Skip to content

GitLab

Commit 57f3be7e authored by peastman's avatar peastman Committed by GitHub
Browse files

Merge pull request #1908 from JoaoRodrigues/asym_chain_fix 

Fixed chain labeling in mmCIF files IO.
parents f3e727df 8d59a6be
Hide whitespace changes
Inline Side-by-side
Showing with 87 additions and 13 deletions
wrappers/python/CMakeLists.txt
View file @ 57f3be7e
...@@ -55,6 +55,7 @@ foreach(SUBDIR ${SUBDIRS}) ...@@ -55,6 +55,7 @@ foreach(SUBDIR ${SUBDIRS})
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.xml" "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.xml"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.pdb" "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.pdb"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.pdbx" "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.pdbx"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.cif"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prmtop" "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prmtop"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prm" "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.prm"
"${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.inpcrd" "${CMAKE_CURRENT_SOURCE_DIR}/${SUBDIR}/*.inpcrd"
......
wrappers/python/simtk/openmm/app/pdbxfile.py
View file @ 57f3be7e
...@@ -80,13 +80,11 @@ class PDBxFile(object): ...@@ -80,13 +80,11 @@ class PDBxFile(object):
# Build the topology. # Build the topology.
atomData = block.getObj('atom_site') atomData = block.getObj('atom_site')
atomNameCol = atomData.getAttributeIndex('label_atom_id') atomNameCol = atomData.getAttributeIndex('auth_atom_id')
atomIdCol = atomData.getAttributeIndex('id') atomIdCol = atomData.getAttributeIndex('id')
resNameCol = atomData.getAttributeIndex('label_comp_id') resNameCol = atomData.getAttributeIndex('auth_comp_id')
resIdCol = atomData.getAttributeIndex('label_seq_id')
resNumCol = atomData.getAttributeIndex('auth_seq_id') resNumCol = atomData.getAttributeIndex('auth_seq_id')
asymIdCol = atomData.getAttributeIndex('label_asym_id') chainIdCol = atomData.getAttributeIndex('auth_asym_id')
chainIdCol = atomData.getAttributeIndex('label_entity_id')
elementCol = atomData.getAttributeIndex('type_symbol') elementCol = atomData.getAttributeIndex('type_symbol')
altIdCol = atomData.getAttributeIndex('label_alt_id') altIdCol = atomData.getAttributeIndex('label_alt_id')
modelCol = atomData.getAttributeIndex('pdbx_PDB_model_num') modelCol = atomData.getAttributeIndex('pdbx_PDB_model_num')
...@@ -95,12 +93,11 @@ class PDBxFile(object): ...@@ -95,12 +93,11 @@ class PDBxFile(object):
zCol = atomData.getAttributeIndex('Cartn_z') zCol = atomData.getAttributeIndex('Cartn_z')
lastChainId = None lastChainId = None
lastResId = None lastResId = None
lastAsymId = None
atomTable = {} atomTable = {}
atomsInResidue = set() atomsInResidue = set()
models = [] models = []
for row in atomData.getRowList(): for row in atomData.getRowList():
atomKey = ((row[resIdCol], row[asymIdCol], row[atomNameCol])) atomKey = ((row[resNumCol], row[chainIdCol], row[atomNameCol]))
model = ('1' if modelCol == -1 else row[modelCol]) model = ('1' if modelCol == -1 else row[modelCol])
if model not in models: if model not in models:
models.append(model) models.append(model)
...@@ -115,15 +112,13 @@ class PDBxFile(object): ...@@ -115,15 +112,13 @@ class PDBxFile(object):
if lastChainId != row[chainIdCol]: if lastChainId != row[chainIdCol]:
