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Commit a1cadf1c authored by Rafal P. Wiewiora's avatar Rafal P. Wiewiora
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extract ordering=amber part to a function

parent 3c819df2
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Showing with 52 additions and 141 deletions
wrappers/python/simtk/openmm/app/forcefield.py
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......@@ -1736,6 +1736,55 @@ def _createResidueTemplate(residue):
template.addExternalBondByName(atom2.name)
return template
def _matchAmberImproper(torsion, data, hasWildcard):
# topology atom indexes
a2 = torsion[t2[1]]
a3 = torsion[t3[1]]
a4 = torsion[t4[1]]
# residue indexes
r2 = data.atoms[a2].residue.index
r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index
# template atom indexes
ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
# elements
e2 = data.atoms[a2].element
e3 = data.atoms[a3].element
e4 = data.atoms[a4].element
if not hasWildcard:
if t2[0] == t4[0] and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(a2, a4) = (a4, a2)
r2 = data.atoms[a2].residue.index
r4 = data.atoms[a4].residue.index
ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if t3[0] == t4[0] and (r3 > r4 or (r3 == r4 and ta3 > ta4)):
(a3, a4) = (a4, a3)
r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if t2[0] == t3[0] and (r2 > r3 or (r2 == r3 and ta2 > ta3)):
(a2, a3) = (a3, a2)
else:
if e2 == e4 and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(a2, a4) = (a4, a2)
r2 = data.atoms[a2].residue.index
r4 = data.atoms[a4].residue.index
ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if e3 == e4 and (r3 > r4 or (r3 == r4 and ta3 > ta4)):
(a3, a4) = (a4, a3)
r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if r2 > r3 or (r2 == r3 and ta2 > ta3):
(a2, a3) = (a3, a2)
match = (a2, a3, torsion[0], a4, tordef)
# The following classes are generators that know how to create Force subclasses and add them to a System that is being
# created. Each generator class must define two methods: 1) a static method that takes an etree Element and a ForceField,
# and returns the corresponding generator object; 2) a createForce() method that constructs the Force object and adds it
......@@ -2001,53 +2050,7 @@ class PeriodicTorsionGenerator(object):
match = (a1, a2, torsion[0], torsion[t4[1]], tordef)
break
elif tordef.ordering == 'amber':
# topology atom indexes
a2 = torsion[t2[1]]
a3 = torsion[t3[1]]
a4 = torsion[t4[1]]
# residue indexes
r2 = data.atoms[a2].residue.index
r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index
# template atom indexes
ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
# elements
e2 = data.atoms[a2].element
e3 = data.atoms[a3].element
e4 = data.atoms[a4].element
if not hasWildcard:
if t2[0] == t4[0] and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(a2, a4) = (a4, a2)
r2 = data.atoms[a2].residue.index
r4 = data.atoms[a4].residue.index
ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if t3[0] == t4[0] and (r3 > r4 or (r3 == r4 and ta3 > ta4)):
(a3, a4) = (a4, a3)
r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if t2[0] == t3[0] and (r2 > r3 or (r2 == r3 and ta2 > ta3)):
(a2, a3) = (a3, a2)
else:
if e2 == e4 and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(a2, a4) = (a4, a2)
r2 = data.atoms[a2].residue.index
r4 = data.atoms[a4].residue.index
ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if e3 == e4 and (r3 > r4 or (r3 == r4 and ta3 > ta4)):
(a3, a4) = (a4, a3)
r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if r2 > r3 or (r2 == r3 and ta2 > ta3):
(a2, a3) = (a3, a2)
match = (a2, a3, torsion[0], a4, tordef)
match = _matchAmberImproper(torsion, data, hasWildcard)
break
if match is not None:
(a1, a2, a3, a4, tordef) = match
......@@ -2167,53 +2170,7 @@ class RBTorsionGenerator(object):
match = (torsion[0], torsion[t2[1]], torsion[t3[1]], torsion[t4[1]], tordef)
break
elif tordef.ordering == 'amber':
# topology atom indexes
a2 = torsion[t2[1]]
a3 = torsion[t3[1]]
a4 = torsion[t4[1]]
# residue indexes
r2 = data.atoms[a2].residue.index
r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index
# template atom indexes
ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
# elements
e2 = data.atoms[a2].element
e3 = data.atoms[a3].element
e4 = data.atoms[a4].element
if not hasWildcard:
if t2[0] == t4[0] and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(a2, a4) = (a4, a2)
r2 = data.atoms[a2].residue.index
r4 = data.atoms[a4].residue.index
ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if t3[0] == t4[0] and (r3 > r4 or (r3 == r4 and ta3 > ta4)):
(a3, a4) = (a4, a3)
r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if t2[0] == t3[0] and (r2 > r3 or (r2 == r3 and ta2 > ta3)):
(a2, a3) = (a3, a2)
else:
if e2 == e4 and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(a2, a4) = (a4, a2)
r2 = data.atoms[a2].residue.index
r4 = data.atoms[a4].residue.index
ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if e3 == e4 and (r3 > r4 or (r3 == r4 and ta3 > ta4)):
(a3, a4) = (a4, a3)
r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if r2 > r3 or (r2 == r3 and ta2 > ta3):
(a2, a3) = (a3, a2)
match = (a2, a3, torsion[0], a4, tordef)
match = _matchAmberImproper(torsion, data, hasWildcard)
break
if match is not None:
(a1, a2, a3, a4, tordef) = match
......@@ -2782,53 +2739,7 @@ class CustomTorsionGenerator(object):
match = (torsion[0], torsion[t2[1]], torsion[t3[1]], torsion[t4[1]], tordef)
break
elif tordef.ordering == 'amber':
# topology atom indexes
a2 = torsion[t2[1]]
a3 = torsion[t3[1]]
a4 = torsion[t4[1]]
# residue indexes
r2 = data.atoms[a2].residue.index
r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index
# template atom indexes
ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
# elements
e2 = data.atoms[a2].element
e3 = data.atoms[a3].element
e4 = data.atoms[a4].element
if not hasWildcard:
if t2[0] == t4[0] and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(a2, a4) = (a4, a2)
r2 = data.atoms[a2].residue.index
r4 = data.atoms[a4].residue.index
ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if t3[0] == t4[0] and (r3 > r4 or (r3 == r4 and ta3 > ta4)):
(a3, a4) = (a4, a3)
r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if t2[0] == t3[0] and (r2 > r3 or (r2 == r3 and ta2 > ta3)):
(a2, a3) = (a3, a2)
else:
if e2 == e4 and (r2 > r4 or (r2 == r4 and ta2 > ta4)):
(a2, a4) = (a4, a2)
r2 = data.atoms[a2].residue.index
r4 = data.atoms[a4].residue.index
ta2 = data.atomTemplateIndexes[data.atoms[a2]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if e3 == e4 and (r3 > r4 or (r3 == r4 and ta3 > ta4)):
(a3, a4) = (a4, a3)
r3 = data.atoms[a3].residue.index
r4 = data.atoms[a4].residue.index
ta3 = data.atomTemplateIndexes[data.atoms[a3]]
ta4 = data.atomTemplateIndexes[data.atoms[a4]]
if r2 > r3 or (r2 == r3 and ta2 > ta3):
(a2, a3) = (a3, a2)
match = (a2, a3, torsion[0], a4, tordef)
match = _matchAmberImproper(torsion, data, hasWildcard)
break
if match is not None:
(a1, a2, a3, a4, tordef) = match
......
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