Skip to content

GitLab

"platforms/reference/tests/TestReferenceSettle.cpp" did not exist on "ed1fb1923aeff2fe99e090bab87aeddd63115043"
Commit 11082d76 authored by peastman's avatar peastman
Browse files

Merge pull request #478 from mpharrigan/vs 

Add virtual sites
parents 8185f64b 65f0a591
Hide whitespace changes
Inline Side-by-side
Showing with 5 additions and 5 deletions
wrappers/python/simtk/openmm/app/modeller.py
View file @ 11082d76
...@@ -952,14 +952,14 @@ class Modeller(object): ...@@ -952,14 +952,14 @@ 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[site.atoms[1]] - templateAtomPositions[site.atoms[0]]
v2 = templateAtomPositions[index+site.atoms[2]] - templateAtomPositions[index+site.atoms[0]] v2 = templateAtomPositions[site.atoms[2]] - templateAtomPositions[site.atoms[0]]
cross = Vec3(v1[1]*v2[2]-v1[2]*v2[1], v1[2]*v2[0]-v1[0]*v2[2], v1[0]*v2[1]-v1[1]*v2[0]) cross = Vec3(v1[1]*v2[2]-v1[2]*v2[1], v1[2]*v2[0]-v1[0]*v2[2], v1[0]*v2[1]-v1[1]*v2[0])
position = templateAtomPositions[index+site.atoms[0]] + site.weights[0]*v1 + site.weights[1]*v2 + site.weights[2]*cross position = templateAtomPositions[site.atoms[0]] + site.weights[0]*v1 + site.weights[1]*v2 + site.weights[2]*cross
if position is None and atom.type in drudeTypeMap: if position is None and atom.type in drudeTypeMap:
# This is a Drude particle. Put it on top of its parent atom. # This is a Drude particle. Put it on top of its parent atom.
......
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