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Commit f00953b7 authored by peastman's avatar peastman
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Merge pull request #158 from rmcgibbo/pdbbug-bugfix 

Fix to PR #152
parents e0966c78 25d8559f
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wrappers/python/simtk/openmm/app/pdbfile.py
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...@@ -287,10 +287,14 @@ class PDBFile(object): ...@@ -287,10 +287,14 @@ class PDBFile(object):
else: else:
atomName = atom.name atomName = atom.name
coords = positions[posIndex] coords = positions[posIndex]
if atom.element is not None:
symbol = atom.element.symbol
else:
symbol = ' '
line = "ATOM %5d %-4s %3s %s%4d %s%s%s 1.00 0.00 %2s " % ( line = "ATOM %5d %-4s %3s %s%4d %s%s%s 1.00 0.00 %2s " % (
atomIndex%100000, atomName, resName, chainName, atomIndex%100000, atomName, resName, chainName,
(resIndex+1)%10000, _format_83(coords[0]), (resIndex+1)%10000, _format_83(coords[0]),
_format_83(coords[1]), _format_83(coords[2]), atom.element.symbol) _format_83(coords[1]), _format_83(coords[2]), symbol)
assert len(line) == 80, 'Fixed width overflow detected' assert len(line) == 80, 'Fixed width overflow detected'
print >>file, line print >>file, line
posIndex += 1 posIndex += 1
......
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