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"platforms/opencl/src/OpenCLKernelSources.h.in" did not exist on "10379a9a4405bc4efa5f1ba0ab93b85b21404e44"
Commit 89635b86 authored by Rafal P. Wiewiora's avatar Rafal P. Wiewiora
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fix writeFile for extraParticleIdentifier=None

parent c8cbc3d5
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Showing with 8 additions and 6 deletions
wrappers/python/simtk/openmm/app/pdbfile.py
View file @ 89635b86
......@@ -329,17 +329,19 @@ class PDBFile(object):
else:
resId = "%4d" % ((resIndex+1)%10000)
for atom in res.atoms():
if len(atom.name) < 4 and atom.name[:1].isalpha() and ((atom.element is None and extraParticleIdentifier is not None) or len(atom.element.symbol) < 2):
if atom.element is not None:
symbol = atom.element.symbol
elif atom.element is None and extraParticleIdentifier is not None:
symbol = extraParticleIdentifier
else:
symbol = ' '
if len(atom.name) < 4 and atom.name[:1].isalpha() and len(symbol) < 2:
atomName = ' '+atom.name
elif len(atom.name) > 4:
atomName = atom.name[:4]
else:
atomName = atom.name
coords = positions[posIndex]
if atom.element is not None:
symbol = atom.element.symbol
else:
symbol = extraParticleIdentifier
line = "ATOM %5d %-4s %3s %s%4s %s%s%s 1.00 0.00 %2s " % (
atomIndex%100000, atomName, resName, chainName, resId, _format_83(coords[0]),
_format_83(coords[1]), _format_83(coords[2]), symbol)
......
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