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modified_files #22

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17 changes: 17 additions & 0 deletions src/colbuilder/core/geometry/crosslink.py
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Original file line number Diff line number Diff line change
Expand Up @@ -137,4 +137,21 @@ def read_crosslink(pdb_file: Union[str, Path]) -> List[Crosslink]:
)
)

elif (line[17:20] in ("LZD") and line[13:15] == "CE") or (
line[17:20] in ("LZS") and line[13:15] == "NZ1"
):
crosslinks.append(
Crosslink(
resid=line[22:26].strip(),
resname=line[17:20],
chain=line[21],
position=[
float(line[29:38]),
float(line[38:46]),
float(line[46:56]),
],
type="D",
)
)

return crosslinks
6 changes: 5 additions & 1 deletion src/colbuilder/core/topology/amber.py
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Original file line number Diff line number Diff line change
Expand Up @@ -276,6 +276,10 @@ def _is_crosslink_atom(
return True
elif resname in ("AGS", "APD") and atom_name == "NZ":
return True
elif resname in ("LZD") and atom_name == "CE":
return True
elif resname in ("LZS") and atom_name == "NZ1":
return True

return False

Expand Down Expand Up @@ -1059,4 +1063,4 @@ async def build_amber99(system: System, config: ColbuilderConfig, file_manager:
original_error=e,
error_code="TOP_ERR_001",
context={"force_field": ff}
)
)
2,803 changes: 2,798 additions & 5 deletions src/colbuilder/data/sequence/crosslinks.csv
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79 changes: 51 additions & 28 deletions src/colbuilder/data/sequence/modeller/top_heav_mod.lib
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Original file line number Diff line number Diff line change
Expand Up @@ -833,39 +833,62 @@ IC C18 O19 *C19 C20 2.405 37.83 -124.49 108.85 1.524
IC C20 NH1 *C16 C15 2.458 30.12 179.55 112.23 1.496


PRES RAPD 1.00000
ATOM NE NH1 -0.16000
ATOM NH1 NR1 -0.04000
ATOM NH2 NR2 -0.70000
PRESI RAPD 1.00000
ATOM NZ NH3 0.69000
ATOM CZ CE1 0.00000
ATOM C23 CPT 0.13000
ATOM C23 CPT 0.13000
ATOM C24 CPT 0.13000
ATOM C27 CA 0.16000
ATOM C26 CA 0.16000
ATOM C25 CA 0.16000
DELETE ATOM NE
DELETE ATOM NH1
DELETE ATOM NH2
DELETE ATOM CZ
BOND CZ NE NH1 CZ NH2 CZ C24 NH1 C23 NH2 C24 C23 C27 C24 C26 C27 C25 C26 NZ C25 NZ C23
IC CG CD NE CZ 1.5375 110.4600 0.0000 119.7200 1.3735
IC CD NE CZ NH1 1.4640 119.7200 180.0000 117.2800 1.3802
IC CD NE CZ NH2 1.4640 119.7200 180.0000 117.2300 1.3694
IC NE CZ NH1 C24 1.3735 117.2800 180.0000 128.0100 1.3802
IC NE CZ NH2 C23 1.3735 117.2300 180.0000 105.4900 1.3172
IC CZ NH1 C24 C23 1.3802 128.0100 180.0000 117.7700 1.4278
IC CZ NH1 C24 C27 1.3802 128.0100 180.0000 106.9900 1.3729
IC CZ NH2 C23 NZ 1.3694 105.4900 180.0000 112.2200 1.3802
IC CZ NH2 C23 C24 1.3694 105.4900 180.0000 112.5600 1.4278
IC NH1 C24 C23 NH2 1.3802 117.7700 180.0000 112.5600 1.3172
IC NH1 C24 C27 C26 1.3802 106.9900 180.0000 1141.900 1.4278
IC C24 C27 C26 C25 1.3729 114.1900 180.0000 114.1900 1.3729
IC C27 C26 C25 NZ 1.4278 114.1900 180.0000 106.9900 1.3802
IC C26 C25 NZ C23 1.3729 106.9900 180.0000 109.9000 1.3802
IC C25 NZ C23 C24 1.3802 109.9000 180.0000 117.7700 1.4278
IC C25 NZ C23 NH2 1.3802 109.9000 180.0000 112.2200 1.3170
IC C15 C20 *C16 NH1 1.4000 115.6500 180.0000 120.7100 1.4000
BOND NH2 C23 ! 1.368
BOND C23 NZ ! 1.352
BOND NZ C25 ! 1.350
BOND C25 C26 ! 1.392
BOND C26 C27 ! 1.394
BOND C27 C24 ! 1.391
BOND C24 NH1 ! 1.368
BOND C24 C23 ! 1.390
IMPR NE CZ NH2 C23 ! 178.74
IMPR NH1 CZ NH2 C23 ! 1.38
IMPR CZ NH2 C23 NZ ! 179.27
IMPR CZ NH2 C23 C24 ! -0.87
IMPR NH2 C23 NZ C25 ! 179.61
IMPR C24 C23 NZ C25 ! -0.22
IMPR C23 NZ C25 C26 ! 0.04
IMPR NZ C25 C26 C27 ! 0.03
IMPR C25 C26 C27 C24 ! 0.08
IMPR C26 C27 C24 NH1 ! -179.66
IMPR C26 C27 C24 C23 ! -0.26
IMPR C27 C24 NH1 CZ ! -179.76
IMPR C23 C24 NH1 CZ ! 0.77
IMPR C27 C24 C23 NH2 ! -179.50
IMPR C27 C24 C23 NZ ! 0.36
IMPR NH1 C24 C23 NH2 ! 0.05
IMPR NH1 C24 C23 NZ ! 179.91
IMPR C24 NH1 CZ NE ! -178.89
IMPR C24 NH1 CZ NH2 ! -1.40
IC NE CZ NH2 C23 1.351 126.35 178.74 105.13 1.368
IC NH1 CZ NNH2 C23 1.371 111.54 1.38 105.13 1.368
IC CZ NH2 C23 NZ 1.310 105.13 179.27 125.46 1.352
IC CZ NH2 C23 C24 1.310 105.13 -0.87 111.40 1.390
IC NH2 C23 NZ C25 1.368 125.46 179.61 114.25 1.350
IC C24 C23 NZ C25 1.390 123.14 -0.22 114.25 1.350
IC C23 NZ C25 C26 1.352 114.25 0.04 125.80 1.392
IC NZ C25 C26 C27 1.350 125.80 0.03 119.62 1.394
IC C25 C26 C27 C24 1.392 119.62 0.08 114.86 1.391
IC C26 C27 C24 NH1 1.394 114.86 -179.66 133.85 1.368
IC C26 C27 C24 C23 1.394 114.86 -0.26 122.32 1.390
IC C27 C24 NH1 CZ 1.391 133.85 -179.76 108.09 1.371
IC C23 C24 NH1 CZ 1.390 103.82 0.77 108.09 1.371
IC C27 C24 C23 NH2 1.391 122.32 -179.50 111.40 1.368
IC C27 C24 C23 NZ 1.391 122.32 0.36 123.14 1.352
IC NH1 C24 C23 NH2 1.368 103.82 0.05 111.40 1.368
IC NH1 C24 C23 NZ 1.368 103.82 179.91 123.14 1.352
IC C24 NH1 CZ NE 1.368 108.09 -178.89 122.06 1.351
IC C24 NH1 CZ NH2 1.368 108.09 -1.40 111.54 1.310
IC NE NH2 *CZ NH1 2.374 27.28 -177.36 111.54 1.371
IC NH2 NZ *C23 C24 2.417 27.44 -179.84 123.14 1.390
IC C27 NH1 *C24 C23 2.539 23.28 -179.47 103.82 1.390


RESI SER 0.00000
Expand Down
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