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Commit c1158f40 authored by Matthew Harrigan's avatar Matthew Harrigan
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Add virtual sites

parent 8185f64b
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wrappers/python/simtk/openmm/app/modeller.py
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...@@ -952,9 +952,9 @@ class Modeller(object): ...@@ -952,9 +952,9 @@ class Modeller(object):
# This is a virtual site. Compute its position by the correct rule. # This is a virtual site. Compute its position by the correct rule.
if site.type == 'average2': if site.type == 'average2':
position = site.weights[0]*templateAtomPositions[index+site.atoms[0]] + site.weights[1]*templateAtomPositions[index+site.atoms[1]] position = site.weights[0]*templateAtomPositions[site.atoms[0]] + site.weights[1]*templateAtomPositions[site.atoms[1]]
elif site.type == 'average3': elif site.type == 'average3':
position = site.weights[0]*templateAtomPositions[index+site.atoms[0]] + site.weights[1]*templateAtomPositions[index+site.atoms[1]] + site.weights[2]*templateAtomPositions[index+site.atoms[2]] position = site.weights[0]*templateAtomPositions[site.atoms[0]] + site.weights[1]*templateAtomPositions[site.atoms[1]] + site.weights[2]*templateAtomPositions[site.atoms[2]]
elif site.type == 'outOfPlane': elif site.type == 'outOfPlane':
v1 = templateAtomPositions[index+site.atoms[1]] - templateAtomPositions[index+site.atoms[0]] v1 = templateAtomPositions[index+site.atoms[1]] - templateAtomPositions[index+site.atoms[0]]
v2 = templateAtomPositions[index+site.atoms[2]] - templateAtomPositions[index+site.atoms[0]] v2 = templateAtomPositions[index+site.atoms[2]] - templateAtomPositions[index+site.atoms[0]]
......
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