# The start of a new chain. # The start of a new chain.
chain = top.addChain(row[asymIdCol]) chain = top.addChain(row[chainIdCol])
lastChainId = row[chainIdCol] lastChainId = row[chainIdCol]
lastResId = None lastResId = None
lastAsymId = None if lastResId != row[resNumCol] or lastChainId != row[chainIdCol] or (lastResId == '.' and row[atomNameCol] in atomsInResidue):
if lastResId != row[resIdCol] or lastAsymId != row[asymIdCol] or (lastResId == '.' and row[atomNameCol] in atomsInResidue):
# The start of a new residue. # The start of a new residue.
res = top.addResidue(row[resNameCol], chain, None if resNumCol == -1 else row[resNumCol]) res = top.addResidue(row[resNameCol], chain, None if resNumCol == -1 else row[resNumCol])
lastResId = row[resIdCol] lastResId = row[resNumCol]
lastAsymId = row[asymIdCol]
atomsInResidue.clear() atomsInResidue.clear()
element = None element = None
try: try:
...@@ -139,7 +134,7 @@ class PDBxFile(object): ...@@ -139,7 +134,7 @@ class PDBxFile(object):
try: try:
atom = atomTable[atomKey] atom = atomTable[atomKey]
except KeyError: except KeyError:
raise ValueError('Unknown atom %s in residue %s %s for model %s' % (row[atomNameCol], row[resNameCol], row[resIdCol], model)) raise ValueError('Unknown atom %s in residue %s %s for model %s' % (row[atomNameCol], row[resNameCol], row[resNumCol], model))
if atom.index != len(self._positions[modelIndex]): if atom.index != len(self._positions[modelIndex]):
raise ValueError('Atom %s for model %s does not match the order of atoms for model %s' % (row[atomIdCol], model, models[0])) raise ValueError('Atom %s for model %s does not match the order of atoms for model %s' % (row[atomIdCol], model, models[0]))
self._positions[modelIndex].append(Vec3(float(row[xCol]), float(row[yCol]), float(row[zCol]))*0.1) self._positions[modelIndex].append(Vec3(float(row[xCol]), float(row[yCol]), float(row[zCol]))*0.1)
......
wrappers/python/tests/TestPdbxFile.py
View file @ 57f3be7e
...@@ -133,5 +133,21 @@ class TestPdbxFile(unittest.TestCase): ...@@ -133,5 +133,21 @@ class TestPdbxFile(unittest.TestCase):
self.assertEqual(bond1[0].name, bond2[0].name) self.assertEqual(bond1[0].name, bond2[0].name)
self.assertEqual(bond1[1].name, bond2[1].name) self.assertEqual(bond1[1].name, bond2[1].name)
def testMultiChain(self):
"""Test reading and writing a file that includes multiple chains"""
cif_ori = PDBxFile('systems/multichain.pdbx')
output = StringIO()
PDBxFile.writeFile(cif_ori.topology, cif_ori.positions, output, keepIds=True)
input = StringIO(output.getvalue())
cif_new = PDBxFile(input)
output.close()
input.close()
self.assertEqual(cif_ori.topology.getNumChains(), cif_new.topology.getNumChains())
for chain1, chain2 in zip(cif_ori.topology.chains(), cif_new.topology.chains()):
self.assertEqual(chain1.id, chain2.id)
