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Analysis updates based on manuscript comments #57

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3b2a70f
Updating analysis to NOT include SAMPL8-20 pKa of 11.44 since microst…
aakankschit Feb 13, 2025
f080ba5
Modifying figures-font and figure sizes for manuscript. Adding SI fig…
aakankschit Feb 14, 2025
90b8bd6
Adding updated titration curve plots, updated analysis plots for both…
aakankschit May 27, 2025
ff8eaf5
Updating code to name the .csv data file containing the pKa values fo…
aakankschit May 27, 2025
59a04c0
Updating plots to have standard titles. Modifying scripts to perform …
aakankschit May 29, 2025
2af5d68
Updating Analysis to only evaluate molecules in a submission that hav…
aakankschit Jun 2, 2025
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2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -131,3 +131,5 @@ dmypy.json

# Mac
*.DS_Store
.conda/
.vscode/
291 changes: 291 additions & 0 deletions physical_properties/microstates/all_microstates.csv
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105 changes: 105 additions & 0 deletions physical_properties/microstates/microstate_issues/SAMPL8_12/COSMO_RS_extra003_c0.mol2
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# Created by COSMOvis on Mon Aug 09 22:24:20 CEST 2021
#
#

#
#

@<TRIPOS>MOLECULE
SAMPL8-12_extra003_c0
42 44
SMALL
USER_CHARGES

@<TRIPOS>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
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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
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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
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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 -0.475000 H 38 XO 0.000000
40 H 4.321500 -2.267800 2.248300 H 39 XO 0.000000
41 H 3.389300 -3.703100 1.909000 H 40 XO 0.000000
42 H 3.284400 -0.150900 2.114400 H 41 XO 0.000000

@<TRIPOS>BOND
1 1 3 ar
2 1 6 ar
3 2 4 ar
4 2 6 ar
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@<COSMOlogic>TOTAL_CHARGE
1.0
105 changes: 105 additions & 0 deletions physical_properties/microstates/microstate_issues/SAMPL8_12/COSMO_RS_extra005_c0.mol2
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# Created by COSMOvis on Mon Aug 09 22:24:20 CEST 2021
#
#

#
#

@<TRIPOS>MOLECULE
SAMPL8-12_extra005_c0
42 44
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16 C -0.601400 0.667600 -0.000800 C 15 XO 0.000000
17 N 0.173700 -3.078500 0.200400 N 16 XO 0.000000
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19 N 2.369700 0.483900 -0.025500 N 18 XO 1.000000
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21 O 4.878600 1.908600 -0.102400 O 20 XO 0.000000
22 H -4.789900 0.452400 2.107200 H 21 XO 0.000000
23 H -4.720800 0.166600 -2.193500 H 22 XO 0.000000
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26 H -1.565700 -1.971300 0.160500 H 25 XO 0.000000
27 H 3.864700 -0.217700 1.285800 H 26 XO 0.000000
28 H 2.561300 0.725200 2.083000 H 27 XO 0.000000
29 H 2.576700 0.467300 -2.145300 H 28 XO 0.000000
30 H 3.873700 -0.371200 -1.230800 H 29 XO 0.000000
31 H 4.718500 2.039400 1.935400 H 30 XO 0.000000
32 H 3.392900 2.834300 1.038300 H 31 XO 0.000000
33 H 3.401000 2.688100 -1.357200 H 32 XO 0.000000
34 H 4.732800 1.791100 -2.142000 H 33 XO 0.000000
35 H -6.905000 1.197900 -0.162600 H 34 XO 0.000000
36 H -6.803100 -0.405600 -0.910200 H 35 XO 0.000000
37 H -6.834800 -0.243800 0.865900 H 36 XO 0.000000
38 H -0.312400 1.289500 0.863600 H 37 XO 0.000000
39 H -0.291000 1.218000 -0.905800 H 38 XO 0.000000
40 H 1.716900 -5.060500 0.278200 H 39 XO 0.000000
41 H 3.229800 -4.180900 0.208100 H 40 XO 0.000000
42 H 1.719300 1.284100 -0.077100 H 41 XO 0.000000

@<TRIPOS>BOND
1 1 3 ar
2 1 6 ar
3 2 4 ar
4 2 6 ar
5 3 7 ar
6 4 7 ar
7 5 8 ar
8 5 17 ar
9 6 15 1
10 7 16 1
11 8 9 ar
12 8 16 1
13 9 18 ar
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15 10 17 ar
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17 10 20 1
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22 13 21 1
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36 14 34 1
37 15 35 1
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41 16 39 1
42 19 42 1
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44 20 41 1

