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Unverified Commit 3fdc297c authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #2572 from peastman/hetatm 

PDBxFile marks heterogens with HETATM
parents 421b8f67 9025de4d
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Showing with 8 additions and 2 deletions
wrappers/python/simtk/openmm/app/pdbxfile.py
View file @ 3fdc297c
......@@ -400,6 +400,8 @@ class PDBxFile(object):
raise ValueError('Particle position is NaN')
if any(math.isinf(norm(pos)) for pos in positions):
raise ValueError('Particle position is infinite')
nonHeterogens = PDBFile._standardResidues[:]
nonHeterogens.remove('HOH')
atomIndex = 1
posIndex = 0
for (chainIndex, chain) in enumerate(topology.chains()):
......@@ -415,14 +417,18 @@ class PDBxFile(object):
else:
resId = resIndex + 1
resIC = '.'
if res.name in nonHeterogens:
recordName = "ATOM"
else:
recordName = "HETATM"
for atom in res.atoms():
coords = positions[posIndex]
if atom.element is not None:
symbol = atom.element.symbol
else:
symbol = '?'
line = "ATOM %5d %-3s %-4s . %-4s %s ? %5s %s %10.4f %10.4f %10.4f 0.0 0.0 ? ? ? ? ? . %5s %4s %s %4s %5d"
print(line % (atomIndex, symbol, atom.name, res.name, chainName, resId, resIC, coords[0], coords[1], coords[2],
line = "%s %5d %-3s %-4s . %-4s %s ? %5s %s %10.4f %10.4f %10.4f 0.0 0.0 ? ? ? ? ? . %5s %4s %s %4s %5d"
print(line % (recordName, atomIndex, symbol, atom.name, res.name, chainName, resId, resIC, coords[0], coords[1], coords[2],
resId, res.name, chainName, atom.name, modelIndex), file=file)
posIndex += 1
atomIndex += 1
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