if __name__ == '__main__': if __name__ == '__main__':
unittest.main() unittest.main()
wrappers/python/tests/systems/multichain.pdbx 0 → 100644
View file @ 57f3be7e
# dummy file with multiple chains
# fragment of 1brs
#
data_1brs_AD
_entry.id 1brs_AD
#
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_asym_id
_atom_site.pdbx_PDB_model_num
ATOM 1 N N . VAL A 1 3 ? 16.783 48.812 26.447 1.00 30.15 0 A 1
ATOM 2 C CA . VAL A 1 3 ? 17.591 48.101 25.416 1.00 27.93 0 A 1
ATOM 3 C C . VAL A 1 3 ? 16.643 47.160 24.676 1.00 25.52 0 A 1
ATOM 4 O O . VAL A 1 3 ? 16.213 46.129 25.220 1.00 26.86 0 A 1
ATOM 5 C CB . VAL A 1 3 ? 18.813 47.329 25.940 1.00 28.10 0 A 1
ATOM 6 C CG1 . VAL A 1 3 ? 19.512 46.623 24.799 1.00 29.27 0 A 1
ATOM 7 C CG2 . VAL A 1 3 ? 19.838 48.188 26.670 1.00 28.76 0 A 1
ATOM 8 N N . ILE A 1 4 ? 16.327 47.509 23.466 1.00 23.19 0 A 1
ATOM 9 C CA . ILE A 1 4 ? 15.435 46.625 22.666 1.00 21.26 0 A 1
ATOM 10 C C . ILE A 1 4 ? 16.364 45.902 21.716 1.00 19.99 0 A 1
ATOM 11 O O . ILE A 1 4 ? 16.847 46.590 20.823 1.00 18.74 0 A 1
ATOM 12 C CB . ILE A 1 4 ? 14.415 47.516 21.981 1.00 22.04 0 A 1
ATOM 13 C CG1 . ILE A 1 4 ? 13.710 48.294 23.129 1.00 22.39 0 A 1
ATOM 14 C CG2 . ILE A 1 4 ? 13.485 46.762 21.052 1.00 19.05 0 A 1
ATOM 15 C CD1 . ILE A 1 4 ? 12.870 49.416 22.486 1.00 23.20 0 A 1
ATOM 16 N N . LYS D 2 1 ? 48.330 40.393 9.798 1.00 29.18 0 D 1
ATOM 17 C CA . LYS D 2 1 ? 47.401 39.287 9.370 1.00 29.51 0 D 1
ATOM 18 C C . LYS D 2 1 ? 47.507 38.911 7.890 1.00 28.30 0 D 1
ATOM 19 O O . LYS D 2 1 ? 47.126 39.582 6.905 1.00 28.68 0 D 1
ATOM 20 C CB . LYS D 2 1 ? 45.995 39.632 9.817 1.00 31.06 0 D 1
ATOM 21 C CG . LYS D 2 1 ? 44.801 38.778 9.587 1.00 34.24 0 D 1
ATOM 22 C CD . LYS D 2 1 ? 44.946 37.289 9.712 1.00 37.99 0 D 1
ATOM 23 C CE . LYS D 2 1 ? 44.733 36.789 11.137 1.00 39.74 0 D 1
ATOM 24 N NZ . LYS D 2 1 ? 44.858 35.301 11.250 1.00 39.95 1 D 1
ATOM 25 N N . LYS D 2 2 ? 48.047 37.742 7.642 1.00 26.22 0 D 1
ATOM 26 C CA . LYS D 2 2 ? 48.270 37.151 6.331 1.00 25.12 0 D 1
ATOM 27 C C . LYS D 2 2 ? 47.509 35.851 6.169 1.00 24.31 0 D 1
ATOM 28 O O . LYS D 2 2 ? 47.675 35.055 7.114 1.00 25.51 0 D 1
ATOM 29 C CB . LYS D 2 2 ? 49.764 36.810 6.325 1.00 25.77 0 D 1
ATOM 30 C CG . LYS D 2 2 ? 50.121 35.923 5.159 1.00 27.71 0 D 1
ATOM 31 C CD . LYS D 2 2 ? 50.197 36.783 3.916 1.00 28.44 0 D 1
ATOM 32 C CE . LYS D 2 2 ? 50.902 36.036 2.805 1.00 30.19 0 D 1
ATOM 33 N NZ . LYS D 2 2 ? 52.379 36.102 2.952 1.00 31.01 1 D 1
HETATM 34 O O . HOH G 3 111 ? 25.978 40.412 17.662 1.00 16.91 0 A 1
HETATM 35 O O . HOH G 3 112 ? 24.196 43.521 11.471 1.00 13.10 0 A 1
HETATM 36 O O . HOH J 3 91 ? 25.995 40.067 5.614 1.00 11.53 0 D 1
HETATM 37 O O . HOH J 3 92 ? 36.372 43.366 10.462 1.00 17.15 0 D 1
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment