Skip to content

GitLab

Commit abdc6296 authored by Peter Eastman's avatar Peter Eastman
Browse files

Improper torsions without wildcards override ones with

parent d2fd6cee
Show whitespace changes
Inline Side-by-side
Showing with 33 additions and 21 deletions
wrappers/python/simtk/openmm/app/forcefield.py
View file @ abdc6296
...@@ -1360,14 +1360,16 @@ class PeriodicTorsionGenerator: ...@@ -1360,14 +1360,16 @@ class PeriodicTorsionGenerator:
type2 = data.atomType[data.atoms[torsion[1]]] type2 = data.atomType[data.atoms[torsion[1]]]
type3 = data.atomType[data.atoms[torsion[2]]] type3 = data.atomType[data.atoms[torsion[2]]]
type4 = data.atomType[data.atoms[torsion[3]]] type4 = data.atomType[data.atoms[torsion[3]]]
done = False match = None
for tordef in self.improper: for tordef in self.improper:
if done:
break
types1 = tordef.types1 types1 = tordef.types1
types2 = tordef.types2 types2 = tordef.types2
types3 = tordef.types3 types3 = tordef.types3
types4 = tordef.types4 types4 = tordef.types4
hasWildcard = (wildcard in (types1, types2, types3, types4))
if match is not None and hasWildcard:
# Prefer specific definitions over ones with wildcards
continue
if type1 in types1: if type1 in types1:
for (t2, t3, t4) in itertools.permutations(((type2, 1), (type3, 2), (type4, 3))): for (t2, t3, t4) in itertools.permutations(((type2, 1), (type3, 2), (type4, 3))):
if t2[0] in types2 and t3[0] in types3 and t4[0] in types4: if t2[0] in types2 and t3[0] in types3 and t4[0] in types4:
...@@ -1382,11 +1384,13 @@ class PeriodicTorsionGenerator: ...@@ -1382,11 +1384,13 @@ class PeriodicTorsionGenerator:
(a1, a2) = (a2, a1) (a1, a2) = (a2, a1)
elif e1 != elem.carbon and (e2 == elem.carbon or e1.mass < e2.mass): elif e1 != elem.carbon and (e2 == elem.carbon or e1.mass < e2.mass):
(a1, a2) = (a2, a1) (a1, a2) = (a2, a1)
match = (a1, a2, torsion[0], torsion[t4[1]], tordef)
break
if match is not None:
(a1, a2, a3, a4, tordef) = match
for i in range(len(tordef.phase)): for i in range(len(tordef.phase)):
if tordef.k[i] != 0: if tordef.k[i] != 0:
force.addTorsion(a1, a2, torsion[0], torsion[t4[1]], tordef.periodicity[i], tordef.phase[i], tordef.k[i]) force.addTorsion(a1, a2, a3, a4, tordef.periodicity[i], tordef.phase[i], tordef.k[i])
done = True
break
parsers["PeriodicTorsionForce"] = PeriodicTorsionGenerator.parseElement parsers["PeriodicTorsionForce"] = PeriodicTorsionGenerator.parseElement
...@@ -1457,18 +1461,20 @@ class RBTorsionGenerator: ...@@ -1457,18 +1461,20 @@ class RBTorsionGenerator:
type2 = data.atomType[data.atoms[torsion[1]]] type2 = data.atomType[data.atoms[torsion[1]]]
type3 = data.atomType[data.atoms[torsion[2]]] type3 = data.atomType[data.atoms[torsion[2]]]
type4 = data.atomType[data.atoms[torsion[3]]] type4 = data.atomType[data.atoms[torsion[3]]]
done = False match = None
for tordef in self.improper: for tordef in self.improper:
if done:
break
types1 = tordef.types1 types1 = tordef.types1
types2 = tordef.types2 types2 = tordef.types2
types3 = tordef.types3 types3 = tordef.types3
types4 = tordef.types4 types4 = tordef.types4
hasWildcard = (wildcard in (types1, types2, types3, types4))
if match is not None and hasWildcard:
# Prefer specific definitions over ones with wildcards
continue
if type1 in types1: if type1 in types1:
for (t2, t3, t4) in itertools.permutations(((type2, 1), (type3, 2), (type4, 3))): for (t2, t3, t4) in itertools.permutations(((type2, 1), (type3, 2), (type4, 3))):
if t2[0] in types2 and t3[0] in types3 and t4[0] in types4: if t2[0] in types2 and t3[0] in types3 and t4[0] in types4:
if wildcard in (types1, types2, types3, types4): if hasWildcard:
# Workaround to be more consistent with AMBER. It uses wildcards to define most of its # Workaround to be more consistent with AMBER. It uses wildcards to define most of its
# impropers, which leaves the ordering ambiguous. It then follows some bizarre rules # impropers, which leaves the ordering ambiguous. It then follows some bizarre rules
# to pick the order. # to pick the order.
...@@ -1480,12 +1486,14 @@ class RBTorsionGenerator: ...@@ -1480,12 +1486,14 @@ class RBTorsionGenerator:
