label.,,,,,, +# The `Category:` keyword is required.,,,,,, +Category: +QM+LEC + +# METHOD DESCRIPTION SECTION,,,,,, +#,,,,,, +# Methodology and computational details.,,,,,, +# Level of details should be roughly equivalent to that used in a publication.,,,,,, +# Please include the values of key parameters with units.,,,,,, +# Please explain how statistical uncertainties were estimated.,,,,,, +# Use as many lines of text as you need.,,,,,, +#,,,,,, +# We strongly encourage you to submit your predicted macro pKa values in this section in consecutive lines following this format:,,,,,, +# compound name, macro pKa, initial formal charge, formal charge after transition, e.g.:,, +# SAMPL8-1,3.5,0,1,,, +Method: +Workflow +"1) We used COSMOquick to generate possible tautomeric and ionic states. Irrelevant states where discarded due to an internal energy threshold implemented in COSMOquick. In a subsequent manual check we discarded all dissociated structures. After a first DFT optimization we checked the relative energies of the microstates with same charge and reduced the number of states with an energy threshold. We performed DFT optimizations of the SAMPL8 microstates proposals and checked the structures against the already created microstates. Missing, energetically relevant structures were added to the set." +2) COSMOconf was used to create the conformer set of the microstates. +3) The conformer sets of the microstates were used to calculate the pKa values of the reactions between the microstates. We used the COSMO-RS theory with the BP-TZVPD-FINE 21 parametrization. The pKa values were predicted using a LFER approach based on the fee Gibbs energies of the microstates at infinite dilution in water. +"We normally use two LFER fits, one for the pKa (HA +H2O -> H3O+ + A-) and one for the pKa of the conjugated base (BH+ + H2O -> B + H3O+). Here we used the pKa model for SAMPL8-2 and the base pKa model for SAMPL8-10, SAMPL8-11, SAMPL8-15, SAMPL8-8. All other predictions have been done with a harmonized LFER model (fit of one model for the pKa and base pKa data). The RSME values in kcal/mol are 0.7 for the pKa model, 0.73 for the base pKa model, and 1.4 for the harmonized model." +The COSMO-RS algorithm by itself has no statistical error. The overall workflow including the conformational search (or molecule or state) has a statistical noise smaller than 0.1 kcal/mol. + +#,,,,,, +Macro pKa values +SAMPL8-1,-0.61,1,0 +SAMPL8-1,3.69,0,-1 +SAMPL8-2,3.99,0,-1 +SAMPL8-3,-1.04,1,0 +SAMPL8-3,3.39,0,-1 +SAMPL8-3,7.41,-1,-2 +SAMPL8-4,2.6,1,0 +SAMPL8-4,3.44,0,-1 +SAMPL8-5,-1.58,1,0 +SAMPL8-5,3.23,0,-1 +SAMPL8-6,3.76,1,0 +SAMPL8-6,3.25,0,-1 +SAMPL8-7,8,1,0 +SAMPL8-7,12.04,0,-1 +SAMPL8-8,1.88,1,0 +SAMPL8-9,7.77,1,0 +SAMPL8-9,12.28,0,-1 +SAMPL8-10,8.44,1,0 +SAMPL8-11,3.02,2,1 +SAMPL8-11,11.02,1,0 +SAMPL8-12,2.76,2,1 +SAMPL8-12,8.58,1,0 +SAMPL8-12,14.65,0,-1 +SAMPL8-13,2.69,1,0 +SAMPL8-13,12.62,0,-1 +SAMPL8-14,3.53,2,1 +SAMPL8-14,8.68,1,0 +SAMPL8-14,9.8,0,-1 +SAMPL8-14,13.71,-1,-2 +SAMPL8-15,4.02,1,0 +SAMPL8-16,6.81,1,0 +SAMPL8-16,10.84,0,-1 +SAMPL8-16,12.27,-1,-2 +SAMPL8-17,7.44,1,0 +SAMPL8-17,11.57,0,-1 +SAMPL8-18,5.29,1,0 +SAMPL8-18,11.35,0,-1 +SAMPL8-19,3.45,2,1 +SAMPL8-19,6.12,1,0 +SAMPL8-19,6.67,0,-1 +SAMPL8-20,0.41,2,1 +SAMPL8-20,4.64,1,0 +SAMPL8-20,10.19,0,-1 +SAMPL8-21,2.99,2,1 +SAMPL8-21,7.86,1,0 +SAMPL8-21,8.65,0,-1 +SAMPL8-21,13.2,-1,-2 +SAMPL8-22,-0.84,2,1 +SAMPL8-22,5.52,1,0 +SAMPL8-22,12.61,0,-1 +SAMPL8-23,4.51,1,0 +SAMPL8-23,8.97,0,-1 + +#,,,,,, +#,,,,,, +# All submissions must either be ranked or non-ranked.,,,,,, +# Only one ranked submission per participant is allowed.,,,,,, +# Multiple ranked submissions from the same participant will not be judged.,,,,,, +# Non-ranked submissions are accepted so we can verify that they were made before the deadline.,,,,,, +"# The ""Ranked:"" keyword is required", and expects a Boolean value (True/False),,,,, +Ranked: +True diff --git a/physical_properties/pKa/submissions/pKa-3DS-2_modified.csv b/physical_properties/pKa/submissions/pKa-3DS-2_modified.csv new file mode 100644 index 0000000..30ecd2b --- /dev/null +++ b/physical_properties/pKa/submissions/pKa-3DS-2_modified.csv @@ -0,0 +1,385 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction),,,,,, +#,,,,,, +# This file will be automatically parsed. It must contain the following four elements:,,,,,, +# predictions, name of method, software listing, and method description.,,, +# These elements must be provided in the order shown with their respective headers.,,,,,, +#,,,,,, +# Any line that begins with a # is considered a comment and will be ignored when parsing.,,,,,, +#,,,,,, +# PREDICTION SECTION,,,,,, +#,,,,,, +# It is mandatory to submit relative free energy (RFE) predictions for all 23 molecules. Incomplete submissions will not be accepted.,,,,,, +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty.,,,,,, +# Note that we here follow the same sign convention and submission format as the SAMPL7 pKa challenge.,,,,,, +#,,,,,, +# The data in each prediction line should be structured as follows:,,,,,, +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, +#,,,,,, +# If you have evaluated additional microstates, include the following:,,,,, +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +#,,,,,, +# The molecule ID of the other microstate needs to be in the format: `SAMPL8-X_extra001` (number can vary),,,,,, +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders,,,,,, +# Please send the `.mol2` file to the email listed on the instructions page.,,,,,, +#,,,,,, +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here.,,,,,, +Predictions: +SAMPL8-1_micro000,SAMPL8-1_COSMO-RS_base_pKa_fit_extra001,1,4.48,0.1,0.73 +SAMPL8-1_micro000,SAMPL8-1_COSMO-RS_base_pKa_fit_extra002,1,4.51,1.1,0.73 +SAMPL8-1_micro000,SAMPL8-1_micro000,0,0.0,2.1,0.73 +SAMPL8-1_micro000,SAMPL8-1_micro007,0,18.66,3.1,0.73 +SAMPL8-1_micro000,SAMPL8-1_micro010,0,17.03,4.1,0.73 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,2.93,5.1,1.4 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-11.52,6.1,0.73 +SAMPL8-10_micro000,SAMPL8-10_micro000,0,0.0,7.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_base_pKa_fit_extra001,2,3.32,14.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_base_pKa_fit_extra007,2,-4.46,15.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_base_pKa_fit_extra008,2,-12.4,16.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_base_pKa_fit_extra002,1,-1.51,17.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_base_pKa_fit_extra003,1,-11.0,18.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_base_pKa_fit_extra004,1,-8.28,19.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_base_pKa_fit_extra005,1,-0.58,20.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_base_pKa_fit_extra009,1,-8.26,21.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_micro000,0,0.0,22.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_micro002,0,10.28,23.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_micro003 ,0,7.4,24.1,0.73 +SAMPL8-12_micro000,SAMPL8-12_micro001,-1,21.02,25.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra009,2,-23.92,30.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra001,1,-21.26,31.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra002,1,-18.57,32.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra003,1,-8.42,33.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra004,1,-11.41,34.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra010,1,-12.7,35.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_micro024,0,-10.09,36.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra005,0,-5.4,37.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra006,0,-1.29,38.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra007,0,10.27,39.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_base_pKa_fit_extra008,0,4.21,40.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_micro000,0,0.0,41.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_micro002,0,-1.93,42.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_micro013,0,-2.56,43.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_micro017,0,-0.88,44.1,0.73 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,2.93,45.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro004,-1,17.45,46.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro005,-1,12.0,47.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro010,-1,9.96,48.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro021,-1,16.41,49.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro022,-1,11.45,50.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro027,-1,15.73,51.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro028,-1,11.2,52.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro029,-1,13.01,53.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro032,-1,10.97,54.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro007,-2,28.91,55.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro018,-2,34.82,56.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro020,-2,29.98,57.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro001,-2,24.54,58.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro003,-2,22.46,59.1,1.4 +SAMPL8-15_micro000,SAMPL8-15_micro004,1,-11.73,60.1,0.73 +SAMPL8-15_micro000,SAMPL8-15_micro003,1,-7.07,61.1,0.73 +SAMPL8-15_micro000,SAMPL8-15_micro001,0,-6.24,62.1,0.73 +SAMPL8-15_micro000,SAMPL8-15_micro000,0,0.0,63.1,0.73 +SAMPL8-15_micro000,SAMPL8-15_micro002,0,0.13,64.1,0.73 +SAMPL8-16_micro000,SAMPL8-16_micro004,1,-8.09,65.1,0.73 +SAMPL8-16_micro000,SAMPL8-16_micro008,1,7.67,66.1,0.73 +SAMPL8-16_micro000,SAMPL8-16_micro000,0,0.0,67.1,0.73 +SAMPL8-16_micro000,SAMPL8-16_COSMO-RS_base_pKa_fit_extra002,0,11.85,68.1,0.73 +SAMPL8-16_micro000,SAMPL8-16_micro007,0,13.75,69.1,0.73 +SAMPL8-16_micro000,SAMPL8-16_micro011,0,15.66,70.1,0.73 +SAMPL8-16_micro000,SAMPL8-16_COSMO-RS_base_pKa_fit_extra003,-1,14.74,71.1,1.4 +SAMPL8-16_micro000,SAMPL8-16_COSMO-RS_base_pKa_fit_extra004,-1,18.87,72.1,1.4 +SAMPL8-16_micro000,SAMPL8-16_COSMO-RS_base_pKa_fit_extra005,-2,31.83,73.1,1.4 +SAMPL8-17_micro000,SAMPL8-17_micro002,1,-9.14,74.1,0.73 +SAMPL8-17_micro000,SAMPL8-17_micro003,1,2.81,75.1,0.73 +SAMPL8-17_micro000,SAMPL8-17_micro000,0,0.0,76.1,0.73 +SAMPL8-17_micro000,SAMPL8-17_micro004,0,1.63,77.1,0.73 +SAMPL8-17_micro000,SAMPL8-17_micro001,-1,15.93,78.1,1.4 +SAMPL8-18_micro000,SAMPL8-18_COSMO-RS_base_pKa_fit_extra001,1,-0.81,79.1,0.73 +SAMPL8-18_micro000,SAMPL8-18_micro004,1,-13.07,80.1,0.73 +SAMPL8-18_micro000,SAMPL8-18_micro003,1,-7.65,81.1,0.73 +SAMPL8-18_micro000,SAMPL8-18_micro002,0,-7.5,82.1,0.73 +SAMPL8-18_micro000,SAMPL8-18_micro001,0,-0.01,83.1,0.73 +SAMPL8-18_micro000,SAMPL8-18_micro000,0,0.0,84.1,0.73 +SAMPL8-18_micro000,SAMPL8-18_micro005,-1,8.08,85.1,1.4 +SAMPL8-19_micro000,SAMPL8-19_COSMO-RS_base_pKa_fit_extra001,2,-15.38,86.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_COSMO-RS_base_pKa_fit_extra002,2,-15.0,87.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro002,2,-13.63,88.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro003,2,-8.18,89.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro017,2,-12.57,90.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro005,1,-12.77,91.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro009,1,-12.67,92.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro004,1,-0.1,93.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro022,1,-3.71,94.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro008,1,-8.97,95.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro006,1,-7.5,96.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro019,1,-6.05,97.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro013,0,-5.79,98.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_COSMO-RS_base_pKa_fit_extra003,0,0.56,99.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro024,0,-4.45,100.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro007,0,-5.63,101.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro000,0,0.0,102.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro015,0,-1.94,103.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro020,0,6.79,104.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro025,0,-0.59,105.1,0.73 +SAMPL8-19_micro000,SAMPL8-19_micro011,-1,1.76,106.1,1.4 +SAMPL8-19_micro000,SAMPL8-19_micro010,-1,10.26,107.1,1.4 +SAMPL8-2_micro000,SAMPL8-2_micro000,0,0.0,108.1,0.73 +SAMPL8-2_micro000,SAMPL8-2_micro002,0,18.4,109.1,0.73 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,2.24,110.1,1.4 +SAMPL8-20_micro000,SAMPL8-20_COSMO-RS_base_pKa_fit_extra001,2,-14.19,111.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro006,1,-16.44,112.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro015,1,-9.11,113.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro011,1,-10.1,114.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro002,1,-15.02,115.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro003,1,-16.13,116.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro026,1,-14.9,117.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro016,1,-2.55,118.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro022,0,-12.16,119.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro018,0,-4.9,120.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro017,0,-10.52,121.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_COSMO-RS_base_pKa_fit_extra002,0,-3.11,122.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro000,0,0.0,123.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_micro001,0,1.8,124.1,0.73 +SAMPL8-20_micro000,SAMPL8-20_COSMO-RS_base_pKa_fit_extra003,-1,1.48,125.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra001,2,-14.8,126.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra010,2,-28.07,127.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra011,2,-19.06,128.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra002,1,-26.29,129.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra003,1,-23.99,130.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra004,1,-16.83,131.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra005,1,-17.83,132.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra012,1,-16.34,133.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_micro028,0,-16.48,134.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra006,0,-13.17,135.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra007,0,-12.0,136.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra008,0,-2.16,137.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_base_pKa_fit_extra009,0,-4.34,138.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_micro000,0,0.0,139.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_micro008,0,-4.17,140.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_micro023,0,-8.18,141.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_micro025,0,-8.15,142.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_micro029,0,-4.95,143.1,0.73 +SAMPL8-21_micro000,SAMPL8-21_micro022,-1,-5.35,144.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro016,-1,3.62,145.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro007,-1,14.81,146.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro009,-1,4.18,147.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro018,-1,0.47,148.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro020,-1,3.73,149.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro024,-1,1.94,150.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro026,-1,6.33,151.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro027,-1,8.22,152.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro013,-2,16.73,153.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro004,-2,24.8,154.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro005,-2,13.33,155.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro012,-2,26.14,156.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro015,-2,14.63,157.1,1.4 +SAMPL8-22_micro000,SAMPL8-22_COSMO-RS_base_pKa_fit_extra004,2,-10.62,158.1,0.73 +SAMPL8-22_micro000,SAMPL8-22_COSMO-RS_base_pKa_fit_extra001,1,-15.16,159.1,0.73 +SAMPL8-22_micro000,SAMPL8-22_COSMO-RS_base_pKa_fit_extra002,1,-13.42,160.1,0.73 +SAMPL8-22_micro000,SAMPL8-22_COSMO-RS_base_pKa_fit_extra003,1,-4.66,161.1,0.73 +SAMPL8-22_micro000,SAMPL8-22_micro002,0,-9.21,162.1,0.73 +SAMPL8-22_micro000,SAMPL8-22_micro000,0,0.0,163.1,0.73 +SAMPL8-22_micro000,SAMPL8-22_micro003,0,0.64,164.1,0.73 +SAMPL8-22_micro000,SAMPL8-22_micro001,-1,8.46,165.1,1.4 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-17.25,166.1,0.73 +SAMPL8-23_micro000,SAMPL8-23_micro007,0,-12.97,167.1,0.73 +SAMPL8-23_micro000,SAMPL8-23_micro003,0,-5.73,168.1,0.73 +SAMPL8-23_micro000,SAMPL8-23_micro000,0,0.0,169.1,0.73 +SAMPL8-23_micro000,SAMPL8-23_micro005,-1,-1.31,170.1,1.4 +SAMPL8-23_micro000,SAMPL8-23_micro002,-1,12.11,171.1,1.4 +SAMPL8-3_micro000,SAMPL8-3_COSMO-RS_base_pKa_fit_extra001,1,-27.19,172.1,0.73 +SAMPL8-3_micro000,SAMPL8-3_COSMO-RS_base_pKa_fit_extra003,1,-19.07,173.1,0.73 +SAMPL8-3_micro000,SAMPL8-3_micro000,0,0.0,174.1,0.73 +SAMPL8-3_micro000,SAMPL8-3_micro006,0,-32.06,175.1,0.73 +SAMPL8-3_micro000,SAMPL8-3_COSMO-RS_base_pKa_fit_extra002,0,-18.65,176.1,0.73 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,-23.22,177.1,1.4 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,-29.63,178.1,1.4 +SAMPL8-3_micro000,SAMPL8-3_micro013,-2,-20.55,179.1,1.4 +SAMPL8-4_micro000,SAMPL8-4_micro002,1,-6.54,180.1,0.73 +SAMPL8-4_micro000,SAMPL8-4_micro010,0,-5.09,181.1,0.73 +SAMPL8-4_micro000,SAMPL8-4_COSMO-RS_base_pKa_fit_extra001,0,17.45,182.1,0.73 +SAMPL8-4_micro000,SAMPL8-4_COSMO-RS_base_pKa_fit_extra002,0,15.65,183.1,0.73 +SAMPL8-4_micro000,SAMPL8-4_micro000,0,0.0,184.1,0.73 +SAMPL8-4_micro000,SAMPL8-4_micro001,0,-5.04,185.1,0.73 +SAMPL8-4_micro000,SAMPL8-4_micro005,-1,-2.88,186.1,1.4 +SAMPL8-4_micro000,SAMPL8-4_micro003,-1,1.17,187.1,1.4 +SAMPL8-4_micro000,SAMPL8-4_micro008,-1,8.6,188.1,1.4 +SAMPL8-5_micro000,SAMPL8-5_micro003,1,5.77,189.1,0.73 +SAMPL8-5_micro000,SAMPL8-5_micro006,1,17.05,190.1,0.73 +SAMPL8-5_micro000,SAMPL8-5_micro000,0,0.0,191.1,0.73 +SAMPL8-5_micro000,SAMPL8-5_micro005,0,13.49,192.1,0.73 +SAMPL8-5_micro000,SAMPL8-5_micro001,0,8.58,193.1,0.73 +SAMPL8-5_micro000,SAMPL8-5_micro007,-1,2.17,194.1,1.4 +SAMPL8-6_micro000,SAMPL8-6_micro003,1,-3.35,195.1,0.73 +SAMPL8-6_micro000,SAMPL8-6_micro000,0,0.0,196.1,0.73 +SAMPL8-6_micro000,SAMPL8-6_micro007,0,-0.42,197.1,0.73 +SAMPL8-6_micro000,SAMPL8-6_micro001,-1,1.91,198.1,1.4 +SAMPL8-6_micro000,SAMPL8-6_micro009,-1,25.23,199.1,1.4 +SAMPL8-7_micro000,SAMPL8-7_micro002,1,-10.05,200.1,0.73 +SAMPL8-7_micro000,SAMPL8-7_micro003,1,3.61,201.1,0.73 +SAMPL8-7_micro000,SAMPL8-7_micro000,0,0.0,202.1,0.73 +SAMPL8-7_micro000,SAMPL8-7_micro004,0,2.86,203.1,0.73 +SAMPL8-7_micro000,SAMPL8-7_micro001,-1,16.72,204.1,1.4 +SAMPL8-8_micro000,SAMPL8-8_micro001,1,-2.56,205.1,0.73 +SAMPL8-8_micro000,SAMPL8-8_micro002,1,13.47,206.1,0.73 +SAMPL8-8_micro000,SAMPL8-8_micro000,0,0.0,207.1,0.73 +SAMPL8-9_micro002,SAMPL8-9_micro002,1,-9.67,208.1,0.73 +SAMPL8-9_micro002,SAMPL8-9_micro004,1,3.02,209.1,0.73 +SAMPL8-9_micro002,SAMPL8-9_micro000,0,0.0,210.1,0.73 +SAMPL8-9_micro002,SAMPL8-9_micro003,0,2.66,211.1,0.73 +SAMPL8-9_micro002,SAMPL8-9_micro001,-1,17.12,212.1,1.4 + +#,,,,,, +#,,,,,, +# Please list your name," using only UTF-8 characters as described above. The ""Participant name:"" entry is required.",,,,, +Participant name: +"Michael Diedenhofen, Selman Terzi, Frank Eckert" + +#,,,,,, +#,,,,,, +# Please list your organization/affiliation, using only UTF-8 characters as described above.,,,,, +Participant organization: +Dassault Systemes Deutschland GmbH, BIOVIA + +#,,,,,, +#,,,,,, +# NAME SECTION,,,,,, +#,,,,,, +# Please provide an informal but informative name of the method used.,,,,,, +# The name of the method should not exceed 40 characters.,,,,,, +# The 'Name:' keyword is required as shown here.,,,,,, +Name: +COSMO-RS base pKa fit + +#,,,,,, +#,,,,,, +# COMPUTE TIME SECTION,,,,,, +#,,,,,, +# Please provide the average compute time across all of the molecules.,,,,,, +# For physical methods, report the GPU and/or CPU compute time in hours.,,,,, +# For empirical methods, report the query time in hours.,,,,, +# Create a new line for each processor type.,,,,,, +# The 'Compute time:' keyword is required as shown here.,,,,,, +Compute time: +1076 hours, CPU + +#,,,,,, +# COMPUTING AND HARDWARE SECTION,,,,,, +#,,,,,, +# Please provide details of the computing resources that were used to train models and make predictions.,,,,,, +# Please specify compute time for training models and querying separately for empirical prediction methods.,,,,,, +# Provide a detailed description of the hardware used to run the simulations.,,,,,, +# The 'Computing and hardware:' keyword is required as shown here.,,,,,, +Computing and hardware: +We have use a linux cluster (Intel(R) Xeon(R) Gold 6248R CPU @ 3.00GHz). The calculations could use up to 20 cores. The number of actually use CPU differ during the steps of the conformer search procedure +The timings given above are wall times estimated from 33 structures and extrapolated to 203 microstates + +# SOFTWARE SECTION,,,,,, +#,,,,,, +# List all major software packages used and their versions.,,,,,, +# Create a new line for each software.,,,,,, +# The 'Software:' keyword is required.,,,,,, +Software: +BIOVIA COSMOquick 2021: A proprietary tool of Dassault Systemes to generate tautomeric states. +BIOVIA COSMOconf 2021: A proprietary tool of Dassault Systemes for conformer generation, TURBOMOLE and COSMOtherm. +BIOVIA COSMOtherm 2021: The proprietary software developed and distributed by Dassault Systemes, which uses COSMO-RS. COSMO-RS is a published theory: Klamt A (1995) Conductor-like screening model for real solvents: a new approach to the quantitative calculation of solvation phenomena. J Phys Chem 99:2224-2235. https://doi.org/10.1021/j100007a062 +TURBOMOLE 7.5: The quantum chemistry suite. University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989-2007, TURBOMOLE GmbH, since 2007; available from http://www.turbomole.com: Karlsruhe, Germany,2020, + +# METHOD CATEGORY SECTION,,,,,, +#,,,,,, +# State if your prediction method is better classified as an,,,,,, +# experimental database lookup (DL), linear free energy relationship (LFER),,,,, +# quantitative structure-property relationship or machine learning (QSPR/ML),,,,,, +# quantum mechanics without empirical correction (QM) model, quantum mechanics with,,,,, +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular,,,,, +# mechanics (QM+MM), or Other, using the following category labels:,,,, +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`., +#,,,,,, +# Pick only one category label.,,,,,, +# The `Category:` keyword is required.,,,,,, +Category: +QM+LEC + +# METHOD DESCRIPTION SECTION,,,,,, +#,,,,,, +# Methodology and computational details.,,,,,, +# Level of details should be roughly equivalent to that used in a publication.,,,,,, +# Please include the values of key parameters with units.,,,,,, +# Please explain how statistical uncertainties were estimated.,,,,,, +# Use as many lines of text as you need.,,,,,, +#,,,,,, +# We strongly encourage you to submit your predicted macro pKa values in this section in consecutive lines following this format:,,,,,, +# compound name, macro pKa, initial formal charge, formal charge after transition, e.g.:,, +# SAMPL8-1,3.5,0,1,,, +Method: +Workflow +"1) We used COSMOquick to generate possible tautomeric and ionic states. Irrelevant states where discarded due to an internal energy threshold implemented in COSMOquick. In a subsequent manual check we discarded all dissociated structures. After a first DFT optimization we checked the relative energies of the microstates with same charge and reduced the number of states with an energy threshold. We performed DFT optimizations of the SAMPL8 microstates proposals and checked the structures against the already created microstates. Missing, energetically relevant structures were added to the set." +2) COSMOconf was used to create the conformer set of the microstates. +4) The conformer sets of the microstates were used to calculate the pKa values of the reactions between the microstates. We used the COSMO-RS theory with the BP-TZVPD-FINE 21 parametrization. The pKa values were predicted using a LFER approach based on the fee Gibbs energies of the microstates at infinite dilution in water. +"We normally use two LFER fits, one for the pKa (HA +H2O -> H3O+ + A-) and one for the pKa of the conjugated base (BH+ + H2O -> B + H3O+). Here we used the pKa model for the conjugated base for all reactions. The RSME value of this model for BH+ + H2O -> B + H3O+ reactions is 0.73 kcal/mol." +The COSMO-RS algorithm by itself has no statistical error. The overall workflow including the conformational search (or molecule or state) has a statistical noise smaller than 0.1 kcal/mol. + +#,,,,,, +Macro pKa values +SAMPL8-1,1,0,-3.05 +SAMPL8-1,0,-1,2.15 +SAMPL8-2,0,-1,1.64 +SAMPL8-3,1,0,-3.58 +SAMPL8-3,0,-1,1.78 +SAMPL8-3,-1,-2,6.66 +SAMPL8-4,1,0,0.84 +SAMPL8-4,0,-1,1.84 +SAMPL8-5,1,0,-4.23 +SAMPL8-5,0,-1,1.59 +SAMPL8-6,1,0,2.23 +SAMPL8-6,0,-1,1.62 +SAMPL8-7,1,0,7.36 +SAMPL8-7,0,-1,12.26 +SAMPL8-8,1,0,1.88 +SAMPL8-9,1,0,7.09 +SAMPL8-9,0,-1,12.55 +SAMPL8-10,1,0,8.44 +SAMPL8-11,2,1,3.02 +SAMPL8-11,1,0,11.02 +SAMPL8-12,2,1,1.02 +SAMPL8-12,1,0,8.07 +SAMPL8-12,0,-1,15.41 +SAMPL8-13,1,0,0.93 +SAMPL8-13,0,-1,12.96 +SAMPL8-14,2,1,1.95 +SAMPL8-14,1,0,8.19 +SAMPL8-14,0,-1,9.55 +SAMPL8-14,-1,-2,14.28 +SAMPL8-15,1,0,4.02 +SAMPL8-16,1,0,5.93 +SAMPL8-16,0,-1,10.80 +SAMPL8-16,-1,-2,12.53 +SAMPL8-17,1,0,6.69 +SAMPL8-17,0,-1,11.69 +SAMPL8-18,1,0,4.08 +SAMPL8-18,0,-1,11.42 +SAMPL8-19,2,1,1.86 +SAMPL8-19,1,0,5.09 +SAMPL8-19,0,-1,5.76 +SAMPL8-20,2,1,-1.82 +SAMPL8-20,1,0,3.30 +SAMPL8-20,0,-1,10.01 +SAMPL8-21,2,1,1.30 +SAMPL8-21,1,0,7.19 +SAMPL8-21,0,-1,8.16 +SAMPL8-21,-1,-2,13.66 +SAMPL8-22,2,1,-3.34 +SAMPL8-22,1,0,4.37 +SAMPL8-22,0,-1,12.95 +SAMPL8-23,1,0,3.14 +SAMPL8-23,0,-1,8.55 + +#,,,,,, +#,,,,,, +# All submissions must either be ranked or non-ranked.,,,,,, +# Only one ranked submission per participant is allowed.,,,,,, +# Multiple ranked submissions from the same participant will not be judged.,,,,,, +# Non-ranked submissions are accepted so we can verify that they were made before the deadline.,,,,,, +"# The ""Ranked:"" keyword is required", and expects a Boolean value (True/False),,,,, + +Ranked: +False \ No newline at end of file diff --git a/physical_properties/pKa/submissions/pKa-3DS-3_modified.csv b/physical_properties/pKa/submissions/pKa-3DS-3_modified.csv new file mode 100644 index 0000000..b4a38b4 --- /dev/null +++ b/physical_properties/pKa/submissions/pKa-3DS-3_modified.csv @@ -0,0 +1,382 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction),,,,,, +#,,,,,, +# This file will be automatically parsed. It must contain the following four elements:,,,,,, +# predictions, name of method, software listing, and method description.,,, +# These elements must be provided in the order shown with their respective headers.,,,,,, +#,,,,,, +# Any line that begins with a # is considered a comment and will be ignored when parsing.,,,,,, +#,,,,,, +# PREDICTION SECTION,,,,,, +#,,,,,, +# It is mandatory to submit relative free energy (RFE) predictions for all 23 molecules. Incomplete submissions will not be accepted.,,,,,, +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty.,,,,,, +# Note that we here follow the same sign convention and submission format as the SAMPL7 pKa challenge.,,,,,, +#,,,,,, +# The data in each prediction line should be structured as follows:,,,,,, +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, +#,,,,,, +# If you have evaluated additional microstates, include the following:,,,,, +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +#,,,,,, +# The molecule ID of the other microstate needs to be in the format: `SAMPL8-X_extra001` (number can vary),,,,,, +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders,,,,,, +# Please send the `.mol2` file to the email listed on the instructions page.,,,,,, +#,,,,,, +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here.,,,,,, +Predictions: +SAMPL8-1_micro000,SAMPL8-1_COSMO-RS_pKa_fit_extra001,1,0.01,0.1,1.4 +SAMPL8-1_micro000,SAMPL8-1_COSMO-RS_pKa_fit_extra002,1,0.03,0.1,1.4 +SAMPL8-1_micro000,SAMPL8-1_micro000,0,0.0,0.1,0.7 +SAMPL8-1_micro000,SAMPL8-1_micro007,0,15.13,0.1,0.7 +SAMPL8-1_micro000,SAMPL8-1_micro010,0,13.81,0.1,0.7 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,6.01,0.1,0.7 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-12.96,0.1,1.4 +SAMPL8-10_micro000,SAMPL8-10_micro000,0,0.0,0.1,0.7 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_pKa_fit_extra001,2,-4.57,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_pKa_fit_extra007,2,-10.87,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_pKa_fit_extra008,2,-17.31,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_pKa_fit_extra002,1,-4.85,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_pKa_fit_extra003,1,-12.54,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_pKa_fit_extra004,1,-10.34,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_pKa_fit_extra005,1,-4.09,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_COSMO-RS_pKa_fit_extra009,1,-10.32,0.1,1.4 +SAMPL8-12_micro000,SAMPL8-12_micro000,0,0.0,0.1,0.7 +SAMPL8-12_micro000,SAMPL8-12_micro002,0,8.33,0.1,0.7 +SAMPL8-12_micro000,SAMPL8-12_micro003 ,0,6.0,0.1,0.7 +SAMPL8-12_micro000,SAMPL8-12_micro001,-1,20.67,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra009,2,-26.65,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra001,1,-20.86,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra002,1,-18.68,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra003,1,-10.45,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra004,1,-12.88,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra010,1,-13.92,0.1,1.4 +SAMPL8-14_micro000,SAMPL8-14_micro024,0,-8.18,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra005,0,-4.37,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra006,0,-1.05,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra007,0,8.33,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_COSMO-RS_pKa_fit_extra008,0,3.41,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro000,0,0.0,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro002,0,-1.56,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro013,0,-2.08,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro017,0,-0.71,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,6.01,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro004,-1,17.77,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro005,-1,13.35,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro010,-1,11.7,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro021,-1,16.93,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro022,-1,12.91,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro027,-1,16.38,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro028,-1,12.71,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro029,-1,14.18,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro032,-1,12.52,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro007,-2,30.69,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro018,-2,35.48,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro020,-2,31.56,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro001,-2,27.15,0.1,0.7 +SAMPL8-14_micro000,SAMPL8-14_micro003,-2,25.46,0.1,0.7 +SAMPL8-15_micro000,SAMPL8-15_micro004,1,-13.13,0.1,1.4 +SAMPL8-15_micro000,SAMPL8-15_micro003,1,-9.36,0.1,1.4 +SAMPL8-15_micro000,SAMPL8-15_micro001,0,-5.06,0.1,0.7 +SAMPL8-15_micro000,SAMPL8-15_micro000,0,0.0,0.1,0.7 +SAMPL8-15_micro000,SAMPL8-15_micro002,0,0.11,0.1,0.7 +SAMPL8-16_micro000,SAMPL8-16_micro004,1,-10.18,0.1,1.4 +SAMPL8-16_micro000,SAMPL8-16_micro008,1,2.59,0.1,1.4 +SAMPL8-16_micro000,SAMPL8-16_micro000,0,0.0,0.1,0.7 +SAMPL8-16_micro000,SAMPL8-16_COSMO-RS_pKa_fit_extra002,0,9.6,0.1,0.7 +SAMPL8-16_micro000,SAMPL8-16_micro007,0,11.15,0.1,0.7 +SAMPL8-16_micro000,SAMPL8-16_micro011,0,12.69,0.1,0.7 +SAMPL8-16_micro000,SAMPL8-16_COSMO-RS_pKa_fit_extra003,-1,15.57,0.1,0.7 +SAMPL8-16_micro000,SAMPL8-16_COSMO-RS_pKa_fit_extra004,-1,18.92,0.1,0.7 +SAMPL8-16_micro000,SAMPL8-16_COSMO-RS_pKa_fit_extra005,-2,33.06,0.1,0.7 +SAMPL8-17_micro000,SAMPL8-17_micro002,1,-11.04,0.1,1.4 +SAMPL8-17_micro000,SAMPL8-17_micro003,1,-1.35,0.1,1.4 +SAMPL8-17_micro000,SAMPL8-17_micro000,0,0.0,0.1,0.7 +SAMPL8-17_micro000,SAMPL8-17_micro004,0,1.32,0.1,0.7 +SAMPL8-17_micro000,SAMPL8-17_micro001,-1,16.54,0.1,0.7 +SAMPL8-18_micro000,SAMPL8-18_COSMO-RS_pKa_fit_extra001,1,-4.28,0.1,1.4 +SAMPL8-18_micro000,SAMPL8-18_micro004,1,-14.23,0.1,1.4 +SAMPL8-18_micro000,SAMPL8-18_micro003,1,-9.83,0.1,1.4 +SAMPL8-18_micro000,SAMPL8-18_micro002,0,-6.08,0.1,0.7 +SAMPL8-18_micro000,SAMPL8-18_micro001,0,-0.01,0.1,0.7 +SAMPL8-18_micro000,SAMPL8-18_micro000,0,0.0,0.1,0.7 +SAMPL8-18_micro000,SAMPL8-18_micro005,-1,10.17,0.1,0.7 +SAMPL8-19_micro000,SAMPL8-19_COSMO-RS_pKa_fit_extra001,2,-19.72,0.1,1.4 +SAMPL8-19_micro000,SAMPL8-19_COSMO-RS_pKa_fit_extra002,2,-19.42,0.1,1.4 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+SAMPL8-20_micro000,SAMPL8-20_COSMO-RS_pKa_fit_extra002,0,-2.52,0.1,0.7 +SAMPL8-20_micro000,SAMPL8-20_micro000,0,0.0,0.1,0.7 +SAMPL8-20_micro000,SAMPL8-20_micro001,0,1.46,0.1,0.7 +SAMPL8-20_micro000,SAMPL8-20_COSMO-RS_pKa_fit_extra003,-1,4.83,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_pKa_fit_extra001,2,-19.25,0.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_pKa_fit_extra010,2,-30.01,0.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_pKa_fit_extra011,2,-22.7,0.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_pKa_fit_extra002,1,-24.94,0.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_pKa_fit_extra003,1,-23.08,0.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_pKa_fit_extra004,1,-17.27,0.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_pKa_fit_extra005,1,-18.08,0.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_pKa_fit_extra012,1,-16.87,0.1,1.4 +SAMPL8-21_micro000,SAMPL8-21_micro028,0,-13.36,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_pKa_fit_extra006,0,-10.67,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_pKa_fit_extra007,0,-9.73,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_pKa_fit_extra008,0,-1.75,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_COSMO-RS_pKa_fit_extra009,0,-3.52,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro000,0,0.0,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro008,0,-3.38,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro023,0,-6.63,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro025,0,-6.6,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro029,0,-4.01,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro022,-1,-0.71,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro016,-1,6.56,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro007,-1,15.64,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro009,-1,7.02,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro018,-1,4.01,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro020,-1,6.65,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro024,-1,5.2,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro026,-1,8.76,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro027,-1,10.29,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro013,-2,20.82,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro004,-2,27.36,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro005,-2,18.06,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro012,-2,28.45,0.1,0.7 +SAMPL8-21_micro000,SAMPL8-21_micro015,-2,19.12,0.1,0.7 +SAMPL8-22_micro000,SAMPL8-22_COSMO-RS_pKa_fit_extra004,2,-15.86,0.1,1.4 +SAMPL8-22_micro000,SAMPL8-22_COSMO-RS_pKa_fit_extra001,1,-15.91,0.1,1.4 +SAMPL8-22_micro000,SAMPL8-22_COSMO-RS_pKa_fit_extra002,1,-14.51,0.1,1.4 +SAMPL8-22_micro000,SAMPL8-22_COSMO-RS_pKa_fit_extra003,1,-7.4,0.1,1.4 +SAMPL8-22_micro000,SAMPL8-22_micro002,0,-7.46,0.1,0.7 +SAMPL8-22_micro000,SAMPL8-22_micro000,0,0.0,0.1,0.7 +SAMPL8-22_micro000,SAMPL8-22_micro003,0,0.52,0.1,0.7 +SAMPL8-22_micro000,SAMPL8-22_micro001,-1,10.49,0.1,0.7 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-17.61,0.1,1.4 +SAMPL8-23_micro000,SAMPL8-23_micro007,0,-10.52,0.1,0.7 +SAMPL8-23_micro000,SAMPL8-23_micro003,0,-4.64,0.1,0.7 +SAMPL8-23_micro000,SAMPL8-23_micro000,0,0.0,0.1,0.7 +SAMPL8-23_micro000,SAMPL8-23_micro005,-1,2.56,0.1,0.7 +SAMPL8-23_micro000,SAMPL8-23_micro002,-1,13.45,0.1,0.7 +SAMPL8-3_micro000,SAMPL8-3_COSMO-RS_pKa_fit_extra001,1,-25.67,0.1,1.4 +SAMPL8-3_micro000,SAMPL8-3_COSMO-RS_pKa_fit_extra003,1,-19.09,0.1,1.4 +SAMPL8-3_micro000,SAMPL8-3_micro000,0,0.0,0.1,0.7 +SAMPL8-3_micro000,SAMPL8-3_micro006,0,-25.99,0.1,0.7 +SAMPL8-3_micro000,SAMPL8-3_COSMO-RS_pKa_fit_extra002,0,-15.12,0.1,0.7 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,-15.2,0.1,0.7 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,-20.39,0.1,0.7 +SAMPL8-3_micro000,SAMPL8-3_micro013,-2,-9.4,0.1,0.7 +SAMPL8-4_micro000,SAMPL8-4_micro002,1,-8.93,0.1,1.4 +SAMPL8-4_micro000,SAMPL8-4_micro010,0,-4.13,0.1,0.7 +SAMPL8-4_micro000,SAMPL8-4_COSMO-RS_pKa_fit_extra001,0,14.15,0.1,0.7 +SAMPL8-4_micro000,SAMPL8-4_COSMO-RS_pKa_fit_extra002,0,12.69,0.1,0.7 +SAMPL8-4_micro000,SAMPL8-4_micro000,0,0.0,0.1,0.7 +SAMPL8-4_micro000,SAMPL8-4_micro001,0,-4.09,0.1,0.7 +SAMPL8-4_micro000,SAMPL8-4_micro005,-1,1.29,0.1,0.7 +SAMPL8-4_micro000,SAMPL8-4_micro003,-1,4.58,0.1,0.7 +SAMPL8-4_micro000,SAMPL8-4_micro008,-1,10.6,0.1,0.7 +SAMPL8-5_micro000,SAMPL8-5_micro003,1,1.05,0.1,1.4 +SAMPL8-5_micro000,SAMPL8-5_micro006,1,10.19,0.1,1.4 +SAMPL8-5_micro000,SAMPL8-5_micro000,0,0.0,0.1,0.7 +SAMPL8-5_micro000,SAMPL8-5_micro005,0,10.94,0.1,0.7 +SAMPL8-5_micro000,SAMPL8-5_micro001,0,6.95,0.1,0.7 +SAMPL8-5_micro000,SAMPL8-5_micro007,-1,5.39,0.1,0.7 +SAMPL8-6_micro000,SAMPL8-6_micro003,1,-6.35,0.1,1.4 +SAMPL8-6_micro000,SAMPL8-6_micro000,0,0.0,0.1,0.7 +SAMPL8-6_micro000,SAMPL8-6_micro007,0,-0.34,0.1,0.7 +SAMPL8-6_micro000,SAMPL8-6_micro001,-1,5.17,0.1,0.7 +SAMPL8-6_micro000,SAMPL8-6_micro009,-1,24.08,0.1,0.7 +SAMPL8-7_micro000,SAMPL8-7_micro002,1,-11.77,0.1,1.4 +SAMPL8-7_micro000,SAMPL8-7_micro003,1,-0.7,0.1,1.4 +SAMPL8-7_micro000,SAMPL8-7_micro000,0,0.0,0.1,0.7 +SAMPL8-7_micro000,SAMPL8-7_micro004,0,2.32,0.1,0.7 +SAMPL8-7_micro000,SAMPL8-7_micro001,-1,17.18,0.1,0.7 +SAMPL8-8_micro000,SAMPL8-8_micro001,1,-5.7,0.1,1.4 +SAMPL8-8_micro000,SAMPL8-8_micro002,1,7.29,0.1,1.4 +SAMPL8-8_micro000,SAMPL8-8_micro000,0,0.0,0.1,0.7 +SAMPL8-9_micro002,SAMPL8-9_micro002,1,-11.47,0.1,1.4 +SAMPL8-9_micro002,SAMPL8-9_micro004,1,-1.18,0.1,1.4 +SAMPL8-9_micro002,SAMPL8-9_micro000,0,0.0,0.1,0.7 +SAMPL8-9_micro002,SAMPL8-9_micro003,0,2.16,0.1,0.7 +SAMPL8-9_micro002,SAMPL8-9_micro001,-1,17.5,0.1,0.0 + +#,,,,,, +#,,,,,, +# Please list your name," using only UTF-8 characters as described above. The ""Participant name:"" entry is required.",,,,, +Participant name: +"Michael Diedenhofen, Selman Terzi, Frank Eckert" + +#,,,,,, +#,,,,,, +# Please list your organization/affiliation, using only UTF-8 characters as described above.,,,,, +Participant organization: +Dassault Systemes Deutschland GmbH, BIOVIA + +# NAME SECTION,,,,,, +#,,,,,, +# Please provide an informal but informative name of the method used.,,,,,, +# The name of the method should not exceed 40 characters.,,,,,, +# The 'Name:' keyword is required as shown here.,,,,,, +Name: +COSMO-RS pKa fit + +#,,,,,, +#,,,,,, +# COMPUTE TIME SECTION,,,,,, +#,,,,,, +# Please provide the average compute time across all of the molecules.,,,,,, +# For physical methods, report the GPU and/or CPU compute time in hours.,,,,, +# For empirical methods, report the query time in hours.,,,,, +# Create a new line for each processor type.,,,,,, +# The 'Compute time:' keyword is required as shown here.,,,,,, +Compute time: +1076 hours, CPU + +#,,,,,, +# COMPUTING AND HARDWARE SECTION,,,,,, +#,,,,,, +# Please provide details of the computing resources that were used to train models and make predictions.,,,,,, +# Please specify compute time for training models and querying separately for empirical prediction methods.,,,,,, +# Provide a detailed description of the hardware used to run the simulations.,,,,,, +# The 'Computing and hardware:' keyword is required as shown here.,,,,,, +Computing and hardware: +We have use a linux cluster (Intel(R) Xeon(R) Gold 6248R CPU @ 3.00GHz). The calculations could use up to 20 cores. The number of actually use CPU differ during the steps of the conformer search procedure. +The timings given above are wall times estimated from 33 structures and extrapolated to 203 microstates + +# SOFTWARE SECTION,,,,,, +#,,,,,, +# List all major software packages used and their versions.,,,,,, +# Create a new line for each software.,,,,,, +# The 'Software:' keyword is required.,,,,,, +Software: +BIOVIA COSMOquick 2021: A proprietary tool of Dassault Systemes to generate tautomeric states. +BIOVIA COSMOconf 2021: A proprietary tool of Dassault Systemes for conformer generation (uses TURBOMOLE and COSMOtherm) +BIOVIA COSMOtherm 2021: The proprietary software developed and distributed by Dassault Systemes, which uses COSMO-RS. COSMO-RS is a published theory: Klamt A (1995) Conductor-like screening model for real solvents: a new approach to the quantitative calculation of solvation phenomena. J Phys Chem 99:2224-2235. https://doi.org/10.1021/j100007a062 +TURBOMOLE 7.5: The quantum chemistry suite. University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989-2007, TURBOMOLE GmbH, since 2007; available from http://www.turbomole.com: Karlsruhe, Germany,2020, + +# METHOD CATEGORY SECTION,,,,,, +#,,,,,, +# State if your prediction method is better classified as an,,,,,, +# experimental database lookup (DL), linear free energy relationship (LFER),,,,, +# quantitative structure-property relationship or machine learning (QSPR/ML),,,,,, +# quantum mechanics without empirical correction (QM) model, quantum mechanics with,,,,, +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular,,,,, +# mechanics (QM+MM), or Other, using the following category labels:,,,, +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`., +#,,,,,, +# Pick only one category label.,,,,,, +# The `Category:` keyword is required.,,,,,, +Category: +QM+LEC + +# METHOD DESCRIPTION SECTION,,,,,, +#,,,,,, +# Methodology and computational details.,,,,,, +# Level of details should be roughly equivalent to that used in a publication.,,,,,, +# Please include the values of key parameters with units.,,,,,, +# Please explain how statistical uncertainties were estimated.,,,,,, +# Use as many lines of text as you need.,,,,,, +#,,,,,, +# We strongly encourage you to submit your predicted macro pKa values in this section in consecutive lines following this format:,,,,,, +# compound name, macro pKa, initial formal charge, formal charge after transition, e.g.:,, +# SAMPL8-1,3.5,0,1,,, +Method: +Workflow +"1) We used COSMOquick to generate possible tautomeric and ionic states. Irrelevant states where discarded due to an internal energy threshold implemented in COSMOquick. In a subsequent manual check we discarded all dissociated structures. After a first DFT optimization we checked the relative energies of the microstates with same charge and reduced the number of states with an energy threshold. We performed DFT optimizations of the SAMPL8 microstates proposals and checked the structures against the already created microstates. Missing, energetically relevant structures were added to the set." +2) COSMOconf was used to create the conformer set of the microstates. +4) The conformer sets of the microstates were used to calculate the pKa values of the reactions between the microstates. We used the COSMO-RS theory with the BP-TZVPD-FINE 21 parametrization. The pKa values were predicted using a LFER approach based on the fee Gibbs energies of the microstates at infinite dilution in water. +"We normally use two LFER fits, one for the pKa (HA +H2O -> H3O+ + A-) and one for the pKa of the conjugated base (BH+ + H2O -> B + H3O+). Here we used the pKa model for all reactions. The RSME value of this model in kcal/mol for HA +H2O -> H3O+ + A- reactions is 0.7." +The COSMO-RS algorithm by itself has no statistical error. The overall workflow including the conformational search (or molecule or state) has a statistical noise smaller than 0.1 kcal/mol. +#,,,,,, +Macro pKa values +SAMPL8-1,1,0,0.19 +SAMPL8-1,0,-1,4.40 +SAMPL8-2,0,-1,3.99 +SAMPL8-3,1,0,-0.24 +SAMPL8-3,0,-1,4.11 +SAMPL8-3,-1,-2,8.06 +SAMPL8-4,1,0,3.34 +SAMPL8-4,0,-1,4.15 +SAMPL8-5,1,0,-0.77 +SAMPL8-5,0,-1,3.95 +SAMPL8-6,1,0,4.47 +SAMPL8-6,0,-1,3.97 +SAMPL8-7,1,0,8.63 +SAMPL8-7,0,-1,12.60 +SAMPL8-8,1,0,4.18 +SAMPL8-9,1,0,8.41 +SAMPL8-9,0,-1,12.83 +SAMPL8-10,1,0,9.50 +SAMPL8-11,2,1,5.11 +SAMPL8-11,1,0,11.59 +SAMPL8-12,2,1,3.49 +SAMPL8-12,1,0,9.20 +SAMPL8-12,0,-1,15.15 +SAMPL8-13,1,0,3.42 +SAMPL8-13,0,-1,13.17 +SAMPL8-14,2,1,4.24 +SAMPL8-14,1,0,9.29 +SAMPL8-14,0,-1,10.40 +SAMPL8-14,-1,-2,14.24 +SAMPL8-15,1,0,5.92 +SAMPL8-16,1,0,7.46 +SAMPL8-16,0,-1,11.41 +SAMPL8-16,-1,-2,12.82 +SAMPL8-17,1,0,8.08 +SAMPL8-17,0,-1,12.13 +SAMPL8-18,1,0,5.97 +SAMPL8-18,0,-1,11.92 +SAMPL8-19,2,1,4.16 +SAMPL8-19,1,0,6.79 +SAMPL8-19,0,-1,7.32 +SAMPL8-20,2,1,1.18 +SAMPL8-20,1,0,5.33 +SAMPL8-20,0,-1,10.77 +SAMPL8-21,2,1,3.71 +SAMPL8-21,1,0,8.49 +SAMPL8-21,0,-1,9.27 +SAMPL8-21,-1,-2,13.73 +SAMPL8-22,2,1,-0.04 +SAMPL8-22,1,0,6.20 +SAMPL8-22,0,-1,13.16 +SAMPL8-23,1,0,5.20 +SAMPL8-23,0,-1,9.59 + +#,,,,,, +#,,,,,, +# All submissions must either be ranked or non-ranked.,,,,,, +# Only one ranked submission per participant is allowed.,,,,,, +# Multiple ranked submissions from the same participant will not be judged.,,,,,, +# Non-ranked submissions are accepted so we can verify that they were made before the deadline.,,,,,, +"# The ""Ranked:"" keyword is required", and expects a Boolean value (True/False),,,,, + +Ranked: +False diff --git a/physical_properties/pKa/submissions/pKa-RobertRaddi_AdaBoost_modified.csv b/physical_properties/pKa/submissions/pKa-RobertRaddi_AdaBoost_modified.csv new file mode 100644 index 0000000..93ad03d --- /dev/null +++ b/physical_properties/pKa/submissions/pKa-RobertRaddi_AdaBoost_modified.csv @@ -0,0 +1,285 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction) +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# PREDICTION SECTION +# +# It is mandatory to submit relative free energy (RFE) predictions for all 22 molecules. Incomplete submissions will not be accepted. +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty. +# +# The data in each prediction line should be structured as follows: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty +# +# If you have evaluated additional microstates, include the following: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +# +# The molecule ID of the other microstate needs to be in the format: `SMXX_extra001` (number can vary) +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders, +# Please send the `.mol2` file to the email listed on the instructions page. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: +SAMPL8-1_micro000,SAMPL8-1_micro001,-1,14.01,2.05,2.05 +SAMPL8-1_micro000,SAMPL8-1_micro002,-1,11.74,2.05,2.05 +SAMPL8-1_micro000,SAMPL8-1_micro003,-1,14.01,2.05,2.05 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,7.0,2.05,2.05 +SAMPL8-1_micro000,SAMPL8-1_micro005,-1,12.38,2.05,2.05 +SAMPL8-1_micro000,SAMPL8-1_micro008,-1,14.01,2.05,2.05 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,6.56,2.05,2.05 +SAMPL8-2_micro000,SAMPL8-2_micro003,-1,-0.0,2.05,2.05 +SAMPL8-2_micro000,SAMPL8-2_micro002,0,-9.94,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro001,-1,14.01,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro003,-1,23.05,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro005,-1,12.25,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro009,-1,15.86,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,7.0,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro011,-1,23.05,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro015,-1,27.47,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,14.69,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro017,-1,23.05,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro018,-1,14.01,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro020,-1,10.23,2.05,2.05 +SAMPL8-3_micro000,SAMPL8-3_micro002,0,12.69,2.05,2.05 +SAMPL8-4_micro000,SAMPL8-4_micro003,-1,9.4,2.05,2.05 +SAMPL8-4_micro000,SAMPL8-4_micro005,-1,9.02,2.05,2.05 +SAMPL8-4_micro000,SAMPL8-4_micro006,-1,7.34,2.05,2.05 +SAMPL8-4_micro000,SAMPL8-4_micro008,-1,4.94,2.05,2.05 +SAMPL8-5_micro000,SAMPL8-5_micro002,-1,-0.0,2.05,2.05 +SAMPL8-5_micro000,SAMPL8-5_micro007,-1,6.04,2.05,2.05 +SAMPL8-5_micro000,SAMPL8-5_micro003,1,-5.25,2.05,2.05 +SAMPL8-5_micro000,SAMPL8-5_micro006,1,-19.67,2.05,2.05 +SAMPL8-5_micro000,SAMPL8-5_micro001,0,0.0,2.05,2.05 +SAMPL8-6_micro000,SAMPL8-6_micro001,-1,7.0,2.05,2.05 +SAMPL8-6_micro000,SAMPL8-6_micro006,-1,7.62,2.05,2.05 +SAMPL8-6_micro000,SAMPL8-6_micro009,-1,-0.0,2.05,2.05 +SAMPL8-6_micro000,SAMPL8-6_micro002,1,-19.31,2.05,2.05 +SAMPL8-6_micro000,SAMPL8-6_micro003,1,-12.47,2.05,2.05 +SAMPL8-7_micro000,SAMPL8-7_micro001,-1,11.23,2.05,2.05 +SAMPL8-8_micro000,SAMPL8-8_micro001,1,-5.02,2.05,2.05 +SAMPL8-8_micro000,SAMPL8-8_micro002,1,-7.93,2.05,2.05 +SAMPL8-9_micro000,SAMPL8-9_micro001,-1,11.04,2.05,2.05 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-7.34,2.05,2.05 +SAMPL8-12_micro000,SAMPL8-12_micro001,-1,18.5,2.05,2.05 +SAMPL8-12_micro000,SAMPL8-12_micro002,0,0.46,2.05,2.05 +SAMPL8-12_micro000,SAMPL8-12_micro003,0,-0.0,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro004,-1,21.5,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro005,-1,10.83,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,10.0,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro009,-1,4.12,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro010,-1,5.85,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro012,-1,7.92,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro019,-1,10.83,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro021,-1,8.24,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro022,-1,10.36,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro025,-1,12.24,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro027,-1,11.38,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro028,-1,10.23,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro029,-1,9.13,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro032,-1,10.36,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro001,-2,9.71,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro003,-2,18.82,2.05,2.05 +SAMPL8-14_micro000,SAMPL8-14_micro002,0,-7.14,2.05,2.05 +SAMPL8-15_micro000,SAMPL8-15_micro003,1,-9.13,2.05,2.05 +SAMPL8-15_micro000,SAMPL8-15_micro004,1,-8.85,2.05,2.05 +SAMPL8-15_micro000,SAMPL8-15_micro001,0,0.0,2.05,2.05 +SAMPL8-15_micro000,SAMPL8-15_micro002,0,-0.0,2.05,2.05 +SAMPL8-16_micro000,SAMPL8-16_micro001,1,-11.04,2.05,2.05 +SAMPL8-16_micro000,SAMPL8-16_micro003,1,-15.78,2.05,2.05 +SAMPL8-16_micro000,SAMPL8-16_micro004,1,-7.98,2.05,2.05 +SAMPL8-16_micro000,SAMPL8-16_micro006,1,-7.49,2.05,2.05 +SAMPL8-16_micro000,SAMPL8-16_micro008,1,-11.08,2.05,2.05 +SAMPL8-16_micro000,SAMPL8-16_micro009,1,-12.51,2.05,2.05 +SAMPL8-16_micro000,SAMPL8-16_micro010,1,-9.27,2.05,2.05 +SAMPL8-16_micro000,SAMPL8-16_micro002,0,-5.86,2.05,2.05 +SAMPL8-17_micro000,SAMPL8-17_micro001,-1,16.4,2.05,2.05 +SAMPL8-17_micro000,SAMPL8-17_micro005,-1,7.19,2.05,2.05 +SAMPL8-18_micro000,SAMPL8-18_micro005,-1,5.47,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro010,-1,7.21,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro011,-1,11.67,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro001,1,-10.83,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro004,1,-6.61,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro005,1,-6.61,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro006,1,-0.0,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro008,1,-0.0,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro009,1,-0.0,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro016,1,-5.54,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro018,1,-0.0,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro019,1,-0.0,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro022,1,-1.98,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro023,1,-1.59,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro002,2,-7.34,2.05,2.05 +SAMPL8-19_micro000,SAMPL8-19_micro003,2,-4.16,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro002,1,-4.84,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro003,1,-5.75,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro005,1,4.24,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro006,1,-4.5,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro007,1,0.0,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro011,1,-10.98,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro014,1,5.3,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro015,1,-4.52,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro016,1,-6.28,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro025,1,-0.0,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro026,1,-5.33,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro028,1,-0.0,2.05,2.05 +SAMPL8-20_micro000,SAMPL8-20_micro001,0,-0.0,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro003,-1,9.44,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro006,-1,5.86,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro007,-1,6.98,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro009,-1,11.72,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro011,-1,12.35,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro014,-1,7.34,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro016,-1,19.2,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro018,-1,5.4,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro019,-1,12.92,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro020,-1,4.91,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro022,-1,5.17,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro024,-1,4.91,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro026,-1,5.33,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro027,-1,5.25,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro001,-2,17.14,2.05,2.05 +SAMPL8-21_micro000,SAMPL8-21_micro002,-2,21.92,2.05,2.05 +SAMPL8-22_micro000,SAMPL8-22_micro001,-1,7.34,2.05,2.05 +SAMPL8-22_micro000,SAMPL8-22_micro002,0,-2.41,2.05,2.05 +SAMPL8-22_micro000,SAMPL8-22_micro003,0,-0.0,2.05,2.05 +SAMPL8-23_micro000,SAMPL8-23_micro002,-1,11.08,2.05,2.05 +SAMPL8-23_micro000,SAMPL8-23_micro005,-1,14.99,2.05,2.05 +SAMPL8-23_micro000,SAMPL8-23_micro001,1,-4.41,2.05,2.05 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-4.77,2.05,2.05 +SAMPL8-23_micro000,SAMPL8-23_micro003,0,5.24,2.05,2.05 +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Robert Raddi + +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +Temple University + +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name of the method should not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +AdaBoost + +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +0.16 hr (compute features, 4-6 CPUs) +0.15 hr (prediction calculations, 4-6 CPUs) +0.31 hr (total, 4-6 CPUs) +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +1.0 hr to train the model (4 CPUs) +3 GHz 6-Core Intel Core i5 + +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +In order of usage (1st listed is used the most) +RDKit 2020.03.4 +pandas 1.0.3 +numpy 1.18.2 +scikit-learn 0.22.1 +openeye-toolkits 2019.10.2 +openforcefield 0.6.0 + +# METHOD CATEGORY SECTION +# +# State if your prediction method is better classified as an +# experimental database lookup (DL), linear free energy relationship (LFER), +# quantitative structure-property relationship or machine learning (QSPR/ML), +# quantum mechanics without empirical correction (QM) model, quantum mechanics with +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular +# mechanics (QM+MM), or Other, using the following category labels: +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`. +# +# Pick only one category label. +# The `Category:` keyword is required. +Category: +QSPR/ML + +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# Use as many lines of text as you need. +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. +Method: +This submission uses a method that predicts microscopic pKa values that are directly related to relative free energies following the work by Gunner et al.