@<COSMOlogic>TOTAL_CHARGE
1.0
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96 changes: 96 additions & 0 deletions physical_properties/microstates/microstate_issues/SAMPL8_12/EC_RISM_extra005.mol2
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@<TRIPOS>MOLECULE
SAMPL8-12_extra005
43 45 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
1 C 2.5364 4.6156 -10.5402 C.3 1 LIG1 -0.0397
2 C 2.0516 3.9858 -9.2475 C.ar 1 LIG1 -0.0504
3 C 2.7266 4.2432 -8.0533 C.ar 1 LIG1 -0.0586
4 C 2.2909 3.6564 -6.8678 C.ar 1 LIG1 -0.0580
5 C 1.1777 2.8116 -6.8752 C.ar 1 LIG1 -0.0432
6 C 0.5107 2.5458 -8.0741 C.ar 1 LIG1 -0.0580
7 C 0.9470 3.1328 -9.2590 C.ar 1 LIG1 -0.0586
8 C 0.7013 2.1581 -5.5806 C.3 1 LIG1 -0.0019
9 C -0.6985 2.5993 -5.1286 C.2 1 LIG1 -0.0138
10 C -0.9983 3.9534 -4.8876 C.2 1 LIG1 -0.0054
11 N -2.2438 4.2650 -4.4820 N.pl3 1 LIG1 -0.3162
12 C -3.2344 3.3689 -4.2892 C.3 1 LIG1 0.1881
13 N -2.9580 2.0745 -4.5178 N.3 1 LIG1 -0.2550
14 C -1.7010 1.6838 -4.9318 C.3 1 LIG1 0.1361
15 N -1.5930 0.3130 -5.1119 N.3 1 LIG1 -0.2738
16 C -1.5065 -0.5973 -3.9492 C.3 1 LIG1 0.0245
17 C -0.8726 -1.9551 -4.3363 C.3 1 LIG1 0.0605
18 O -1.5915 -2.5451 -5.4213 O.3 1 LIG1 -0.3772
19 C -1.5496 -1.7119 -6.5815 C.3 1 LIG1 0.0605
20 C -2.2125 -0.3461 -6.2822 C.3 1 LIG1 0.0245
21 N -4.4456 3.7492 -3.8866 N.3 1 LIG1 -0.2937
22 H 2.0913 5.6008 -10.6799 H 1 LIG1 0.0278
23 H 3.6214 4.7245 -10.5388 H 1 LIG1 0.0278
24 H 2.2903 3.9941 -11.4018 H 1 LIG1 0.0278
25 H 3.5882 4.8974 -8.0403 H 1 LIG1 0.0620
26 H 2.8236 3.8642 -5.9494 H 1 LIG1 0.0620
27 H -0.3453 1.8851 -8.0926 H 1 LIG1 0.0620
28 H 0.4248 2.9231 -10.1829 H 1 LIG1 0.0620
29 H 1.4041 2.3699 -4.7720 H 1 LIG1 0.0360
30 H 0.7620 1.0761 -5.7128 H 1 LIG1 0.0360
31 H -0.2816 4.7535 -5.0166 H 1 LIG1 0.0779
32 H -2.4589 5.2389 -4.3191 H 1 LIG1 0.1487
33 H -3.6590 1.3704 -4.3723 H 1 LIG1 0.1275
34 H -2.4578 -0.7135 -3.4246 H 1 LIG1 0.0450
35 H -0.8591 -0.1513 -3.1897 H 1 LIG1 0.0450
36 H 0.1843 -1.8282 -4.5816 H 1 LIG1 0.0572
37 H -0.8882 -2.6266 -3.4767 H 1 LIG1 0.0572
38 H -0.5255 -1.5713 -6.9347 H 1 LIG1 0.0572
39 H -2.0717 -2.2017 -7.4046 H 1 LIG1 0.0572
40 H -2.0645 0.2777 -7.1673 H 1 LIG1 0.0450
41 H -3.3004 -0.4150 -6.2092 H 1 LIG1 0.0450
42 H -5.2678 3.1906 -4.0698 H 1 LIG1 0.1216
43 H -4.5965 4.6101 -3.3784 H 1 LIG1 0.1216
@<TRIPOS>BOND
1 24 1 1
2 22 1 1
3 1 23 1
4 1 2 1
5 28 7 1
6 7 2 ar
7 7 6 ar
8 2 3 ar
9 27 6 1
10 6 5 ar
11 3 25 1
12 3 4 ar
13 39 19 1
14 40 20 1
15 38 19 1
16 5 4 ar
17 5 8 1
18 4 26 1
19 19 20 1
20 19 18 1
21 20 41 1
22 20 15 1
23 30 8 1
24 8 9 1
25 8 29 1
26 18 17 1
27 9 14 1
28 9 10 2
29 15 14 1
30 15 16 1
31 31 10 1
32 14 13 1
33 10 11 1
34 36 17 1
35 13 33 1
36 13 12 1
37 11 32 1
38 11 12 1
39 17 16 1
40 17 37 1
41 12 21 1
42 42 21 1
43 16 34 1
44 16 35 1
45 21 43 1
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