(a1, a2) = (a2, a1) (a1, a2) = (a2, a1)
elif e1 != elem.carbon and (e2 == elem.carbon or e1.mass < e2.mass): elif e1 != elem.carbon and (e2 == elem.carbon or e1.mass < e2.mass):
(a1, a2) = (a2, a1) (a1, a2) = (a2, a1)
force.addTorsion(a1, a2, torsion[0], torsion[t4[1]], tordef.c[0], tordef.c[1], tordef.c[2], tordef.c[3], tordef.c[4], tordef.c[5]) match = (a1, a2, torsion[0], torsion[t4[1]], tordef)
else: else:
# There are no wildcards, so the order is unambiguous. # There are no wildcards, so the order is unambiguous.
force.addTorsion(torsion[0], torsion[t2[1]], torsion[t3[1]], torsion[t4[1]], tordef.c[0], tordef.c[1], tordef.c[2], tordef.c[3], tordef.c[4], tordef.c[5]) match = (torsion[0], torsion[t2[1]], torsion[t3[1]], torsion[t4[1]], tordef)
done = True
break break
if match is not None:
(a1, a2, a3, a4, tordef) = match
force.addTorsion(a1, a2, a3, a4, tordef.c[0], tordef.c[1], tordef.c[2], tordef.c[3], tordef.c[4], tordef.c[5])
parsers["RBTorsionForce"] = RBTorsionGenerator.parseElement parsers["RBTorsionForce"] = RBTorsionGenerator.parseElement
...@@ -1884,18 +1892,20 @@ class CustomTorsionGenerator: ...@@ -1884,18 +1892,20 @@ class CustomTorsionGenerator:
type2 = data.atomType[data.atoms[torsion[1]]] type2 = data.atomType[data.atoms[torsion[1]]]
type3 = data.atomType[data.atoms[torsion[2]]] type3 = data.atomType[data.atoms[torsion[2]]]
type4 = data.atomType[data.atoms[torsion[3]]] type4 = data.atomType[data.atoms[torsion[3]]]
done = False match = None
for tordef in self.improper: for tordef in self.improper:
if done:
break
types1 = tordef.types1 types1 = tordef.types1
types2 = tordef.types2 types2 = tordef.types2
types3 = tordef.types3 types3 = tordef.types3
types4 = tordef.types4 types4 = tordef.types4
hasWildcard = (wildcard in (types1, types2, types3, types4))
if match is not None and hasWildcard:
# Prefer specific definitions over ones with wildcards
continue
if type1 in types1: if type1 in types1:
for (t2, t3, t4) in itertools.permutations(((type2, 1), (type3, 2), (type4, 3))): for (t2, t3, t4) in itertools.permutations(((type2, 1), (type3, 2), (type4, 3))):
if t2[0] in types2 and t3[0] in types3 and t4[0] in types4: if t2[0] in types2 and t3[0] in types3 and t4[0] in types4:
if wildcard in (types1, types2, types3, types4): if hasWildcard:
# Workaround to be more consistent with AMBER. It uses wildcards to define most of its # Workaround to be more consistent with AMBER. It uses wildcards to define most of its
# impropers, which leaves the ordering ambiguous. It then follows some bizarre rules # impropers, which leaves the ordering ambiguous. It then follows some bizarre rules
# to pick the order. # to pick the order.
...@@ -1907,12 +1917,14 @@ class CustomTorsionGenerator: ...@@ -1907,12 +1917,14 @@ class CustomTorsionGenerator:
(a1, a2) = (a2, a1) (a1, a2) = (a2, a1)
elif e1 != elem.carbon and (e2 == elem.carbon or e1.mass < e2.mass): elif e1 != elem.carbon and (e2 == elem.carbon or e1.mass < e2.mass):
(a1, a2) = (a2, a1) (a1, a2) = (a2, a1)
force.addTorsion(a1, a2, torsion[0], torsion[t4[1]], tordef.paramValues) match = (a1, a2, torsion[0], torsion[t4[1]], tordef)
else: else:
# There are no wildcards, so the order is unambiguous. # There are no wildcards, so the order is unambiguous.
force.addTorsion(torsion[0], torsion[t2[1]], torsion[t3[1]], torsion[t4[1]], tordef.paramValues) match = (torsion[0], torsion[t2[1]], torsion[t3[1]], torsion[t4[1]], tordef)
done = True
break break
if match is not None:
(a1, a2, a3, a4, tordef) = match
force.addTorsion(a1, a2, a3, a4, tordef.paramValues)
parsers["CustomTorsionForce"] = CustomTorsionGenerator.parseElement parsers["CustomTorsionForce"] = CustomTorsionGenerator.parseElement
......
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