\cite{gunner2020standard} in units of kcal/mol. Our method uses our publicly avialable database (http://doi.org/10.5281/zenodo.5027418) with recomputed AM1BCC partial charge features (AM1BCCELF10) from OpenEye. Previously, we used a DeepGP model to predict SAMPL6 & SAMPL7 molecules\cite{raddi2021stacking}. Here, we blindly test the DeepGP model on the SAMPL8 small moleculue set in addition to the following machine learning (ML) models: Random Forest, AdaBoost and XGBoost. Model parameters for AdaBoost and XGBoost follow a recent work from Yang et al.\cite{yang2020holistic}. Model parameters for the DeepGP and the Random Forest models are presented in the work from Raddi et al\cite{raddi2021stacking}. Note that similarity filtering was only used for the DeepGP model due to it's slight performance enhancements. The ten feature calculations were closely followed from Bannan et al.\cite{bannan2018sampl6} with the exception of changing AM1BCC to AM1BCCELF10 partial charges. Our hand curated training set consists of approximately 3000 small molecules entirely from open-source databases. 5-fold model validation for each of these ML methods using our database results in very similar performance. +Statistical uncertainty (SEM) for the relative free energies was calculated during model validation and standard errors for each microtransition was calculated using 10-round bootstrapping. The standard Gaussian process model automatically provides uncertainties that correspond to how closely the molecule of interest overlaps with the molecules in the training set, so no bootstrapping was needed here. Note that the predictions reported have have high uncertainty due to the lack of chemical space in the training set as well as the lack of similarity of the molecules of interest to that of the molecules found in the training set. + +//ref.bib +@article{raddi2021stacking, + title={Stacking Gaussian Processes to Improve pKa Predictions in the SAMPL7 Challenge}, + author={Raddi, Robert and Voelz, Vincent}, + year={2021} +} +@article{yang2020holistic, + title={Holistic Prediction of the pKa in Diverse Solvents Based on a Machine-Learning Approach}, + author={Yang, Qi and Li, Yao and Yang, Jin-Dong and Liu, Yidi and Zhang, Long and Luo, Sanzhong and Cheng, Jin-Pei}, + journal={Angewandte Chemie}, + volume={132}, + number={43}, + pages={19444--19453}, + year={2020}, + publisher={Wiley Online Library} +} +@article{bannan2018sampl6, + title={SAMPL6 challenge results from $pK_a$ predictions based on a general Gaussian process model}, + author={Bannan, Caitlin C and Mobley, David L and Skillman, A Geoffrey}, + journal={Journal of computer-aided molecular design}, + volume={32}, + number={10}, + pages={1165--1177}, + year={2018}, + publisher={Springer} +} +@article{gunner2020standard, + title={Standard state free energies, not pK as, are ideal for describing small molecule protonation and tautomeric states}, + author={Gunner, Marilyn R and Murakami, Taichi and Rustenburg, Ari{\"e}n S and I{\c{s}}{\i}k, Mehtap and Chodera, John D}, + journal={Journal of Computer-Aided Molecular Design}, + pages={1--13}, + year={2020}, + publisher={Springer} +} + + + +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) +Ranked: +False + diff --git a/physical_properties/pKa/submissions/pKa-RobertRaddi_DeepGP_modified.csv b/physical_properties/pKa/submissions/pKa-RobertRaddi_DeepGP_modified.csv new file mode 100644 index 0000000..a433f40 --- /dev/null +++ b/physical_properties/pKa/submissions/pKa-RobertRaddi_DeepGP_modified.csv @@ -0,0 +1,267 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction) +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# PREDICTION SECTION +# +# It is mandatory to submit relative free energy (RFE) predictions for all 22 molecules. Incomplete submissions will not be accepted. +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty. +# +# The data in each prediction line should be structured as follows: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty +# +# If you have evaluated additional microstates, include the following: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +# +# The molecule ID of the other microstate needs to be in the format: `SMXX_extra001` (number can vary) +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders, +# Please send the `.mol2` file to the email listed on the instructions page. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: +SAMPL8-1_micro000,SAMPL8-1_micro001,-1,11.61,4.73,4.73 +SAMPL8-1_micro000,SAMPL8-1_micro002,-1,8.08,3.14,3.14 +SAMPL8-1_micro000,SAMPL8-1_micro003,-1,13.16,4.95,4.95 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,6.54,2.46,2.46 +SAMPL8-1_micro000,SAMPL8-1_micro005,-1,7.16,2.83,2.83 +SAMPL8-1_micro000,SAMPL8-1_micro008,-1,13.22,4.97,4.97 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,6.53,2.43,2.43 +SAMPL8-2_micro000,SAMPL8-2_micro002,0,-9.11,2.73,2.73 +SAMPL8-3_micro000,SAMPL8-3_micro001,-1,20.25,5.86,5.86 +SAMPL8-3_micro000,SAMPL8-3_micro003,-1,28.68,8.8,8.8 +SAMPL8-3_micro000,SAMPL8-3_micro005,-1,10.87,2.9,2.9 +SAMPL8-3_micro000,SAMPL8-3_micro009,-1,16.88,5.96,5.96 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,9.98,2.94,2.94 +SAMPL8-3_micro000,SAMPL8-3_micro011,-1,26.76,8.85,8.85 +SAMPL8-3_micro000,SAMPL8-3_micro015,-1,24.59,3.84,3.84 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,21.27,5.79,5.79 +SAMPL8-3_micro000,SAMPL8-3_micro017,-1,28.02,8.82,8.82 +SAMPL8-3_micro000,SAMPL8-3_micro018,-1,20.53,5.84,5.84 +SAMPL8-3_micro000,SAMPL8-3_micro020,-1,10.04,2.94,2.94 +SAMPL8-3_micro000,SAMPL8-3_micro002,0,8.31,3.04,3.04 +SAMPL8-4_micro000,SAMPL8-4_micro003,-1,11.76,1.77,1.77 +SAMPL8-4_micro000,SAMPL8-4_micro005,-1,3.99,2.4,2.4 +SAMPL8-4_micro000,SAMPL8-4_micro006,-1,11.71,2.01,2.01 +SAMPL8-4_micro000,SAMPL8-4_micro008,-1,3.59,2.2,2.2 +SAMPL8-5_micro000,SAMPL8-5_micro007,-1,6.12,2.35,2.35 +SAMPL8-5_micro000,SAMPL8-5_micro003,1,-6.61,2.65,2.65 +SAMPL8-5_micro000,SAMPL8-5_micro006,1,-20.15,5.82,5.82 +SAMPL8-6_micro000,SAMPL8-6_micro001,-1,5.55,2.35,2.35 +SAMPL8-6_micro000,SAMPL8-6_micro006,-1,13.28,2.24,2.24 +SAMPL8-6_micro000,SAMPL8-6_micro002,1,-18.15,4.99,4.99 +SAMPL8-6_micro000,SAMPL8-6_micro003,1,-9.54,2.94,2.94 +SAMPL8-7_micro000,SAMPL8-7_micro001,-1,7.0,2.28,2.28 +SAMPL8-8_micro000,SAMPL8-8_micro001,1,-5.28,1.85,1.85 +SAMPL8-8_micro000,SAMPL8-8_micro002,1,-6.71,2.8,2.8 +SAMPL8-9_micro000,SAMPL8-9_micro001,-1,5.44,2.11,2.11 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-12.64,1.75,1.75 +SAMPL8-12_micro000,SAMPL8-12_micro001,-1,17.32,6.12,6.12 +SAMPL8-12_micro000,SAMPL8-12_micro002,0,-2.41,8.94,8.94 +SAMPL8-14_micro000,SAMPL8-14_micro004,-1,38.73,9.76,9.76 +SAMPL8-14_micro000,SAMPL8-14_micro005,-1,24.81,6.17,6.17 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,12.23,2.23,2.23 +SAMPL8-14_micro000,SAMPL8-14_micro009,-1,11.39,2.83,2.83 +SAMPL8-14_micro000,SAMPL8-14_micro010,-1,10.24,3.38,3.38 +SAMPL8-14_micro000,SAMPL8-14_micro012,-1,26.37,6.41,6.41 +SAMPL8-14_micro000,SAMPL8-14_micro019,-1,28.39,6.09,6.09 +SAMPL8-14_micro000,SAMPL8-14_micro021,-1,26.95,6.27,6.27 +SAMPL8-14_micro000,SAMPL8-14_micro022,-1,12.14,2.32,2.32 +SAMPL8-14_micro000,SAMPL8-14_micro025,-1,21.3,6.91,6.91 +SAMPL8-14_micro000,SAMPL8-14_micro027,-1,12.26,2.21,2.21 +SAMPL8-14_micro000,SAMPL8-14_micro028,-1,12.3,2.2,2.2 +SAMPL8-14_micro000,SAMPL8-14_micro029,-1,12.34,2.11,2.11 +SAMPL8-14_micro000,SAMPL8-14_micro032,-1,12.22,2.24,2.24 +SAMPL8-14_micro000,SAMPL8-14_micro001,-2,21.44,4.2,4.2 +SAMPL8-14_micro000,SAMPL8-14_micro003,-2,17.1,5.55,5.55 +SAMPL8-14_micro000,SAMPL8-14_micro002,0,11.61,13.42,13.42 +SAMPL8-15_micro000,SAMPL8-15_micro003,1,-9.69,2.22,2.22 +SAMPL8-15_micro000,SAMPL8-15_micro004,1,-6.4,2.44,2.44 +SAMPL8-16_micro000,SAMPL8-16_micro001,1,-12.33,2.76,2.76 +SAMPL8-16_micro000,SAMPL8-16_micro003,1,-21.56,5.28,5.28 +SAMPL8-16_micro000,SAMPL8-16_micro004,1,-4.88,2.55,2.55 +SAMPL8-16_micro000,SAMPL8-16_micro006,1,-11.61,2.73,2.73 +SAMPL8-16_micro000,SAMPL8-16_micro008,1,-12.13,2.76,2.76 +SAMPL8-16_micro000,SAMPL8-16_micro009,1,-20.46,5.29,5.29 +SAMPL8-16_micro000,SAMPL8-16_micro010,1,-5.3,2.68,2.68 +SAMPL8-16_micro000,SAMPL8-16_micro002,0,-9.74,2.53,2.53 +SAMPL8-17_micro000,SAMPL8-17_micro001,-1,15.27,4.07,4.07 +SAMPL8-17_micro000,SAMPL8-17_micro005,-1,5.89,1.77,1.77 +SAMPL8-18_micro000,SAMPL8-18_micro005,-1,6.89,2.32,2.32 +SAMPL8-19_micro000,SAMPL8-19_micro010,-1,12.79,3.0,3.0 +SAMPL8-19_micro000,SAMPL8-19_micro011,-1,13.69,3.57,3.57 +SAMPL8-19_micro000,SAMPL8-19_micro001,1,-7.19,1.79,1.79 +SAMPL8-19_micro000,SAMPL8-19_micro004,1,-6.77,1.78,1.78 +SAMPL8-19_micro000,SAMPL8-19_micro005,1,-3.0,2.52,2.52 +SAMPL8-19_micro000,SAMPL8-19_micro016,1,-8.85,2.04,2.04 +SAMPL8-19_micro000,SAMPL8-19_micro022,1,0.08,2.0,2.0 +SAMPL8-19_micro000,SAMPL8-19_micro023,1,-0.34,2.06,2.06 +SAMPL8-19_micro000,SAMPL8-19_micro002,2,-7.34,2.83,2.83 +SAMPL8-19_micro000,SAMPL8-19_micro003,2,-2.27,2.02,2.02 +SAMPL8-20_micro000,SAMPL8-20_micro002,1,-4.45,2.59,2.59 +SAMPL8-20_micro000,SAMPL8-20_micro003,1,-4.51,2.29,2.29 +SAMPL8-20_micro000,SAMPL8-20_micro005,1,5.08,2.08,2.08 +SAMPL8-20_micro000,SAMPL8-20_micro006,1,-5.62,1.94,1.94 +SAMPL8-20_micro000,SAMPL8-20_micro011,1,-8.14,2.57,2.57 +SAMPL8-20_micro000,SAMPL8-20_micro014,1,9.97,2.11,2.11 +SAMPL8-20_micro000,SAMPL8-20_micro015,1,3.92,3.14,3.14 +SAMPL8-20_micro000,SAMPL8-20_micro016,1,-5.7,1.94,1.94 +SAMPL8-20_micro000,SAMPL8-20_micro026,1,-9.36,2.88,2.88 +SAMPL8-21_micro000,SAMPL8-21_micro003,-1,22.82,6.85,6.85 +SAMPL8-21_micro000,SAMPL8-21_micro006,-1,9.8,3.11,3.11 +SAMPL8-21_micro000,SAMPL8-21_micro007,-1,9.12,2.76,2.76 +SAMPL8-21_micro000,SAMPL8-21_micro009,-1,19.4,6.52,6.52 +SAMPL8-21_micro000,SAMPL8-21_micro011,-1,15.02,6.25,6.25 +SAMPL8-21_micro000,SAMPL8-21_micro014,-1,9.23,2.86,2.86 +SAMPL8-21_micro000,SAMPL8-21_micro016,-1,19.03,6.26,6.26 +SAMPL8-21_micro000,SAMPL8-21_micro018,-1,12.59,2.29,2.29 +SAMPL8-21_micro000,SAMPL8-21_micro019,-1,15.97,6.79,6.79 +SAMPL8-21_micro000,SAMPL8-21_micro020,-1,12.73,2.09,2.09 +SAMPL8-21_micro000,SAMPL8-21_micro022,-1,12.59,2.06,2.06 +SAMPL8-21_micro000,SAMPL8-21_micro024,-1,11.85,2.2,2.2 +SAMPL8-21_micro000,SAMPL8-21_micro026,-1,12.51,2.3,2.3 +SAMPL8-21_micro000,SAMPL8-21_micro027,-1,13.1,2.14,2.14 +SAMPL8-21_micro000,SAMPL8-21_micro001,-2,35.43,7.9,7.9 +SAMPL8-21_micro000,SAMPL8-21_micro002,-2,48.96,10.56,10.56 +SAMPL8-22_micro000,SAMPL8-22_micro001,-1,4.99,2.14,2.14 +SAMPL8-22_micro000,SAMPL8-22_micro002,0,-2.18,3.26,3.26 +SAMPL8-23_micro000,SAMPL8-23_micro002,-1,12.66,2.01,2.01 +SAMPL8-23_micro000,SAMPL8-23_micro005,-1,25.01,4.79,4.79 +SAMPL8-23_micro000,SAMPL8-23_micro001,1,-3.17,2.56,2.56 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-5.72,3.9,3.9 +SAMPL8-23_micro000,SAMPL8-23_micro003,0,5.31,3.27,3.27 +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Robert Raddi + +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +Temple University + +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name of the method should not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +Deep Gaussian Process + +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +0.16 hr (compute features, 4-6 CPUs) +0.15 hr (prediction calculations, 4-6 CPUs) +0.31 hr (total, 4-6 CPUs) +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +1.0 hr to train the model (4 CPUs) +3 GHz 6-Core Intel Core i5 + +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +In order of usage (1st listed is used the most) +RDKit 2020.03.4 +pandas 1.0.3 +numpy 1.18.2 +scikit-learn 0.22.1 +openeye-toolkits 2019.10.2 +openforcefield 0.6.0 + +# METHOD CATEGORY SECTION +# +# State if your prediction method is better classified as an +# experimental database lookup (DL), linear free energy relationship (LFER), +# quantitative structure-property relationship or machine learning (QSPR/ML), +# quantum mechanics without empirical correction (QM) model, quantum mechanics with +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular +# mechanics (QM+MM), or Other, using the following category labels: +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`. +# +# Pick only one category label. +# The `Category:` keyword is required. +Category: +QSPR/ML + +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# Use as many lines of text as you need. +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. +Method: +This submission uses a method that predicts microscopic pKa values that are directly related to relative free energies following the work by Gunner et al.\cite{gunner2020standard} in units of kcal/mol. Our method uses our publicly avialable database (http://doi.org/10.5281/zenodo.5027418) with recomputed AM1BCC partial charge features (AM1BCCELF10) from OpenEye. Previously, we used a DeepGP model to predict SAMPL6 & SAMPL7 molecules\cite{raddi2021stacking}. Here, we blindly test the DeepGP model on the SAMPL8 small moleculue set in addition to the following machine learning (ML) models: Random Forest, AdaBoost and XGBoost. Model parameters for AdaBoost and XGBoost follow a recent work from Yang et al.\cite{yang2020holistic}. Model parameters for the DeepGP and the Random Forest models are presented in the work from Raddi et al\cite{raddi2021stacking}. Note that similarity filtering was only used for the DeepGP model due to it's slight performance enhancements. The ten feature calculations were closely followed from Bannan et al.\cite{bannan2018sampl6} with the exception of changing AM1BCC to AM1BCCELF10 partial charges. Our hand curated training set consists of approximately 3000 small molecules entirely from open-source databases. 5-fold model validation for each of these ML methods using our database results in very similar performance. +Statistical uncertainty (SEM) for the relative free energies was calculated during model validation and standard errors for each microtransition was calculated using 10-round bootstrapping. The standard Gaussian process model automatically provides uncertainties that correspond to how closely the molecule of interest overlaps with the molecules in the training set, so no bootstrapping was needed here. Note that the predictions reported have have high uncertainty due to the lack of chemical space in the training set as well as the lack of similarity of the molecules of interest to that of the molecules found in the training set. + +//ref.bib +@article{raddi2021stacking, + title={Stacking Gaussian Processes to Improve pKa Predictions in the SAMPL7 Challenge}, + author={Raddi, Robert and Voelz, Vincent}, + year={2021} +} +@article{yang2020holistic, + title={Holistic Prediction of the pKa in Diverse Solvents Based on a Machine-Learning Approach}, + author={Yang, Qi and Li, Yao and Yang, Jin-Dong and Liu, Yidi and Zhang, Long and Luo, Sanzhong and Cheng, Jin-Pei}, + journal={Angewandte Chemie}, + volume={132}, + number={43}, + pages={19444--19453}, + year={2020}, + publisher={Wiley Online Library} +} +@article{bannan2018sampl6, + title={SAMPL6 challenge results from $pK_a$ predictions based on a general Gaussian process model}, + author={Bannan, Caitlin C and Mobley, David L and Skillman, A Geoffrey}, + journal={Journal of computer-aided molecular design}, + volume={32}, + number={10}, + pages={1165--1177}, + year={2018}, + publisher={Springer} +} +@article{gunner2020standard, + title={Standard state free energies, not pK as, are ideal for describing small molecule protonation and tautomeric states}, + author={Gunner, Marilyn R and Murakami, Taichi and Rustenburg, Ari{\"e}n S and I{\c{s}}{\i}k, Mehtap and Chodera, John D}, + journal={Journal of Computer-Aided Molecular Design}, + pages={1--13}, + year={2020}, + publisher={Springer} +} + + +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) +Ranked: +True + diff --git a/physical_properties/pKa/submissions/pKa-RobertRaddi_RF_modified.csv b/physical_properties/pKa/submissions/pKa-RobertRaddi_RF_modified.csv new file mode 100644 index 0000000..b91fb90 --- /dev/null +++ b/physical_properties/pKa/submissions/pKa-RobertRaddi_RF_modified.csv @@ -0,0 +1,285 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction) +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# PREDICTION SECTION +# +# It is mandatory to submit relative free energy (RFE) predictions for all 22 molecules. Incomplete submissions will not be accepted. +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty. +# +# The data in each prediction line should be structured as follows: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty +# +# If you have evaluated additional microstates, include the following: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +# +# The molecule ID of the other microstate needs to be in the format: `SMXX_extra001` (number can vary) +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders, +# Please send the `.mol2` file to the email listed on the instructions page. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: +SAMPL8-1_micro000,SAMPL8-1_micro001,-1,16.54,2.02,0.57 +SAMPL8-1_micro000,SAMPL8-1_micro002,-1,7.53,2.02,0.28 +SAMPL8-1_micro000,SAMPL8-1_micro003,-1,15.76,2.02,0.61 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,6.62,2.02,0.3 +SAMPL8-1_micro000,SAMPL8-1_micro005,-1,7.62,2.02,0.4 +SAMPL8-1_micro000,SAMPL8-1_micro008,-1,18.65,2.02,0.57 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,6.65,2.02,0.21 +SAMPL8-2_micro000,SAMPL8-2_micro003,-1,-0.0,2.02,0.01 +SAMPL8-2_micro000,SAMPL8-2_micro002,0,-6.73,2.02,0.29 +SAMPL8-3_micro000,SAMPL8-3_micro001,-1,12.46,2.02,0.53 +SAMPL8-3_micro000,SAMPL8-3_micro003,-1,29.12,2.02,1.35 +SAMPL8-3_micro000,SAMPL8-3_micro005,-1,9.47,2.02,0.43 +SAMPL8-3_micro000,SAMPL8-3_micro009,-1,18.58,2.02,0.79 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,6.6,2.02,0.32 +SAMPL8-3_micro000,SAMPL8-3_micro011,-1,28.1,2.02,1.0 +SAMPL8-3_micro000,SAMPL8-3_micro015,-1,25.36,2.02,0.29 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,12.28,2.02,0.55 +SAMPL8-3_micro000,SAMPL8-3_micro017,-1,28.02,2.02,1.24 +SAMPL8-3_micro000,SAMPL8-3_micro018,-1,12.74,2.02,0.61 +SAMPL8-3_micro000,SAMPL8-3_micro020,-1,7.8,2.02,0.45 +SAMPL8-3_micro000,SAMPL8-3_micro002,0,10.22,2.02,0.36 +SAMPL8-4_micro000,SAMPL8-4_micro003,-1,6.68,2.02,0.43 +SAMPL8-4_micro000,SAMPL8-4_micro005,-1,7.63,2.02,0.53 +SAMPL8-4_micro000,SAMPL8-4_micro006,-1,6.62,2.02,0.43 +SAMPL8-4_micro000,SAMPL8-4_micro008,-1,4.7,2.02,0.46 +SAMPL8-5_micro000,SAMPL8-5_micro002,-1,-0.0,2.02,0.01 +SAMPL8-5_micro000,SAMPL8-5_micro007,-1,6.24,2.02,0.1 +SAMPL8-5_micro000,SAMPL8-5_micro003,1,-4.1,2.02,0.28 +SAMPL8-5_micro000,SAMPL8-5_micro006,1,-13.54,2.02,0.56 +SAMPL8-5_micro000,SAMPL8-5_micro001,0,0.0,2.02,0.01 +SAMPL8-6_micro000,SAMPL8-6_micro001,-1,6.31,2.02,0.29 +SAMPL8-6_micro000,SAMPL8-6_micro006,-1,8.33,2.02,0.31 +SAMPL8-6_micro000,SAMPL8-6_micro009,-1,-0.0,2.02,0.01 +SAMPL8-6_micro000,SAMPL8-6_micro002,1,-19.15,2.02,0.58 +SAMPL8-6_micro000,SAMPL8-6_micro003,1,-10.53,2.02,0.41 +SAMPL8-7_micro000,SAMPL8-7_micro001,-1,10.48,2.02,0.35 +SAMPL8-8_micro000,SAMPL8-8_micro001,1,-4.42,2.02,0.35 +SAMPL8-8_micro000,SAMPL8-8_micro002,1,-5.49,2.02,0.29 +SAMPL8-9_micro000,SAMPL8-9_micro001,-1,10.99,2.02,0.29 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-8.88,2.02,0.27 +SAMPL8-12_micro000,SAMPL8-12_micro001,-1,17.6,2.02,0.41 +SAMPL8-12_micro000,SAMPL8-12_micro002,0,0.14,2.02,0.83 +SAMPL8-12_micro000,SAMPL8-12_micro003,0,-0.0,2.02,0.01 +SAMPL8-14_micro000,SAMPL8-14_micro004,-1,31.69,2.02,0.58 +SAMPL8-14_micro000,SAMPL8-14_micro005,-1,13.82,2.02,0.69 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,8.01,2.02,0.25 +SAMPL8-14_micro000,SAMPL8-14_micro009,-1,5.74,2.02,0.34 +SAMPL8-14_micro000,SAMPL8-14_micro010,-1,7.83,2.02,0.41 +SAMPL8-14_micro000,SAMPL8-14_micro012,-1,10.02,2.02,0.63 +SAMPL8-14_micro000,SAMPL8-14_micro019,-1,10.86,2.02,0.6 +SAMPL8-14_micro000,SAMPL8-14_micro021,-1,10.34,2.02,0.5 +SAMPL8-14_micro000,SAMPL8-14_micro022,-1,8.3,2.02,0.4 +SAMPL8-14_micro000,SAMPL8-14_micro025,-1,15.99,2.02,0.77 +SAMPL8-14_micro000,SAMPL8-14_micro027,-1,8.47,2.02,0.37 +SAMPL8-14_micro000,SAMPL8-14_micro028,-1,8.29,2.02,0.3 +SAMPL8-14_micro000,SAMPL8-14_micro029,-1,8.01,2.02,0.33 +SAMPL8-14_micro000,SAMPL8-14_micro032,-1,8.23,2.02,0.45 +SAMPL8-14_micro000,SAMPL8-14_micro001,-2,11.29,2.02,0.55 +SAMPL8-14_micro000,SAMPL8-14_micro003,-2,18.06,2.02,0.83 +SAMPL8-14_micro000,SAMPL8-14_micro002,0,3.58,2.02,1.06 +SAMPL8-15_micro000,SAMPL8-15_micro003,1,-7.86,2.02,0.37 +SAMPL8-15_micro000,SAMPL8-15_micro004,1,-7.99,2.02,0.3 +SAMPL8-15_micro000,SAMPL8-15_micro001,0,0.0,2.02,0.01 +SAMPL8-15_micro000,SAMPL8-15_micro002,0,-0.0,2.02,0.01 +SAMPL8-16_micro000,SAMPL8-16_micro001,1,-10.18,2.02,0.32 +SAMPL8-16_micro000,SAMPL8-16_micro003,1,-17.65,2.02,0.7 +SAMPL8-16_micro000,SAMPL8-16_micro004,1,-7.19,2.02,0.25 +SAMPL8-16_micro000,SAMPL8-16_micro006,1,-6.78,2.02,0.33 +SAMPL8-16_micro000,SAMPL8-16_micro008,1,-10.47,2.02,0.36 +SAMPL8-16_micro000,SAMPL8-16_micro009,1,-17.69,2.02,0.81 +SAMPL8-16_micro000,SAMPL8-16_micro010,1,-6.93,2.02,0.39 +SAMPL8-16_micro000,SAMPL8-16_micro002,0,-9.46,2.02,0.38 +SAMPL8-17_micro000,SAMPL8-17_micro001,-1,15.0,2.02,0.85 +SAMPL8-17_micro000,SAMPL8-17_micro005,-1,6.29,2.02,0.31 +SAMPL8-18_micro000,SAMPL8-18_micro005,-1,6.26,2.02,0.63 +SAMPL8-19_micro000,SAMPL8-19_micro010,-1,7.4,2.02,0.4 +SAMPL8-19_micro000,SAMPL8-19_micro011,-1,12.4,2.02,0.17 +SAMPL8-19_micro000,SAMPL8-19_micro001,1,-7.65,2.02,0.4 +SAMPL8-19_micro000,SAMPL8-19_micro004,1,-7.73,2.02,0.17 +SAMPL8-19_micro000,SAMPL8-19_micro005,1,-5.61,2.02,0.34 +SAMPL8-19_micro000,SAMPL8-19_micro006,1,-0.0,2.02,0.01 +SAMPL8-19_micro000,SAMPL8-19_micro008,1,-0.0,2.02,0.01 +SAMPL8-19_micro000,SAMPL8-19_micro009,1,-0.0,2.02,0.01 +SAMPL8-19_micro000,SAMPL8-19_micro016,1,-6.18,2.02,0.26 +SAMPL8-19_micro000,SAMPL8-19_micro018,1,-0.0,2.02,0.01 +SAMPL8-19_micro000,SAMPL8-19_micro019,1,-0.0,2.02,0.01 +SAMPL8-19_micro000,SAMPL8-19_micro022,1,-3.44,2.02,0.53 +SAMPL8-19_micro000,SAMPL8-19_micro023,1,-1.55,2.02,0.29 +SAMPL8-19_micro000,SAMPL8-19_micro002,2,-6.35,2.02,0.26 +SAMPL8-19_micro000,SAMPL8-19_micro003,2,-4.36,2.02,0.42 +SAMPL8-20_micro000,SAMPL8-20_micro002,1,-5.03,2.02,0.16 +SAMPL8-20_micro000,SAMPL8-20_micro003,1,-11.06,2.02,0.4 +SAMPL8-20_micro000,SAMPL8-20_micro005,1,4.06,2.02,0.57 +SAMPL8-20_micro000,SAMPL8-20_micro006,1,-4.79,2.02,0.2 +SAMPL8-20_micro000,SAMPL8-20_micro007,1,0.0,2.02,0.01 +SAMPL8-20_micro000,SAMPL8-20_micro011,1,-8.68,2.02,0.36 +SAMPL8-20_micro000,SAMPL8-20_micro014,1,4.16,2.02,0.47 +SAMPL8-20_micro000,SAMPL8-20_micro015,1,-8.88,2.02,0.47 +SAMPL8-20_micro000,SAMPL8-20_micro016,1,-6.16,2.02,0.34 +SAMPL8-20_micro000,SAMPL8-20_micro025,1,-0.0,2.02,0.01 +SAMPL8-20_micro000,SAMPL8-20_micro026,1,-7.22,2.02,0.45 +SAMPL8-20_micro000,SAMPL8-20_micro028,1,-0.0,2.02,0.01 +SAMPL8-20_micro000,SAMPL8-20_micro001,0,-0.0,2.02,0.01 +SAMPL8-21_micro000,SAMPL8-21_micro003,-1,11.85,2.02,0.72 +SAMPL8-21_micro000,SAMPL8-21_micro006,-1,6.65,2.02,0.16 +SAMPL8-21_micro000,SAMPL8-21_micro007,-1,6.92,2.02,0.4 +SAMPL8-21_micro000,SAMPL8-21_micro009,-1,13.37,2.02,0.71 +SAMPL8-21_micro000,SAMPL8-21_micro011,-1,12.56,2.02,0.57 +SAMPL8-21_micro000,SAMPL8-21_micro014,-1,6.77,2.02,0.35 +SAMPL8-21_micro000,SAMPL8-21_micro016,-1,19.59,2.02,0.81 +SAMPL8-21_micro000,SAMPL8-21_micro018,-1,4.22,2.02,0.31 +SAMPL8-21_micro000,SAMPL8-21_micro019,-1,13.61,2.02,0.72 +SAMPL8-21_micro000,SAMPL8-21_micro020,-1,4.92,2.02,0.41 +SAMPL8-21_micro000,SAMPL8-21_micro022,-1,4.02,2.02,0.43 +SAMPL8-21_micro000,SAMPL8-21_micro024,-1,4.66,2.02,0.35 +SAMPL8-21_micro000,SAMPL8-21_micro026,-1,4.51,2.02,0.37 +SAMPL8-21_micro000,SAMPL8-21_micro027,-1,4.92,2.02,0.51 +SAMPL8-21_micro000,SAMPL8-21_micro001,-2,17.12,2.02,1.12 +SAMPL8-21_micro000,SAMPL8-21_micro002,-2,25.77,2.02,1.26 +SAMPL8-22_micro000,SAMPL8-22_micro001,-1,7.95,2.02,0.5 +SAMPL8-22_micro000,SAMPL8-22_micro002,0,-2.8,2.02,0.58 +SAMPL8-22_micro000,SAMPL8-22_micro003,0,-0.0,2.02,0.01 +SAMPL8-23_micro000,SAMPL8-23_micro002,-1,7.6,2.02,0.39 +SAMPL8-23_micro000,SAMPL8-23_micro005,-1,15.23,2.02,1.04 +SAMPL8-23_micro000,SAMPL8-23_micro001,1,-1.21,2.02,0.74 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-2.3,2.02,0.63 +SAMPL8-23_micro000,SAMPL8-23_micro003,0,5.43,2.02,0.35 +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Robert Raddi + +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +Temple University + +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name of the method should not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +Random Forest + +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +0.16 hr (compute features, 4-6 CPUs) +0.15 hr (prediction calculations, 4-6 CPUs) +0.31 hr (total, 4-6 CPUs) +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +1.0 hr to train the model (4 CPUs) +3 GHz 6-Core Intel Core i5 + +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +In order of usage (1st listed is used the most) +RDKit 2020.03.4 +pandas 1.0.3 +numpy 1.18.2 +scikit-learn 0.22.1 +openeye-toolkits 2019.10.2 +openforcefield 0.6.0 + +# METHOD CATEGORY SECTION +# +# State if your prediction method is better classified as an +# experimental database lookup (DL), linear free energy relationship (LFER), +# quantitative structure-property relationship or machine learning (QSPR/ML), +# quantum mechanics without empirical correction (QM) model, quantum mechanics with +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular +# mechanics (QM+MM), or Other, using the following category labels: +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`. +# +# Pick only one category label. +# The `Category:` keyword is required. +Category: +QSPR/ML + +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# Use as many lines of text as you need. +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. +Method: +This submission uses a method that predicts microscopic pKa values that are directly related to relative free energies following the work by Gunner et al.\cite{gunner2020standard} in units of kcal/mol. Our method uses our publicly avialable database (http://doi.org/10.5281/zenodo.5027418) with recomputed AM1BCC partial charge features (AM1BCCELF10) from OpenEye. Previously, we used a DeepGP model to predict SAMPL6 & SAMPL7 molecules\cite{raddi2021stacking}. Here, we blindly test the DeepGP model on the SAMPL8 small moleculue set in addition to the following machine learning (ML) models: Random Forest, AdaBoost and XGBoost. Model parameters for AdaBoost and XGBoost follow a recent work from Yang et al.\cite{yang2020holistic}. Model parameters for the DeepGP and the Random Forest models are presented in the work from Raddi et al\cite{raddi2021stacking}. Note that similarity filtering was only used for the DeepGP model due to it's slight performance enhancements. The ten feature calculations were closely followed from Bannan et al.\cite{bannan2018sampl6} with the exception of changing AM1BCC to AM1BCCELF10 partial charges. Our hand curated training set consists of approximately 3000 small molecules entirely from open-source databases. 5-fold model validation for each of these ML methods using our database results in very similar performance. +Statistical uncertainty (SEM) for the relative free energies was calculated during model validation and standard errors for each microtransition was calculated using 10-round bootstrapping. The standard Gaussian process model automatically provides uncertainties that correspond to how closely the molecule of interest overlaps with the molecules in the training set, so no bootstrapping was needed here. Note that the predictions reported have have high uncertainty due to the lack of chemical space in the training set as well as the lack of similarity of the molecules of interest to that of the molecules found in the training set. + +//ref.bib +@article{raddi2021stacking, + title={Stacking Gaussian Processes to Improve pKa Predictions in the SAMPL7 Challenge}, + author={Raddi, Robert and Voelz, Vincent}, + year={2021} +} +@article{yang2020holistic, + title={Holistic Prediction of the pKa in Diverse Solvents Based on a Machine-Learning Approach}, + author={Yang, Qi and Li, Yao and Yang, Jin-Dong and Liu, Yidi and Zhang, Long and Luo, Sanzhong and Cheng, Jin-Pei}, + journal={Angewandte Chemie}, + volume={132}, + number={43}, + pages={19444--19453}, + year={2020}, + publisher={Wiley Online Library} +} +@article{bannan2018sampl6, + title={SAMPL6 challenge results from $pK_a$ predictions based on a general Gaussian process model}, + author={Bannan, Caitlin C and Mobley, David L and Skillman, A Geoffrey}, + journal={Journal of computer-aided molecular design}, + volume={32}, + number={10}, + pages={1165--1177}, + year={2018}, + publisher={Springer} +} +@article{gunner2020standard, + title={Standard state free energies, not pK as, are ideal for describing small molecule protonation and tautomeric states}, + author={Gunner, Marilyn R and Murakami, Taichi and Rustenburg, Ari{\"e}n S and I{\c{s}}{\i}k, Mehtap and Chodera, John D}, + journal={Journal of Computer-Aided Molecular Design}, + pages={1--13}, + year={2020}, + publisher={Springer} +} + + + +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) +Ranked: +False + diff --git a/physical_properties/pKa/submissions/pKa-RobertRaddi_XGBoost_modified.csv b/physical_properties/pKa/submissions/pKa-RobertRaddi_XGBoost_modified.csv new file mode 100644 index 0000000..b83d36c --- /dev/null +++ b/physical_properties/pKa/submissions/pKa-RobertRaddi_XGBoost_modified.csv @@ -0,0 +1,285 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction) +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# PREDICTION SECTION +# +# It is mandatory to submit relative free energy (RFE) predictions for all 22 molecules. Incomplete submissions will not be accepted. +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty. +# +# The data in each prediction line should be structured as follows: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty +# +# If you have evaluated additional microstates, include the following: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +# +# The molecule ID of the other microstate needs to be in the format: `SMXX_extra001` (number can vary) +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders, +# Please send the `.mol2` file to the email listed on the instructions page. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: +SAMPL8-1_micro000,SAMPL8-1_micro001,-1,13.45,1.98,1.98 +SAMPL8-1_micro000,SAMPL8-1_micro002,-1,8.96,1.98,1.98 +SAMPL8-1_micro000,SAMPL8-1_micro003,-1,12.2,1.98,1.98 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,6.79,1.98,1.98 +SAMPL8-1_micro000,SAMPL8-1_micro005,-1,7.87,1.98,1.98 +SAMPL8-1_micro000,SAMPL8-1_micro008,-1,14.17,1.98,1.98 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,6.75,1.98,1.98 +SAMPL8-2_micro000,SAMPL8-2_micro003,-1,-0.0,1.98,1.98 +SAMPL8-2_micro000,SAMPL8-2_micro002,0,-6.64,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro001,-1,12.4,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro003,-1,22.52,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro005,-1,6.51,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro009,-1,15.6,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,7.81,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro011,-1,23.36,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro015,-1,25.37,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,13.55,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro017,-1,22.35,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro018,-1,12.79,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro020,-1,8.32,1.98,1.98 +SAMPL8-3_micro000,SAMPL8-3_micro002,0,8.09,1.98,1.98 +SAMPL8-4_micro000,SAMPL8-4_micro003,-1,9.89,1.98,1.98 +SAMPL8-4_micro000,SAMPL8-4_micro005,-1,7.18,1.98,1.98 +SAMPL8-4_micro000,SAMPL8-4_micro006,-1,10.04,1.98,1.98 +SAMPL8-4_micro000,SAMPL8-4_micro008,-1,5.01,1.98,1.98 +SAMPL8-5_micro000,SAMPL8-5_micro002,-1,-0.0,1.98,1.98 +SAMPL8-5_micro000,SAMPL8-5_micro007,-1,6.88,1.98,1.98 +SAMPL8-5_micro000,SAMPL8-5_micro003,1,-2.98,1.98,1.98 +SAMPL8-5_micro000,SAMPL8-5_micro006,1,-12.13,1.98,1.98 +SAMPL8-5_micro000,SAMPL8-5_micro001,0,0.0,1.98,1.98 +SAMPL8-6_micro000,SAMPL8-6_micro001,-1,5.99,1.98,1.98 +SAMPL8-6_micro000,SAMPL8-6_micro006,-1,8.87,1.98,1.98 +SAMPL8-6_micro000,SAMPL8-6_micro009,-1,-0.0,1.98,1.98 +SAMPL8-6_micro000,SAMPL8-6_micro002,1,-21.74,1.98,1.98 +SAMPL8-6_micro000,SAMPL8-6_micro003,1,-9.4,1.98,1.98 +SAMPL8-7_micro000,SAMPL8-7_micro001,-1,10.5,1.98,1.98 +SAMPL8-8_micro000,SAMPL8-8_micro001,1,-6.38,1.98,1.98 +SAMPL8-8_micro000,SAMPL8-8_micro002,1,-5.3,1.98,1.98 +SAMPL8-9_micro000,SAMPL8-9_micro001,-1,11.43,1.98,1.98 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-10.79,1.98,1.98 +SAMPL8-12_micro000,SAMPL8-12_micro001,-1,19.85,1.98,1.98 +SAMPL8-12_micro000,SAMPL8-12_micro002,0,2.25,1.98,1.98 +SAMPL8-12_micro000,SAMPL8-12_micro003,0,-0.0,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro004,-1,27.84,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro005,-1,17.16,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,6.82,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro009,-1,5.4,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro010,-1,6.49,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro012,-1,9.15,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro019,-1,10.53,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro021,-1,10.37,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro022,-1,6.22,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro025,-1,12.97,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro027,-1,8.43,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro028,-1,7.73,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro029,-1,6.12,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro032,-1,7.04,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro001,-2,11.21,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro003,-2,21.04,1.98,1.98 +SAMPL8-14_micro000,SAMPL8-14_micro002,0,-3.16,1.98,1.98 +SAMPL8-15_micro000,SAMPL8-15_micro003,1,-8.01,1.98,1.98 +SAMPL8-15_micro000,SAMPL8-15_micro004,1,-9.04,1.98,1.98 +SAMPL8-15_micro000,SAMPL8-15_micro001,0,0.0,1.98,1.98 +SAMPL8-15_micro000,SAMPL8-15_micro002,0,-0.0,1.98,1.98 +SAMPL8-16_micro000,SAMPL8-16_micro001,1,-8.16,1.98,1.98 +SAMPL8-16_micro000,SAMPL8-16_micro003,1,-14.41,1.98,1.98 +SAMPL8-16_micro000,SAMPL8-16_micro004,1,-6.64,1.98,1.98 +SAMPL8-16_micro000,SAMPL8-16_micro006,1,-5.24,1.98,1.98 +SAMPL8-16_micro000,SAMPL8-16_micro008,1,-8.69,1.98,1.98 +SAMPL8-16_micro000,SAMPL8-16_micro009,1,-16.21,1.98,1.98 +SAMPL8-16_micro000,SAMPL8-16_micro010,1,-8.06,1.98,1.98 +SAMPL8-16_micro000,SAMPL8-16_micro002,0,-6.58,1.98,1.98 +SAMPL8-17_micro000,SAMPL8-17_micro001,-1,14.39,1.98,1.98 +SAMPL8-17_micro000,SAMPL8-17_micro005,-1,7.45,1.98,1.98 +SAMPL8-18_micro000,SAMPL8-18_micro005,-1,5.78,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro010,-1,8.86,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro011,-1,13.01,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro001,1,-6.39,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro004,1,-6.95,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro005,1,-6.0,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro006,1,-0.0,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro008,1,-0.0,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro009,1,-0.0,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro016,1,-4.83,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro018,1,-0.0,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro019,1,-0.0,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro022,1,-5.7,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro023,1,-2.95,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro002,2,-7.34,1.98,1.98 +SAMPL8-19_micro000,SAMPL8-19_micro003,2,-3.97,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro002,1,-5.16,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro003,1,-8.88,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro005,1,5.35,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro006,1,-4.89,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro007,1,0.0,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro011,1,-10.36,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro014,1,5.4,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro015,1,-8.26,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro016,1,-6.77,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro025,1,-0.0,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro026,1,-8.31,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro028,1,-0.0,1.98,1.98 +SAMPL8-20_micro000,SAMPL8-20_micro001,0,-0.0,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro003,-1,16.22,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro006,-1,7.19,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro007,-1,5.38,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro009,-1,14.88,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro011,-1,12.8,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro014,-1,6.51,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro016,-1,20.11,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro018,-1,5.88,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro019,-1,13.1,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro020,-1,6.57,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro022,-1,4.97,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro024,-1,6.74,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro026,-1,6.07,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro027,-1,6.37,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro001,-2,14.82,1.98,1.98 +SAMPL8-21_micro000,SAMPL8-21_micro002,-2,22.5,1.98,1.98 +SAMPL8-22_micro000,SAMPL8-22_micro001,-1,7.67,1.98,1.98 +SAMPL8-22_micro000,SAMPL8-22_micro002,0,-3.19,1.98,1.98 +SAMPL8-22_micro000,SAMPL8-22_micro003,0,-0.0,1.98,1.98 +SAMPL8-23_micro000,SAMPL8-23_micro002,-1,7.18,1.98,1.98 +SAMPL8-23_micro000,SAMPL8-23_micro005,-1,17.2,1.98,1.98 +SAMPL8-23_micro000,SAMPL8-23_micro001,1,-2.01,1.98,1.98 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-0.91,1.98,1.98 +SAMPL8-23_micro000,SAMPL8-23_micro003,0,5.21,1.98,1.98 +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Robert Raddi + +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +Temple University + +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name of the method should not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +XGBoost + +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +0.16 hr (compute features, 4-6 CPUs) +0.15 hr (prediction calculations, 4-6 CPUs) +0.31 hr (total, 4-6 CPUs) +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +1.0 hr to train the model (4 CPUs) +3 GHz 6-Core Intel Core i5 + +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +In order of usage (1st listed is used the most) +RDKit 2020.03.4 +pandas 1.0.3 +numpy 1.18.2 +scikit-learn 0.22.1 +openeye-toolkits 2019.10.2 +openforcefield 0.6.0 + +# METHOD CATEGORY SECTION +# +# State if your prediction method is better classified as an +# experimental database lookup (DL), linear free energy relationship (LFER), +# quantitative structure-property relationship or machine learning (QSPR/ML), +# quantum mechanics without empirical correction (QM) model, quantum mechanics with +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular +# mechanics (QM+MM), or Other, using the following category labels: +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`. +# +# Pick only one category label. +# The `Category:` keyword is required. +Category: +QSPR/ML + +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# Use as many lines of text as you need. +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. +Method: +This submission uses a method that predicts microscopic pKa values that are directly related to relative free energies following the work by Gunner et al.\cite{gunner2020standard} in units of kcal/mol. Our method uses our publicly avialable database (http://doi.org/10.5281/zenodo.5027418) with recomputed AM1BCC partial charge features (AM1BCCELF10) from OpenEye. Previously, we used a DeepGP model to predict SAMPL6 & SAMPL7 molecules\cite{raddi2021stacking}. Here, we blindly test the DeepGP model on the SAMPL8 small moleculue set in addition to the following machine learning (ML) models: Random Forest, AdaBoost and XGBoost. Model parameters for AdaBoost and XGBoost follow a recent work from Yang et al.\cite{yang2020holistic}. Model parameters for the DeepGP and the Random Forest models are presented in the work from Raddi et al\cite{raddi2021stacking}. Note that similarity filtering was only used for the DeepGP model due to it's slight performance enhancements. The ten feature calculations were closely followed from Bannan et al.\cite{bannan2018sampl6} with the exception of changing AM1BCC to AM1BCCELF10 partial charges. Our hand curated training set consists of approximately 3000 small molecules entirely from open-source databases. 5-fold model validation for each of these ML methods using our database results in very similar performance. +Statistical uncertainty (SEM) for the relative free energies was calculated during model validation and standard errors for each microtransition was calculated using 10-round bootstrapping. The standard Gaussian process model automatically provides uncertainties that correspond to how closely the molecule of interest overlaps with the molecules in the training set, so no bootstrapping was needed here. Note that the predictions reported have have high uncertainty due to the lack of chemical space in the training set as well as the lack of similarity of the molecules of interest to that of the molecules found in the training set. + +//ref.bib +@article{raddi2021stacking, + title={Stacking Gaussian Processes to Improve pKa Predictions in the SAMPL7 Challenge}, + author={Raddi, Robert and Voelz, Vincent}, + year={2021} +} +@article{yang2020holistic, + title={Holistic Prediction of the pKa in Diverse Solvents Based on a Machine-Learning Approach}, + author={Yang, Qi and Li, Yao and Yang, Jin-Dong and Liu, Yidi and Zhang, Long and Luo, Sanzhong and Cheng, Jin-Pei}, + journal={Angewandte Chemie}, + volume={132}, + number={43}, + pages={19444--19453}, + year={2020}, + publisher={Wiley Online Library} +} +@article{bannan2018sampl6, + title={SAMPL6 challenge results from $pK_a$ predictions based on a general Gaussian process model}, + author={Bannan, Caitlin C and Mobley, David L and Skillman, A Geoffrey}, + journal={Journal of computer-aided molecular design}, + volume={32}, + number={10}, + pages={1165--1177}, + year={2018}, + publisher={Springer} +} +@article{gunner2020standard, + title={Standard state free energies, not pK as, are ideal for describing small molecule protonation and tautomeric states}, + author={Gunner, Marilyn R and Murakami, Taichi and Rustenburg, Ari{\"e}n S and I{\c{s}}{\i}k, Mehtap and Chodera, John D}, + journal={Journal of Computer-Aided Molecular Design}, + pages={1--13}, + year={2020}, + publisher={Springer} +} + + + +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) +Ranked: +False + diff --git a/physical_properties/pKa/submissions/pKa-ZhiyiWu-1_modified.csv b/physical_properties/pKa/submissions/pKa-ZhiyiWu-1_modified.csv new file mode 100644 index 0000000..b05e3c7 --- /dev/null +++ b/physical_properties/pKa/submissions/pKa-ZhiyiWu-1_modified.csv @@ -0,0 +1,375 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction) +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# PREDICTION SECTION +# +# It is mandatory to submit relative free energy (RFE) predictions for all 22 molecules. Incomplete submissions will not be accepted. +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty. +# Note that we here follow the same sign convention and submission format as the SAMPL7 pKa challenge. +# +# The data in each prediction line should be structured as follows: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty +# +# If you have evaluated additional microstates, include the following: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +# +# The molecule ID of the other microstate needs to be in the format: `SAMPL8-X_extra001` (number can vary) +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders, +# Please send the `.mol2` file to the email listed on the instructions page. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: +SAMPL8-1_micro000,SAMPL8-1_micro001,-1,23.04,1.00,1.00 +SAMPL8-1_micro000,SAMPL8-1_micro002,-1,16.82,1.00,1.00 +SAMPL8-1_micro000,SAMPL8-1_micro003,-1,24.10,1.00,1.00 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,6.25,1.00,1.00 +SAMPL8-1_micro000,SAMPL8-1_micro005,-1,6.01,1.00,1.00 +SAMPL8-1_micro000,SAMPL8-1_micro006,0,19.72,1.00,1.00 +SAMPL8-1_micro000,SAMPL8-1_micro007,0,13.06,1.00,1.00 +SAMPL8-1_micro000,SAMPL8-1_micro008,-1,22.79,1.00,1.00 +SAMPL8-1_micro000,SAMPL8-1_micro009,0,16.23,1.00,1.00 +SAMPL8-1_micro000,SAMPL8-1_micro010,0,11.71,1.00,1.00 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,8.38,1.00,1.00 +SAMPL8-2_micro000,SAMPL8-2_micro002,0,12.24,1.00,1.00 +SAMPL8-2_micro000,SAMPL8-2_micro003,-1,25.16,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro001,-1,6.70,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro002,0,-1.94,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro003,-1,1.29,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro004,0,-7.02,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro005,-1,-0.16,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro006,0,-23.19,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro007,-2,14.47,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro008,0,-2.14,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro009,-1,-3.40,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,-13.41,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro011,-1,4.85,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro012,-2,13.18,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro013,-2,-1.25,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro014,-2,-1.25,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro015,-1,17.31,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,-7.45,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro017,-1,11.90,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro018,-1,4.88,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro019,-2,18.24,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro020,-1,-13.51,1.00,1.00 +SAMPL8-3_micro000,SAMPL8-3_micro021,-2,17.30,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro001,0,3.01,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro002,1,-1.39,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro003,-1,8.14,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro004,0,0.02,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro005,-1,8.19,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro006,-1,8.34,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro007,1,-1.41,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro008,-1,10.19,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro009,-1,8.09,1.00,1.00 +SAMPL8-4_micro000,SAMPL8-4_micro010,0,-1.62,1.00,1.00 +SAMPL8-5_micro000,SAMPL8-5_micro001,0,0.31,1.00,1.00 +SAMPL8-5_micro000,SAMPL8-5_micro002,-1,18.53,1.00,1.00 +SAMPL8-5_micro000,SAMPL8-5_micro003,1,1.31,1.00,1.00 +SAMPL8-5_micro000,SAMPL8-5_micro004,0,20.90,1.00,1.00 +SAMPL8-5_micro000,SAMPL8-5_micro005,0,9.52,1.00,1.00 +SAMPL8-5_micro000,SAMPL8-5_micro006,1,12.15,1.00,1.00 +SAMPL8-5_micro000,SAMPL8-5_micro007,-1,5.93,1.00,1.00 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+SAMPL8-23_micro000,SAMPL8-23_micro005,-1,4.20,1.00,1.00 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-14.11,1.00,1.00 +SAMPL8-23_micro000,SAMPL8-23_micro007,0,-9.56,1.00,1.00 + + + +# +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Zhiyi Wu; Philip Biggin + +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +University of Oxford + +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name of the method should not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +QM with linear fitting + +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +7000 hours, CPU + +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used to run the simulations. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +All the simulations were performed on 48 core Cascade Lake (Intel Xeon Platinum +8268 CPU @ 2.90GHz) with 392GB RAM on a single node. + +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +Gaussian/16.A.03 +ORCA/4.2.1 +ORCA/5.0.0 +Multiwfn/3.8 +MDAnalysis/develop +uESE/xESE +crest/2.11 +xTB/6.4.1 +obabel/3.1.1 +RDKit/Q1 2021 +shermo/2.2 + + +# METHOD CATEGORY SECTION +# +# State if your prediction method is better classified as an +# experimental database lookup (DL), linear free energy relationship (LFER), +# quantitative structure-property relationship or machine learning (QSPR/ML), +# quantum mechanics without empirical correction (QM) model, quantum mechanics with +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular +# mechanics (QM+MM), or Other, using the following category labels: +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`. +# +# Pick only one category label. +# The `Category:` keyword is required. +Category: +QM + +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# Use as many lines of text as you need. +# +# We strongly encourage you to submit your predicted macro pKa values in this section in consecutive lines following this format: +# compound name, macro pKa, initial formal charge, formal charge after transition, e.g.: +# SAMPL8-1, 3.5, 0, +1 +# This will allow us to check that our analysis of your free energies leads to the same endpoint as your analysis. +# +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. + +Method: +The 3D molecule is generated with obabel and is minimised with xTB at GFN2-xTB +level using alpb implicit water model. Crest is used to generate additional +conformers at the same theoretical level and implicit solvent model. The conformers +are then geometry optimised and vibration analysis are done at B3LYP-D3(BJ)/def2-TZVP +with water as implicit solvent model with Gaussian. The conformer that are +within 6 kcal/mol of the lowest energy conformer are retained. +The conformer that are within 0.1 A RMSD are discarded. +The final energy of these conformer is the sum of +electron energy computed at PWPB95-D3(BJ)/def2-QZVPP with ORCA +thermal correction computed at B3LYP-D3(BJ)/def2-TZVP with Gaussian +solvation free energy computed with uESE/xESE + +The ensemble free energy of all the conformers are then computed with shermo ( +Grimme's entropy interpolation and Truhlar ZPE scaling factor). + + +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) + +Ranked: +True diff --git a/physical_properties/pKa/submissions/pKa_Chemaxon_modified.csv b/physical_properties/pKa/submissions/pKa_Chemaxon_modified.csv new file mode 100644 index 0000000..1539585 --- /dev/null +++ b/physical_properties/pKa/submissions/pKa_Chemaxon_modified.csv @@ -0,0 +1,166 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction) +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# PREDICTION SECTION +# +# It is mandatory to submit relative free energy (RFE) predictions for all 22 molecules. Incomplete submissions will not be accepted. +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty. +# Note that we here follow the same sign convention and submission format as the SAMPL7 pKa challenge. +# +# The data in each prediction line should be structured as follows: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty +# +# If you have evaluated additional microstates, include the following: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +# +# The molecule ID of the other microstate needs to be in the format: `SAMPL8-X_extra001` (number can vary) +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders, +# Please send the `.mol2` file to the email listed on the instructions page. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: + +SAMPL8-1_micro000,SAMPL8-1_micro001,-1,3.88,0,0 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,3.49,0,0 +SAMPL8-3_micro000,SAMPL8-3_micro001,-1,4.25,0,0 +SAMPL8-3_micro000,SAMPL8-3_micro007,-2,14.08,0,0 +SAMPL8-3_micro000,SAMPL8-3_Chemaxon_extra001,-3,12.56,0,0 +SAMPL8-4_micro000,SAMPL8-4_micro002,1,-1.02,0,0 +SAMPL8-4_micro000,SAMPL8-4_micro003,-1,3.75,0,0 +SAMPL8-4_micro000,SAMPL8-4_Chemaxon_extra001,-2,18.5,0,0 +SAMPL8-5_micro000,SAMPL8-5_micro007,-1,4.00,0,0 +SAMPL8-6_micro000,SAMPL8-6_micro001,-1,3.50,0,0 +SAMPL8-6_micro000,SAMPL8-6_micro003,1,-2.83,0,0 +SAMPL8-7_micro000,SAMPL8-7_Chemaxon_extra001,1,-7.55,0,0 +SAMPL8-7_micro000,SAMPL8-7_Chemaxon_extra002,-1,14.16,0,0 +SAMPL8-8_micro000,SAMPL8-8_Chemaxon_extra001,1,-2.72,0,0 +SAMPL8-9_micro000,SAMPL8-9_Chemaxon_extra001,1,-7.55,0,0 +SAMPL8-9_micro000,SAMPL8-9_Chemaxon_extra002,-1,14.31,0,0 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-7.11,0,0 +SAMPL8-12_micro000,SAMPL8-12_micro002,1,-6.59,0,0 +SAMPL8-12_micro000,SAMPL8-12_micro003,1,-6.89,0,0 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,11.06,0,0 +SAMPL8-14_micro000,SAMPL8-14_dortmund002,1,-7.16,0,0 +SAMPL8-14_micro000,SAMPL8-14_dortmund001,1,-7.26,0,0 +SAMPL8-15_micro000,SAMPL8-15_micro004,1,-1.53,0,0 +SAMPL8-16_micro000,SAMPL8-16_micro004,1,-5.05,0,0 +SAMPL8-16_micro000,SAMPL8-16_Chemaxon_extra001,-1,11.47,0,0 +SAMPL8-16_micro000,SAMPL8-16_Chemaxon_extra002,-1,25.83,0,0 +SAMPL8-17_micro000,SAMPL8-17_micro002,1,-7.59,0,0 +SAMPL8-17_micro000,SAMPL8-17_micro005,-1,15.05,0,0 +SAMPL8-18_micro000,SAMPL8-18_micro004,1,-1.51,0,0 +SAMPL8-19_micro000,SAMPL8-19_Chemaxon_extra001,-1,9.54,0,0 +SAMPL8-19_micro000,SAMPL8-19_micro009,1,-4.77,0,0 +SAMPL8-19_micro000,SAMPL8-19_Chemaxon_extra002,1,-6.49,0,0 +SAMPL8-20_micro000,SAMPL8-20_micro011,1,-1.33,0,0 +SAMPL8-20_micro000,SAMPL8-20_micro018,-1,13.72,0,0 +SAMPL8-21_micro000,SAMPL8-21_micro027,-1,9.44,0,0 +SAMPL8-21_micro000,SAMPL8-21_Chemaxon_extra001,1,-6.85,0,0 +SAMPL8-21_micro000,SAMPL8-21_dortmund001,2,-8.07,0,0 +SAMPL8-22_micro000,SAMPL8-22_dortmund002,1,-2.94,0,0 +SAMPL8-23_micro000,SAMPL8-23_micro001,1,-3.46,0,0 +SAMPL8-23_micro000,SAMPL8-23_micro002,-1,9.15,0,0 + + + +# +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Dhiman Ray + +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +University of California Irvine + +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name of the method should not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +Chemaxon + +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +None + +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used to run the simulations. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +None + +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +Chemaxon + +# METHOD CATEGORY SECTION +# +# State if your prediction method is better classified as an +# experimental database lookup (DL), linear free energy relationship (LFER), +# quantitative structure-property relationship or machine learning (QSPR/ML), +# quantum mechanics without empirical correction (QM) model, quantum mechanics with +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular +# mechanics (QM+MM), or Other, using the following category labels: +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`. +# +# Pick only one category label. +# The `Category:` keyword is required. +Category: +Other + +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# Use as many lines of text as you need. +# +# We strongly encourage you to submit your predicted macro pKa values in this section in consecutive lines following this format: +# compound name, macro pKa, initial formal charge, formal charge after transition, e.g.: +# SAMPL8-1, 3.5, 0, +1 +# This will allow us to check that our analysis of your free energies leads to the same endpoint as your analysis. +# +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. + +Method: +Reference calculations obtained using ChemAxon softwear + + +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) + +Ranked: +True diff --git a/physical_properties/pKa/submissions/pKa_SabatinoRodriguezPaluch_uESE_extra_modified.csv b/physical_properties/pKa/submissions/pKa_SabatinoRodriguezPaluch_uESE_extra_modified.csv new file mode 100644 index 0000000..1bc63ef --- /dev/null +++ b/physical_properties/pKa/submissions/pKa_SabatinoRodriguezPaluch_uESE_extra_modified.csv @@ -0,0 +1,429 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction) +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# PREDICTION SECTION +# +# It is mandatory to submit relative free energy (RFE) predictions for all 23 molecules. Incomplete submissions will not be accepted. +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty. +# Note that we here follow the same sign convention and submission format as the SAMPL7 pKa challenge. +# +# The data in each prediction line should be structured as follows: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty +# +# If you have evaluated additional microstates, include the following: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +# +# The molecule ID of the other microstate needs to be in the format: `SAMPL8-X_extra001` (number can vary) +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders, +# Please send the `.mol2` file to the email listed on the instructions page. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: +SAMPL8-1_micro000,SAMPL8-1_micro001,-1,44.96,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro002,-1,31.07,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro003,-1,40.94,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,10.86,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro005,-1,10.87,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro006,0,45.04,0.10,1.40 +SAMPL8-1_micro000,SAMPL8-1_micro007,0,29.74,0.10,1.40 +SAMPL8-1_micro000,SAMPL8-1_micro008,-1,40.06,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro009,0,33.75,0.10,1.40 +SAMPL8-1_micro000,SAMPL8-1_micro010,0,31.74,0.10,1.40 +SAMPL8-1_micro000,SAMPL8-1_RFE-uESE-extra_extra001,1,15.16,0.10,2.90 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,11.25,0.10,3.00 +SAMPL8-2_micro000,SAMPL8-2_micro002,0,26.87,0.10,1.40 +SAMPL8-2_micro000,SAMPL8-2_micro003,-1,37.87,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro001,-1,-1.36,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro002,0,-13.75,0.10,1.40 +SAMPL8-3_micro000,SAMPL8-3_micro003,-1,1.03,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro004,0,-14.19,0.10,1.40 +SAMPL8-3_micro000,SAMPL8-3_micro005,-1,-15.42,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro006,0,-49.40,0.10,1.40 +SAMPL8-3_micro000,SAMPL8-3_micro007,-2,28.73,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro008,0,-12.06,0.10,1.40 +SAMPL8-3_micro000,SAMPL8-3_micro009,-1,-3.57,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,-40.63,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro011,-1,4.97,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro012,-2,48.91,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro013,-2,58.77,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro014,-2,41.40,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro015,-1,17.35,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,-30.76,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro017,-1,5.39,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro018,-1,-2.62,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro019,-2,42.96,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro020,-1,-36.60,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro021,-2,47.42,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_RFE-uESE-extra_extra001,1,-26.31,0.10,2.90 +SAMPL8-4_micro000,SAMPL8-4_micro001,0,9.21,0.10,1.40 +SAMPL8-4_micro000,SAMPL8-4_micro002,1,1.72,0.10,2.90 +SAMPL8-4_micro000,SAMPL8-4_micro003,-1,6.69,0.10,3.00 +SAMPL8-4_micro000,SAMPL8-4_micro004,0,0.00,0.10,1.40 +SAMPL8-4_micro000,SAMPL8-4_micro005,-1,6.17,0.10,3.00 +SAMPL8-4_micro000,SAMPL8-4_micro006,-1,6.38,0.10,3.00 +SAMPL8-4_micro000,SAMPL8-4_micro007,1,1.42,0.10,2.90 +SAMPL8-4_micro000,SAMPL8-4_micro008,-1,10.14,0.10,3.00 +SAMPL8-4_micro000,SAMPL8-4_micro009,-1,6.16,0.10,3.00 +SAMPL8-4_micro000,SAMPL8-4_micro010,0,-9.81,0.10,1.40 +SAMPL8-5_micro000,SAMPL8-5_micro001,0,20.67,0.10,1.40 +SAMPL8-5_micro000,SAMPL8-5_micro002,-1,32.28,0.10,3.00 +SAMPL8-5_micro000,SAMPL8-5_micro003,1,13.74,0.10,2.90 +SAMPL8-5_micro000,SAMPL8-5_micro004,0,40.59,0.10,1.40 +SAMPL8-5_micro000,SAMPL8-5_micro005,0,22.16,0.10,1.40 +SAMPL8-5_micro000,SAMPL8-5_micro006,1,33.80,0.10,2.90 +SAMPL8-5_micro000,SAMPL8-5_micro007,-1,10.51,0.10,3.00 +SAMPL8-6_micro000,SAMPL8-6_micro001,-1,8.09,0.10,3.00 +SAMPL8-6_micro000,SAMPL8-6_micro002,1,41.73,0.10,2.90 +SAMPL8-6_micro000,SAMPL8-6_micro003,1,7.22,0.10,2.90 +SAMPL8-6_micro000,SAMPL8-6_micro004,0,41.17,0.10,1.40 +SAMPL8-6_micro000,SAMPL8-6_micro005,0,29.53,0.10,1.40 +SAMPL8-6_micro000,SAMPL8-6_micro006,-1,45.64,0.10,3.00 +SAMPL8-6_micro000,SAMPL8-6_micro007,0,20.63,0.10,1.40 +SAMPL8-6_micro000,SAMPL8-6_micro008,0,23.12,0.10,1.40 +SAMPL8-6_micro000,SAMPL8-6_micro009,-1,31.06,0.10,3.00 +SAMPL8-7_micro000,SAMPL8-7_micro001,-1,31.11,0.10,3.00 +SAMPL8-7_micro000,SAMPL8-7_micro002,1,-12.12,0.10,2.90 +SAMPL8-7_micro000,SAMPL8-7_micro003,1,10.42,0.10,2.90 +SAMPL8-7_micro000,SAMPL8-7_micro004,0,7.19,0.10,1.40 +SAMPL8-8_micro000,SAMPL8-8_micro001,1,-6.33,0.10,2.90 +SAMPL8-8_micro000,SAMPL8-8_micro002,1,10.83,0.10,2.90 +SAMPL8-9_micro000,SAMPL8-9_micro001,-1,31.63,0.10,3.00 +SAMPL8-9_micro000,SAMPL8-9_micro002,1,-8.14,0.10,2.90 +SAMPL8-9_micro000,SAMPL8-9_micro003,0,7.42,0.10,1.40 +SAMPL8-9_micro000,SAMPL8-9_micro004,1,10.00,0.10,2.90 +SAMPL8-10_micro000,SAMPL8-10_micro001,1,-9.03,0.10,2.90 +SAMPL8-12_micro000,SAMPL8-12_micro001,-1,43.81,0.10,3.00 +SAMPL8-12_micro000,SAMPL8-12_micro002,0,22.45,0.10,1.40 +SAMPL8-12_micro000,SAMPL8-12_micro003,0,18.11,0.10,1.40 +SAMPL8-12_micro000,SAMPL8-12_RFE-uESE-extra_extra001,2,52.58,0.10,2.90 +SAMPL8-12_micro000,SAMPL8-12_RFE-uESE-extra_extra002,1,-8.02,0.10,2.90 +SAMPL8-12_micro000,SAMPL8-12_RFE-uESE-extra_extra003,2,61.45,0.10,2.90 +SAMPL8-12_micro000,SAMPL8-12_RFE-uESE-extra_extra004,1,-8.28,0.10,2.90 +SAMPL8-12_micro000,SAMPL8-12_RFE-uESE-extra_extra005,2,52.63,0.10,2.90 +SAMPL8-12_micro000,SAMPL8-12_RFE-uESE-extra_extra006,1,-2.09,0.10,2.90 +SAMPL8-14_micro000,SAMPL8-14_micro001,-2,92.53,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro002,0,-10.93,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro003,-2,93.03,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro004,-1,32.10,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro005,-1,19.33,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro006,0,-0.87,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro007,-2,96.52,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro008,-1,-1.80,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro09,-1,28.00,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro010,-1,13.28,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro011,-2,95.29,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro012,-1,19.18,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro013,0,-6.00,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro014,-3,78.18,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro015,-2,95.92,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro016,0,-0.12,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro017,0,-4.80,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro018,-2,119.33,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro019,-1,15.37,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro020,-2,103.45,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro021,-1,21.78,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro022,-1,13.77,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro023,0,-10.90,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro024,0,-22.63,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro025,-1,21.93,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro026,-2,103.38,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro027,-1,18.28,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro028,-1,14.07,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro029,-1,19.15,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro030,0,-4.80,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro031,-2,90.72,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro032,-1,15.96,0.10,3.00 +SAMPL8-14_micro000,SAMPL8-14_micro033,0,-6.00,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_micro034,0,-0.96,0.10,1.40 +SAMPL8-14_micro000,SAMPL8-14_RFE-uESE-extra_extra001,2,23.43,0.10,2.90 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+SAMPL8-18_micro000,SAMPL8-18_micro001,0,0.85,0.10,1.40 +SAMPL8-18_micro000,SAMPL8-18_micro002,0,-8.77,0.10,1.40 +SAMPL8-18_micro000,SAMPL8-18_micro003,1,-5.14,0.10,2.90 +SAMPL8-18_micro000,SAMPL8-18_micro004,1,-11.00,0.10,2.90 +SAMPL8-18_micro000,SAMPL8-18_micro005,-1,14.39,0.10,3.00 +SAMPL8-19_micro000,SAMPL8-19_micro001,1,-7.43,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro002,2,50.36,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro003,2,59.54,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro004,1,1.98,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro005,1,-17.62,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro006,1,-13.69,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro007,0,-13.34,0.10,1.40 +SAMPL8-19_micro000,SAMPL8-19_micro008,1,-16.06,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro009,1,-14.65,0.10,2.90 +SAMPL8-19_micro000,SAMPL8-19_micro010,-1,19.43,0.10,3.00 +SAMPL8-19_micro000,SAMPL8-19_micro011,-1,3.14,0.10,3.00 +SAMPL8-19_micro000,SAMPL8-19_micro012,2,76.06,0.10,2.90 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+SAMPL8-20_micro000,SAMPL8-20_micro005,1,41.96,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro006,1,-19.44,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro007,1,13.13,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro008,0,43.83,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro009,0,15.10,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro010,0,29.50,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro011,1,-0.73,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro012,0,33.63,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro013,0,23.39,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro014,1,38.65,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro015,1,-2.40,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro016,1,19.76,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro017,0,-10.64,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro018,0,-2.25,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro019,0,31.17,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro020,0,47.57,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro021,0,23.95,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro022,0,-17.77,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro023,0,36.76,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro024,0,36.54,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro025,1,27.32,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro026,1,-12.61,0.10,2.90 +SAMPL8-20_micro000,SAMPL8-20_micro027,0,40.21,0.10,1.40 +SAMPL8-20_micro000,SAMPL8-20_micro028,1,39.16,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_micro001,-2,103.60,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro002,-2,111.91,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro003,-1,8.20,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro004,-2,106.42,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro005,-2,94.90,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro006,-1,16.87,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro007,-1,30.27,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro008,0,-1.70,0.10,1.40 +SAMPL8-21_micro000,SAMPL8-21_micro009,-1,12.19,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro010,-3,72.81,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro011,-1,17.03,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro012,-2,114.74,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro013,-2,104.09,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro014,-1,12.17,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro015,-2,106.20,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro016,-1,9.41,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro017,-2,98.71,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro018,-1,12.60,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro019,-1,30.43,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro020,-1,20.23,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro021,-2,95.78,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro022,-1,-3.93,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro023,0,-12.47,0.10,1.40 +SAMPL8-21_micro000,SAMPL8-21_micro024,-1,15.64,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro025,0,-8.76,0.10,1.40 +SAMPL8-21_micro000,SAMPL8-21_micro026,-1,24.29,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro027,-1,26.47,0.10,3.00 +SAMPL8-21_micro000,SAMPL8-21_micro028,0,-27.68,0.10,1.40 +SAMPL8-21_micro000,SAMPL8-21_micro029,0,-6.32,0.10,1.40 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra001,2,24.42,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra002,1,-33.95,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra003,2,23.92,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra004,1,-18.52,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra005,1,-18.45,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra006,1,-33.93,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra007,2,32.59,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra008,1,-29.00,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra009,1,-32.95,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra010,2,23.74,0.10,2.90 +SAMPL8-21_micro000,SAMPL8-21_RFE-uESE-extra_extra011,1,-33.93,0.10,2.90 +SAMPL8-22_micro000,SAMPL8-22_micro001,-1,16.72,0.10,3.00 +SAMPL8-22_micro000,SAMPL8-22_micro002,0,-7.32,0.10,1.40 +SAMPL8-22_micro000,SAMPL8-22_micro003,0,1.89,0.10,1.40 +SAMPL8-22_micro000,SAMPL8-22_RFE-uESE-extra_extra001,2,41.34,0.10,2.90 +SAMPL8-22_micro000,SAMPL8-22_RFE-uESE-extra_extra002,1,-19.99,0.10,2.90 +SAMPL8-22_micro000,SAMPL8-22_RFE-uESE-extra_extra003,2,41.36,0.10,2.90 +SAMPL8-22_micro000,SAMPL8-22_RFE-uESE-extra_extra004,1,-15.69,0.10,2.90 +SAMPL8-22_micro000,SAMPL8-22_RFE-uESE-extra_extra005,1,-20.04,0.10,2.90 +SAMPL8-23_micro000,SAMPL8-23_micro001,1,15.50,0.10,2.90 +SAMPL8-23_micro000,SAMPL8-23_micro002,-1,16.88,0.10,3.00 +SAMPL8-23_micro000,SAMPL8-23_micro003,0,2.15,0.10,1.40 +SAMPL8-23_micro000,SAMPL8-23_micro004,0,36.98,0.10,1.40 +SAMPL8-23_micro000,SAMPL8-23_micro005,-1,1.59,0.10,3.00 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-19.98,0.10,2.90 +SAMPL8-23_micro000,SAMPL8-23_micro007,0,-17.07,0.10,1.40 + +# +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Spencer J. Sabatino +Sergio Antonio Rodriguez +Andrew S. Paluch + +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +Miami University +University of Santiago del Estero, Argentina +Miami University + +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name of the method should not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +RFE-uESE-extra + +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +60 hours, CPU + +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used to run the simulations. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +All simulations were performed on the Pitzer Cluster at the Ohio Supercomputer Center +(https://www.osc.edu/resources/technical_support/supercomputers/pitzer). +The reported compute time is taken as the walltime times the number of processors (core hours). +Pitzer has a mix of processors. We did not specify the processor type upon submission, so a mix was used. +The original Pitzer cluster was installed in late 2018 and +is a Dell-built, Intel Xeon Skylake processor-based supercomputer with 260 nodes. +In September 2020, OSC installed an additional 398 Intel Xeon Cascade Lake processor-based +nodes as part of a Pitzer Expansion cluster. + +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +Gaussian 16 + +# METHOD CATEGORY SECTION +# +# State if your prediction method is better classified as an +# experimental database lookup (DL), linear free energy relationship (LFER), +# quantitative structure-property relationship or machine learning (QSPR/ML), +# quantum mechanics without empirical correction (QM) model, quantum mechanics with +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular +# mechanics (QM+MM), or Other, using the following category labels: +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`. +# +# Pick only one category label. +# The `Category:` keyword is required. +Category: +QM + +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# Use as many lines of text as you need. +# +# We strongly encourage you to submit your predicted macro pKa values in this section in consecutive lines following this format: +# compound name, macro pKa, initial formal charge, formal charge after transition, e.g.: +# SAMPL8-1, 3.5, 0, +1 +# This will allow us to check that our analysis of your free energies leads to the same endpoint as your analysis. +# +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. + +Method: +Starting with the initial structures provided by the SAMPL8 organizers, geometries were first optimized with the PM7 method. +The geometries were then further optimized at the B3LYP/def2-TZVP level of theory/basis set, followed by frequency calculation. +A single point energy calculation was then performed to computed CM5 charges. The final structure and CM5 charges were used to predict +hydration free energies using the uESE method (DOI: 10.1002/jcc.26531) using code provided by the authors of the uESE manuscript. +The gas phase total free energy of each microstate was computed from the frequency calculation. +The relative free energies in water were computed from this information based on the proton dissociation reaction. +All of the electronic structure calculations were perfomed with Gaussian 16. + +This submission includes the extra microstates provided by the challenge organizers. + +Macro pKa values +SAMPL8-1,7.97,0,-1 +SAMPL8-2,8.25,0,-1 +SAMPL8-3,0.76,0,-1 +SAMPL8-3,6.43,0,0 +SAMPL8-4,4.52,0,-1 +SAMPL8-5,7.71,0,-1 +SAMPL8-6,5.93,0,-1 +SAMPL8-7,8.89,0,1 +SAMPL8-8,4.64,0,1 +SAMPL8-9,5.97,0,1 +SAMPL8-11,10.63,0,1 +SAMPL8-11,0.81,0,1 +SAMPL8-12,6.07,0,1 +SAMPL8-13,3.63,0,1 +SAMPL8-14,10.32,0,-1 +SAMPL8-15,7.94,0,1 +SAMPL8-16,3.72,0,1 +SAMPL8-17,5.24,0,1 +SAMPL8-18,3.77,0,1 +SAMPL8-18,8.07,0,1 +SAMPL8-19,5.73,0,1 +SAMPL8-20,12.62,0,1 +SAMPL8-21,12.37,0,-1 +SAMPL8-22,12.26,0,-1 +SAMPL8-23,12.38,0,-1 + +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) + +Ranked: +True diff --git a/physical_properties/pKa/submissions/pKa_SabatinoRodriguezPaluch_uESE_modified.csv b/physical_properties/pKa/submissions/pKa_SabatinoRodriguezPaluch_uESE_modified.csv new file mode 100644 index 0000000..186daad --- /dev/null +++ b/physical_properties/pKa/submissions/pKa_SabatinoRodriguezPaluch_uESE_modified.csv @@ -0,0 +1,364 @@ +# RELATIVE FREE ENERGY PREDICTIONS (for pKa prediction) +# +# This file will be automatically parsed. It must contain the following four elements: +# predictions, name of method, software listing, and method description. +# These elements must be provided in the order shown with their respective headers. +# +# Any line that begins with a # is considered a comment and will be ignored when parsing. +# +# PREDICTION SECTION +# +# It is mandatory to submit relative free energy (RFE) predictions for all 23 molecules. Incomplete submissions will not be accepted. +# Please report RFE standard error of the mean (SEM) and RFE model uncertainty. +# Note that we here follow the same sign convention and submission format as the SAMPL7 pKa challenge. +# +# The data in each prediction line should be structured as follows: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty +# +# If you have evaluated additional microstates, include the following: +# Microstate ID of reference state, Microstate ID of the predicted microstate, total charge, RFE, RFE SEM, RFE model uncertainty, SMILES string of the predicted microstate +# +# The molecule ID of the other microstate needs to be in the format: `SAMPL8-X_extra001` (number can vary) +# Also email us the `.mol2` file of your microstate with explicit hydrogens and correct bond orders, +# Please send the `.mol2` file to the email listed on the instructions page. +# +# The list of predictions must begin with the 'Predictions:' keyword as illustrated here. +Predictions: +SAMPL8-1_micro000,SAMPL8-1_micro001,-1,44.96,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro002,-1,31.07,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro003,-1,40.94,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro004,-1,10.86,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro005,-1,10.87,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro006,0,45.04,0.10,1.40 +SAMPL8-1_micro000,SAMPL8-1_micro007,0,29.74,0.10,1.40 +SAMPL8-1_micro000,SAMPL8-1_micro008,-1,40.06,0.10,3.00 +SAMPL8-1_micro000,SAMPL8-1_micro009,0,33.75,0.10,1.40 +SAMPL8-1_micro000,SAMPL8-1_micro010,0,31.74,0.10,1.40 +SAMPL8-2_micro000,SAMPL8-2_micro001,-1,11.25,0.10,3.00 +SAMPL8-2_micro000,SAMPL8-2_micro002,0,26.87,0.10,1.40 +SAMPL8-2_micro000,SAMPL8-2_micro003,-1,37.87,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro001,-1,-1.36,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro002,0,-13.75,0.10,1.40 +SAMPL8-3_micro000,SAMPL8-3_micro003,-1,1.03,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro004,0,-14.19,0.10,1.40 +SAMPL8-3_micro000,SAMPL8-3_micro005,-1,-15.42,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro006,0,-49.4,0.10,1.40 +SAMPL8-3_micro000,SAMPL8-3_micro007,-2,28.73,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro008,0,-12.06,0.10,1.40 +SAMPL8-3_micro000,SAMPL8-3_micro009,-1,-3.57,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro010,-1,-40.63,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro011,-1,4.97,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro012,-2,48.91,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro013,-2,58.77,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro014,-2,41.4,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro015,-1,17.35,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro016,-1,-30.76,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro017,-1,5.39,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro018,-1,-2.62,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro019,-2,42.96,0.10,3.00 +SAMPL8-3_micro000,SAMPL8-3_micro020,-1,-36.6,0.10,3.00 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+SAMPL8-23_micro000,SAMPL8-23_micro005,-1,1.59,0.10,3.00 +SAMPL8-23_micro000,SAMPL8-23_micro006,1,-19.98,0.10,2.90 +SAMPL8-23_micro000,SAMPL8-23_micro007,0,-17.07,0.10,1.40 + +# +# +# Please list your name, using only UTF-8 characters as described above. The "Participant name:" entry is required. +Participant name: +Spencer J. Sabatino +Sergio Antonio Rodriguez +Andrew S. Paluch + +# +# +# Please list your organization/affiliation, using only UTF-8 characters as described above. +Participant organization: +Miami University +University of Santiago del Estero, Argentina +Miami University + +# +# +# NAME SECTION +# +# Please provide an informal but informative name of the method used. +# The name of the method should not exceed 40 characters. +# The 'Name:' keyword is required as shown here. +Name: +RFE-uESE + +# +# +# COMPUTE TIME SECTION +# +# Please provide the average compute time across all of the molecules. +# For physical methods, report the GPU and/or CPU compute time in hours. +# For empirical methods, report the query time in hours. +# Create a new line for each processor type. +# The 'Compute time:' keyword is required as shown here. +Compute time: +60 hours, CPU + +# +# COMPUTING AND HARDWARE SECTION +# +# Please provide details of the computing resources that were used to train models and make predictions. +# Please specify compute time for training models and querying separately for empirical prediction methods. +# Provide a detailed description of the hardware used to run the simulations. +# The 'Computing and hardware:' keyword is required as shown here. +Computing and hardware: +All simulations were performed on the Pitzer Cluster at the Ohio Supercomputer Center +(https://www.osc.edu/resources/technical_support/supercomputers/pitzer). +The reported compute time is taken as the walltime times the number of processors (core hours). +Pitzer has a mix of processors. We did not specify the processor type upon submission, so a mix was used. +The original Pitzer cluster was installed in late 2018 and +is a Dell-built, Intel Xeon Skylake processor-based supercomputer with 260 nodes. +In September 2020, OSC installed an additional 398 Intel Xeon Cascade Lake processor-based +nodes as part of a Pitzer Expansion cluster. + +# SOFTWARE SECTION +# +# List all major software packages used and their versions. +# Create a new line for each software. +# The 'Software:' keyword is required. +Software: +Gaussian 16 + +# METHOD CATEGORY SECTION +# +# State if your prediction method is better classified as an +# experimental database lookup (DL), linear free energy relationship (LFER), +# quantitative structure-property relationship or machine learning (QSPR/ML), +# quantum mechanics without empirical correction (QM) model, quantum mechanics with +# linear empirical correction (QM+LEC), and combined quantum mechanics and molecular +# mechanics (QM+MM), or Other, using the following category labels: +# `DL`, `LFER`, `QSPR/ML`, `QM`, `QM+LEC`, `QM+MM` or `Other`. +# +# Pick only one category label. +# The `Category:` keyword is required. +Category: +QM + +# METHOD DESCRIPTION SECTION +# +# Methodology and computational details. +# Level of details should be roughly equivalent to that used in a publication. +# Please include the values of key parameters with units. +# Please explain how statistical uncertainties were estimated. +# Use as many lines of text as you need. +# +# We strongly encourage you to submit your predicted macro pKa values in this section in consecutive lines following this format: +# compound name, macro pKa, initial formal charge, formal charge after transition, e.g.: +# SAMPL8-1, 3.5, 0, +1 +# This will allow us to check that our analysis of your free energies leads to the same endpoint as your analysis. +# +# All text following the 'Method:' keyword will be regarded as part of your free text methods description. + +Method: +Starting with the initial structures provided by the SAMPL8 organizers, geometries were first optimized with the PM7 method. +The geometries were then further optimized at the B3LYP/def2-TZVP level of theory/basis set, followed by frequency calculation. +A single point energy calculation was then performed to computed CM5 charges. The final structure and CM5 charges were used to predict +hydration free energies using the uESE method (DOI: 10.1002/jcc.26531) using code provided by the authors of the uESE manuscript. +The gas phase total free energy of each microstate was computed from the frequency calculation. +The relative free energies in water were computed from this information based on the proton dissociation reaction. +All of the electronic structure calculations were perfomed with Gaussian 16. + +# +# +# All submissions must either be ranked or non-ranked. +# Only one ranked submission per participant is allowed. +# Multiple ranked submissions from the same participant will not be judged. +# Non-ranked submissions are accepted so we can verify that they were made before the deadline. +# The "Ranked:" keyword is required, and expects a Boolean value (True/False) + +Ranked: +False diff --git a/test.csv b/test.csv new file mode 100644 index 0000000..5314d88 --- /dev/null +++ b/test.csv @@ -0,0 +1,291 @@ +microstate ID,Estimated Formal Charge +SAMPL8-16_micro000,0 +SAMPL8-16_micro001,1 +SAMPL8-16_micro002,0 +SAMPL8-16_micro003,1 +SAMPL8-16_micro004,1 +SAMPL8-16_micro005,0 +SAMPL8-16_micro006,1 +SAMPL8-16_micro007,0 +SAMPL8-16_micro008,1 +SAMPL8-16_micro009,1 +SAMPL8-16_micro010,1 +SAMPL8-16_micro011,0 +SAMPL8-7_micro000,0 +SAMPL8-7_micro001,-1 +SAMPL8-7_micro002,1 +SAMPL8-7_micro003,1 +SAMPL8-7_micro004,0 +SAMPL8-8_micro000,0 +SAMPL8-8_micro001,1 +SAMPL8-8_micro002,1 +SAMPL8-19_micro000,0 +SAMPL8-19_micro001,1 +SAMPL8-19_micro002,2 +SAMPL8-19_micro003,2 +SAMPL8-19_micro004,1 +SAMPL8-19_micro005,1 +SAMPL8-19_micro006,1 +SAMPL8-19_micro007,0 +SAMPL8-19_micro008,1 +SAMPL8-19_micro009,1 +SAMPL8-19_micro010,-1 +SAMPL8-19_micro011,-1 +SAMPL8-19_micro012,2 +SAMPL8-19_micro013,0 +SAMPL8-19_micro014,0 +SAMPL8-19_micro015,0 +SAMPL8-19_micro016,1 +SAMPL8-19_micro017,2 +SAMPL8-19_micro018,1 +SAMPL8-19_micro019,1 +SAMPL8-19_micro020,0 +SAMPL8-19_micro021,2 +SAMPL8-19_micro022,1 +SAMPL8-19_micro023,1 +SAMPL8-19_micro024,0 +SAMPL8-19_micro025,0 +SAMPL8-23_micro000,0 +SAMPL8-23_micro001,1 +SAMPL8-23_micro002,-1 +SAMPL8-23_micro003,0 +SAMPL8-23_micro004,0 +SAMPL8-23_micro005,-1 +SAMPL8-23_micro006,1 +SAMPL8-23_micro007,0 +SAMPL8-11_micro000,0 +SAMPL8-11_micro001,1 +SAMPL8-11_micro002,1 +SAMPL8-11_micro003,2 +SAMPL8-11_micro004,1 +SAMPL8-11_micro005,2 +SAMPL8-22_micro000,0 +SAMPL8-22_micro001,-1 +SAMPL8-22_micro002,0 +SAMPL8-22_micro003,0 +SAMPL8-22_dortmund002,1 +SAMPL8-22_dortmund004,1 +SAMPL8-22_dortmund005,1 +SAMPL8-22_dortmund001,2 +SAMPL8-22_dortmund003,2 +SAMPL8-1_micro000,0 +SAMPL8-1_micro001,-1 +SAMPL8-1_micro002,-1 +SAMPL8-1_micro003,-1 +SAMPL8-1_micro004,-1 +SAMPL8-1_micro005,-1 +SAMPL8-1_micro006,0 +SAMPL8-1_micro007,0 +SAMPL8-1_micro008,-1 +SAMPL8-1_micro009,0 +SAMPL8-1_micro010,0 +SAMPL8-1_dortmund001,1 +SAMPL8-10_micro000,0 +SAMPL8-10_micro001,1 +SAMPL8-17_micro000,0 +SAMPL8-17_micro001,-1 +SAMPL8-17_micro002,1 +SAMPL8-17_micro003,1 +SAMPL8-17_micro004,0 +SAMPL8-17_micro005,-1 +SAMPL8-6_micro000,0 +SAMPL8-6_micro001,-1 +SAMPL8-6_micro002,1 +SAMPL8-6_micro003,1 +SAMPL8-6_micro004,0 +SAMPL8-6_micro005,0 +SAMPL8-6_micro006,-1 +SAMPL8-6_micro007,0 +SAMPL8-6_micro008,0 +SAMPL8-6_micro009,-1 +SAMPL8-9_micro000,0 +SAMPL8-9_micro001,-1 +SAMPL8-9_micro002,1 +SAMPL8-9_micro003,0 +SAMPL8-9_micro004,1 +SAMPL8-18_micro000,0 +SAMPL8-18_micro001,0 +SAMPL8-18_micro002,0 +SAMPL8-18_micro003,1 +SAMPL8-18_micro004,1 +SAMPL8-18_micro005,-1 +SAMPL8-20_micro000,0 +SAMPL8-20_micro001,0 +SAMPL8-20_micro002,1 +SAMPL8-20_micro003,1 +SAMPL8-20_micro004,0 +SAMPL8-20_micro005,1 +SAMPL8-20_micro006,1 +SAMPL8-20_micro007,1 +SAMPL8-20_micro008,0 +SAMPL8-20_micro009,0 +SAMPL8-20_micro010,0 +SAMPL8-20_micro011,1 +SAMPL8-20_micro012,0 +SAMPL8-20_micro013,0 +SAMPL8-20_micro014,1 +SAMPL8-20_micro015,1 +SAMPL8-20_micro016,1 +SAMPL8-20_micro017,0 +SAMPL8-20_micro018,0 +SAMPL8-20_micro019,0 +SAMPL8-20_micro020,0 +SAMPL8-20_micro021,0 +SAMPL8-20_micro022,0 +SAMPL8-20_micro023,0 +SAMPL8-20_micro024,0 +SAMPL8-20_micro025,1 +SAMPL8-20_micro026,1 +SAMPL8-20_micro027,0 +SAMPL8-20_micro028,1 +SAMPL8-3_micro000,0 +SAMPL8-3_micro001,-1 +SAMPL8-3_micro002,0 +SAMPL8-3_micro003,-1 +SAMPL8-3_micro004,0 +SAMPL8-3_micro005,-1 +SAMPL8-3_micro006,0 +SAMPL8-3_micro007,-2 +SAMPL8-3_micro008,0 +SAMPL8-3_micro009,-1 +SAMPL8-3_micro010,-1 +SAMPL8-3_micro011,-1 +SAMPL8-3_micro012,-2 +SAMPL8-3_micro013,-2 +SAMPL8-3_micro014,-2 +SAMPL8-3_micro015,-1 +SAMPL8-3_micro016,-1 +SAMPL8-3_micro017,-1 +SAMPL8-3_micro018,-1 +SAMPL8-3_micro019,-2 +SAMPL8-3_micro020,-1 +SAMPL8-3_micro021,-2 +SAMPL8-3_dortmund001,1 +SAMPL8-12_micro000,0 +SAMPL8-12_micro001,-1 +SAMPL8-12_micro002,0 +SAMPL8-12_micro003,0 +SAMPL8-12_dortmund002,1 +SAMPL8-12_dortmund004,1 +SAMPL8-12_dortmund006,1 +SAMPL8-12_dortmund001,2 +SAMPL8-12_dortmund003,2 +SAMPL8-12_dortmund005,2 +SAMPL8-15_micro000,0 +SAMPL8-15_micro001,0 +SAMPL8-15_micro002,0 +SAMPL8-15_micro003,1 +SAMPL8-15_micro004,1 +SAMPL8-4_micro000,0 +SAMPL8-4_micro001,0 +SAMPL8-4_micro002,1 +SAMPL8-4_micro003,-1 +SAMPL8-4_micro004,0 +SAMPL8-4_micro005,-1 +SAMPL8-4_micro006,-1 +SAMPL8-4_micro007,1 +SAMPL8-4_micro008,-1 +SAMPL8-4_micro009,-1 +SAMPL8-4_micro010,0 +SAMPL8-14_micro000,0 +SAMPL8-14_micro001,-2 +SAMPL8-14_micro002,0 +SAMPL8-14_micro003,-2 +SAMPL8-14_micro004,-1 +SAMPL8-14_micro005,-1 +SAMPL8-14_micro006,0 +SAMPL8-14_micro007,-2 +SAMPL8-14_micro008,-1 +SAMPL8-14_micro09,-1 +SAMPL8-14_micro010,-1 +SAMPL8-14_micro011,-2 +SAMPL8-14_micro012,-1 +SAMPL8-14_micro013,0 +SAMPL8-14_micro014,-3 +SAMPL8-14_micro015,-2 +SAMPL8-14_micro016,0 +SAMPL8-14_micro017,0 +SAMPL8-14_micro018,-2 +SAMPL8-14_micro019,-1 +SAMPL8-14_micro020,-2 +SAMPL8-14_micro021,-1 +SAMPL8-14_micro022,-1 +SAMPL8-14_micro023,0 +SAMPL8-14_micro024,0 +SAMPL8-14_micro025,-1 +SAMPL8-14_micro026,-2 +SAMPL8-14_micro027,-1 +SAMPL8-14_micro028,-1 +SAMPL8-14_micro029,-1 +SAMPL8-14_micro030,0 +SAMPL8-14_micro031,-2 +SAMPL8-14_micro032,-1 +SAMPL8-14_micro033,0 +SAMPL8-14_micro034,0 +SAMPL8-14_dortmund002,1 +SAMPL8-14_dortmund004,1 +SAMPL8-14_dortmund006,1 +SAMPL8-14_dortmund007,1 +SAMPL8-14_dortmund009,1 +SAMPL8-14_dortmund011,1 +SAMPL8-14_dortmund012,1 +SAMPL8-14_dortmund001,2 +SAMPL8-14_dortmund003,2 +SAMPL8-14_dortmund005,2 +SAMPL8-14_dortmund008,2 +SAMPL8-14_dortmund010,2 +SAMPL8-5_micro000,0 +SAMPL8-5_micro001,0 +SAMPL8-5_micro002,-1 +SAMPL8-5_micro003,1 +SAMPL8-5_micro004,0 +SAMPL8-5_micro005,0 +SAMPL8-5_micro006,1 +SAMPL8-5_micro007,-1 +SAMPL8-21_micro000,0 +SAMPL8-21_micro001,-2 +SAMPL8-21_micro002,-2 +SAMPL8-21_micro003,-1 +SAMPL8-21_micro004,-2 +SAMPL8-21_micro005,-2 +SAMPL8-21_micro006,-1 +SAMPL8-21_micro007,-1 +SAMPL8-21_micro008,0 +SAMPL8-21_micro009,-1 +SAMPL8-21_micro010,-3 +SAMPL8-21_micro011,-1 +SAMPL8-21_micro012,-2 +SAMPL8-21_micro013,-2 +SAMPL8-21_micro014,-1 +SAMPL8-21_micro015,-2 +SAMPL8-21_micro016,-1 +SAMPL8-21_micro017,-2 +SAMPL8-21_micro018,-1 +SAMPL8-21_micro019,-1 +SAMPL8-21_micro020,-1 +SAMPL8-21_micro021,-2 +SAMPL8-21_micro022,-1 +SAMPL8-21_micro023,0 +SAMPL8-21_micro024,-1 +SAMPL8-21_micro025,0 +SAMPL8-21_micro026,-1 +SAMPL8-21_micro027,-1 +SAMPL8-21_micro028,0 +SAMPL8-21_micro029,0 +SAMPL8-21_dortmund002,1 +SAMPL8-21_dortmund004,1 +SAMPL8-21_dortmund006,1 +SAMPL8-21_dortmund008,1 +SAMPL8-21_dortmund009,1 +SAMPL8-21_dortmund011,1 +SAMPL8-21_dortmund001,2 +SAMPL8-21_dortmund003,2 +SAMPL8-21_dortmund007,2 +SAMPL8-21_dortmund010,2 +SAMPL8-2_micro000,0 +SAMPL8-2_micro001,-1 +SAMPL8-2_micro002,0 +SAMPL8-2_micro003,-1 +SAMPL8-13_micro000,0 +SAMPL8-13_micro001,1 +SAMPL8-13_micro002,-1