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Unverified Commit cb4f2016 authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #2508 from peastman/insertion 

Fixed handling of insertion codes in PDBx/mmCIF files
parents f6431a42 c16db8e9
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Showing with 111 additions and 2 deletions
wrappers/python/simtk/openmm/app/pdbxfile.py
View file @ cb4f2016
...@@ -106,6 +106,7 @@ class PDBxFile(object): ...@@ -106,6 +106,7 @@ class PDBxFile(object):
zCol = atomData.getAttributeIndex('Cartn_z') zCol = atomData.getAttributeIndex('Cartn_z')
lastChainId = None lastChainId = None
lastResId = None lastResId = None
lastInsertionCode = ''
atomTable = {} atomTable = {}
atomsInResidue = set() atomsInResidue = set()
models = [] models = []
...@@ -123,17 +124,24 @@ class PDBxFile(object): ...@@ -123,17 +124,24 @@ class PDBxFile(object):
if modelIndex == 0: if modelIndex == 0:
# This row defines a new atom. # This row defines a new atom.
if resInsertionCol == -1:
insertionCode = ''
else:
insertionCode = row[resInsertionCol]
if insertionCode in ('.', '?'):
insertionCode = ''
if lastChainId != row[chainIdCol]: if lastChainId != row[chainIdCol]:
# The start of a new chain. # The start of a new chain.
chain = top.addChain(row[chainIdCol]) chain = top.addChain(row[chainIdCol])
lastChainId = row[chainIdCol] lastChainId = row[chainIdCol]
lastResId = None lastResId = None
if lastResId != row[resNumCol] or lastChainId != row[chainIdCol] or (lastResId == '.' and row[atomNameCol] in atomsInResidue): if lastResId != row[resNumCol] or lastChainId != row[chainIdCol] or lastInsertionCode != insertionCode or (lastResId == '.' and row[atomNameCol] in atomsInResidue):
# The start of a new residue. # The start of a new residue.
resId = (None if resNumCol == -1 else row[resNumCol]) resId = (None if resNumCol == -1 else row[resNumCol])
resIC = ('' if resInsertionCol == -1 else row[resInsertionCol]) resIC = insertionCode
res = top.addResidue(row[resNameCol], chain, resId, resIC) res = top.addResidue(row[resNameCol], chain, resId, resIC)
lastResId = row[resNumCol] lastResId = row[resNumCol]
lastInsertionCode = insertionCode
atomsInResidue.clear() atomsInResidue.clear()
element = None element = None
try: try:
......
wrappers/python/tests/TestPdbxFile.py
View file @ cb4f2016
...@@ -171,5 +171,18 @@ class TestPdbxFile(unittest.TestCase): ...@@ -171,5 +171,18 @@ class TestPdbxFile(unittest.TestCase):
for chain1, chain2 in zip(cif_ori.topology.chains(), cif_new.topology.chains()): for chain1, chain2 in zip(cif_ori.topology.chains(), cif_new.topology.chains()):
self.assertEqual(chain1.id, chain2.id) self.assertEqual(chain1.id, chain2.id)
def testInsertionCodes(self):
"""Test reading a file that uses insertion codes."""
pdbx = PDBxFile('systems/insertions.pdbx')
residues = list(pdbx.topology.residues())
self.assertEqual(7, len(residues))
names = ['PHE', 'ASP', 'LYS', 'ILE', 'LYS', 'ASN', 'TRP']
ids = ['59', '60', '60', '60', '60', '60', '61']
codes = ['', '', 'A', 'B', 'C', 'D', '']
for res, name, id, code in zip(residues, names, ids, codes):
self.assertEqual(name, res.name)
self.assertEqual(id, res.id)
self.assertEqual(code, res.insertionCode)
if __name__ == '__main__': if __name__ == '__main__':
unittest.main() unittest.main()
wrappers/python/tests/systems/insertions.pdbx 0 → 100644
View file @ cb4f2016
# extract from 4X8U involving insertion codes
#
data_4X8U
#
_entry.id 4X8U
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
ATOM 315 N N . PHE A 1 43 ? 6.537 37.168 14.751 1.00 16.93 ? 59 PHE H N 1
ATOM 316 C CA . PHE A 1 43 ? 6.141 37.813 13.496 1.00 16.64 ? 59 PHE H CA 1
ATOM 317 C C . PHE A 1 43 ? 4.851 38.633 13.566 1.00 21.61 ? 59 PHE H C 1
ATOM 318 O O . PHE A 1 43 ? 4.428 39.140 12.532 1.00 22.06 ? 59 PHE H O 1
ATOM 319 C CB . PHE A 1 43 ? 6.074 36.749 12.371 1.00 17.35 ? 59 PHE H CB 1
ATOM 320 C CG . PHE A 1 43 ? 7.366 35.948 12.334 1.00 17.99 ? 59 PHE H CG 1
ATOM 321 C CD1 . PHE A 1 43 ? 8.485 36.434 11.667 1.00 21.29 ? 59 PHE H CD1 1
ATOM 322 C CD2 . PHE A 1 43 ? 7.494 34.770 13.064 1.00 18.58 ? 59 PHE H CD2 1
ATOM 323 C CE1 . PHE A 1 43 ? 9.699 35.741 11.709 1.00 22.04 ? 59 PHE H CE1 1
ATOM 324 C CE2 . PHE A 1 43 ? 8.706 34.079 13.107 1.00 20.43 ? 59 PHE H CE2 1
ATOM 325 C CZ . PHE A 1 43 ? 9.803 34.575 12.437 1.00 18.31 ? 59 PHE H CZ 1
ATOM 326 N N . ASP A 1 44 ? 4.265 38.799 14.760 1.00 19.41 ? 60 ASP H N 1
ATOM 327 C CA . ASP A 1 44 ? 3.019 39.561 14.964 1.00 21.98 ? 60 ASP H CA 1
ATOM 328 C C . ASP A 1 44 ? 3.076 41.011 14.488 1.00 31.37 ? 60 ASP H C 1
ATOM 329 O O . ASP A 1 44 ? 2.061 41.541 14.068 1.00 32.54 ? 60 ASP H O 1
ATOM 330 C CB . ASP A 1 44 ? 2.633 39.555 16.453 1.00 23.09 ? 60 ASP H CB 1
ATOM 331 C CG . ASP A 1 44 ? 1.999 38.275 16.944 1.00 28.33 ? 60 ASP H CG 1
ATOM 332 O OD1 . ASP A 1 44 ? 1.911 37.306 16.147 1.00 29.31 ? 60 ASP H OD1 1
ATOM 333 O OD2 . ASP A 1 44 ? 1.619 38.224 18.133 1.00 29.53 ? 60 ASP H OD2 1
ATOM 334 N N . LYS A 1 45 A 4.240 41.656 14.575 1.00 30.66 ? 60 LYS H N 1
ATOM 335 C CA . LYS A 1 45 A 4.388 43.071 14.222 1.00 31.68 ? 60 LYS H CA 1
ATOM 336 C C . LYS A 1 45 A 5.294 43.324 13.023 1.00 38.11 ? 60 LYS H C 1
ATOM 337 O O . LYS A 1 45 A 5.726 44.457 12.828 1.00 39.40 ? 60 LYS H O 1
ATOM 338 C CB . LYS A 1 45 A 4.853 43.870 15.449 1.00 33.51 ? 60 LYS H CB 1
ATOM 339 C CG . LYS A 1 45 A 3.731 44.096 16.449 1.00 48.38 ? 60 LYS H CG 1
ATOM 340 C CD . LYS A 1 45 A 4.257 44.404 17.833 1.00 64.54 ? 60 LYS H CD 1
ATOM 341 C CE . LYS A 1 45 A 3.124 44.673 18.792 1.00 76.49 ? 60 LYS H CE 1
ATOM 342 N N . ILE A 1 46 B 5.552 42.303 12.196 1.00 34.95 ? 60 ILE H N 1
ATOM 343 C CA . ILE A 1 46 B 6.382 42.504 11.005 1.00 35.67 ? 60 ILE H CA 1
ATOM 344 C C . ILE A 1 46 B 5.550 43.159 9.885 1.00 40.88 ? 60 ILE H C 1
ATOM 345 O O . ILE A 1 46 B 4.442 42.696 9.581 1.00 39.95 ? 60 ILE H O 1
ATOM 346 C CB . ILE A 1 46 B 7.097 41.190 10.495 1.00 38.06 ? 60 ILE H CB 1
ATOM 347 C CG1 . ILE A 1 46 B 7.974 40.487 11.586 1.00 37.99 ? 60 ILE H CG1 1
ATOM 348 C CG2 . ILE A 1 46 B 7.916 41.436 9.212 1.00 37.97 ? 60 ILE H CG2 1
ATOM 349 C CD1 . ILE A 1 46 B 9.078 41.330 12.278 1.00 43.63 ? 60 ILE H CD1 1
ATOM 350 N N . LYS A 1 47 C 6.112 44.208 9.256 1.00 38.12 ? 60 LYS H N 1
ATOM 351 C CA . LYS A 1 47 C 5.533 44.859 8.069 1.00 39.21 ? 60 LYS H CA 1
ATOM 352 C C . LYS A 1 47 C 6.548 44.763 6.937 1.00 45.85 ? 60 LYS H C 1
ATOM 353 O O . LYS A 1 47 C 6.177 44.543 5.787 1.00 46.49 ? 60 LYS H O 1
ATOM 354 C CB . LYS A 1 47 C 5.139 46.313 8.343 1.00 41.67 ? 60 LYS H CB 1
ATOM 355 C CG . LYS A 1 47 C 3.789 46.433 9.040 1.00 58.21 ? 60 LYS H CG 1
ATOM 356 N N . ASN A 1 48 D 7.844 44.865 7.289 1.00 43.92 ? 60 ASN H N 1
ATOM 357 C CA . ASN A 1 48 D 8.992 44.777 6.384 1.00 43.65 ? 60 ASN H CA 1
ATOM 358 C C . ASN A 1 48 D 9.414 43.301 6.208 1.00 44.11 ? 60 ASN H C 1
ATOM 359 O O . ASN A 1 48 D 10.515 42.927 6.608 1.00 42.37 ? 60 ASN H O 1
ATOM 360 C CB . ASN A 1 48 D 10.151 45.643 6.923 1.00 45.00 ? 60 ASN H CB 1
ATOM 361 N N . TRP A 1 49 ? 8.528 42.473 5.599 1.00 39.73 ? 61 TRP H N 1
ATOM 362 C CA . TRP A 1 49 ? 8.763 41.044 5.361 1.00 39.08 ? 61 TRP H CA 1
ATOM 363 C C . TRP A 1 49 ? 10.028 40.746 4.537 1.00 42.50 ? 61 TRP H C 1
ATOM 364 O O . TRP A 1 49 ? 10.652 39.719 4.780 1.00 44.39 ? 61 TRP H O 1
ATOM 365 C CB . TRP A 1 49 ? 7.534 40.355 4.762 1.00 37.55 ? 61 TRP H CB 1
ATOM 366 C CG . TRP A 1 49 ? 6.391 40.245 5.727 1.00 38.53 ? 61 TRP H CG 1
ATOM 367 C CD1 . TRP A 1 49 ? 5.337 41.106 5.851 1.00 41.76 ? 61 TRP H CD1 1
ATOM 368 C CD2 . TRP A 1 49 ? 6.204 39.232 6.731 1.00 37.95 ? 61 TRP H CD2 1
ATOM 369 N NE1 . TRP A 1 49 ? 4.486 40.675 6.847 1.00 41.50 ? 61 TRP H NE1 1
ATOM 370 C CE2 . TRP A 1 49 ? 5.002 39.534 7.413 1.00 42.54 ? 61 TRP H CE2 1
ATOM 371 C CE3 . TRP A 1 49 ? 6.950 38.109 7.140 1.00 38.20 ? 61 TRP H CE3 1
ATOM 372 C CZ2 . TRP A 1 49 ? 4.534 38.758 8.486 1.00 41.36 ? 61 TRP H CZ2 1
ATOM 373 C CZ3 . TRP A 1 49 ? 6.468 37.325 8.175 1.00 38.85 ? 61 TRP H CZ3 1
ATOM 374 C CH2 . TRP A 1 49 ? 5.277 37.648 8.837 1.00 39.68 ? 61 TRP H CH2 1
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