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Commit 9a167d05 authored by peastman's avatar peastman
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Removed inappropriate error checks that forced all AMOEBA parameters to be in a single file

parent fa6025df
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wrappers/python/simtk/openmm/app/forcefield.py
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...@@ -1341,7 +1341,6 @@ class GBVIGenerator: ...@@ -1341,7 +1341,6 @@ class GBVIGenerator:
for bond in data.bonds: for bond in data.bonds:
type1 = data.atomType[data.atoms[bond.atom1]] type1 = data.atomType[data.atoms[bond.atom1]]
type2 = data.atomType[data.atoms[bond.atom2]] type2 = data.atomType[data.atoms[bond.atom2]]
hit = 0
for i in range(len(hbGenerator.types1)): for i in range(len(hbGenerator.types1)):
types1 = hbGenerator.types1[i] types1 = hbGenerator.types1[i]
types2 = hbGenerator.types2[i] types2 = hbGenerator.types2[i]
...@@ -1945,23 +1944,17 @@ class AmoebaBondGenerator: ...@@ -1945,23 +1944,17 @@ class AmoebaBondGenerator:
for bond in data.bonds: for bond in data.bonds:
type1 = data.atomType[data.atoms[bond.atom1]] type1 = data.atomType[data.atoms[bond.atom1]]
type2 = data.atomType[data.atoms[bond.atom2]] type2 = data.atomType[data.atoms[bond.atom2]]
hit = 0
for i in range(len(self.types1)): for i in range(len(self.types1)):
types1 = self.types1[i] types1 = self.types1[i]
types2 = self.types2[i] types2 = self.types2[i]
if (type1 in types1 and type2 in types2) or (type1 in types2 and type2 in types1): if (type1 in types1 and type2 in types2) or (type1 in types2 and type2 in types1):
bond.length = self.length[i] bond.length = self.length[i]
hit = 1
if bond.isConstrained: if bond.isConstrained:
sys.addConstraint(bond.atom1, bond.atom2, self.length[i]) sys.addConstraint(bond.atom1, bond.atom2, self.length[i])
elif self.k[i] != 0: elif self.k[i] != 0:
force.addBond(bond.atom1, bond.atom2, self.length[i], self.k[i]) force.addBond(bond.atom1, bond.atom2, self.length[i], self.k[i])
break break
if (hit == 0):
outputString = "AmoebaBondGenerator missing: types=[%5s %5s] atoms=[%6d %6d] " % (type1, type2, bond.atom1, bond.atom2)
raise ValueError(outputString)
parsers["AmoebaBondForce"] = AmoebaBondGenerator.parseElement parsers["AmoebaBondForce"] = AmoebaBondGenerator.parseElement
#============================================================================================= #=============================================================================================
...@@ -2093,13 +2086,11 @@ class AmoebaAngleGenerator: ...@@ -2093,13 +2086,11 @@ class AmoebaAngleGenerator:
type1 = data.atomType[data.atoms[angle[0]]] type1 = data.atomType[data.atoms[angle[0]]]
type2 = data.atomType[data.atoms[angle[1]]] type2 = data.atomType[data.atoms[angle[1]]]
type3 = data.atomType[data.atoms[angle[2]]] type3 = data.atomType[data.atoms[angle[2]]]
hit = 0
for i in range(len(self.types1)): for i in range(len(self.types1)):
types1 = self.types1[i] types1 = self.types1[i]
types2 = self.types2[i] types2 = self.types2[i]
types3 = self.types3[i] types3 = self.types3[i]
if (type1 in types1 and type2 in types2 and type3 in types3) or (type1 in types3 and type2 in types2 and type3 in types1): if (type1 in types1 and type2 in types2 and type3 in types3) or (type1 in types3 and type2 in types2 and type3 in types1):
hit = 1
if isConstrained and self.k[i] != 0.0: if isConstrained and self.k[i] != 0.0:
angleDict['idealAngle'] = self.angle[i][0] angleDict['idealAngle'] = self.angle[i][0]
addAngleConstraint(angle, self.angle[i][0]*math.pi/180.0, data, sys) addAngleConstraint(angle, self.angle[i][0]*math.pi/180.0, data, sys)
...@@ -2127,13 +2118,6 @@ class AmoebaAngleGenerator: ...@@ -2127,13 +2118,6 @@ class AmoebaAngleGenerator:
angleDict['idealAngle'] = angleValue angleDict['idealAngle'] = angleValue
force.addAngle(angle[0], angle[1], angle[2], angleValue, self.k[i]) force.addAngle(angle[0], angle[1], angle[2], angleValue, self.k[i])
break break
if (hit == 0):
outputString = "AmoebaAngleGenerator missing types: [%s %s %s] for atoms: " % (type1, type2, type3)
outputString += getAtomPrint( data, angle[0] ) + ' '
outputString += getAtomPrint( data, angle[1] ) + ' '
outputString += getAtomPrint( data, angle[2] )
outputString += " indices: [%6d %6d %6d]" % (angle[0], angle[1], angle[2])
raise ValueError(outputString)
#============================================================================================= #=============================================================================================
# createForcePostOpBendInPlaneAngle is called by AmoebaOutOfPlaneBendForce with the list of # createForcePostOpBendInPlaneAngle is called by AmoebaOutOfPlaneBendForce with the list of
...@@ -2169,7 +2153,6 @@ class AmoebaAngleGenerator: ...@@ -2169,7 +2153,6 @@ class AmoebaAngleGenerator:
type2 = data.atomType[data.atoms[angle[1]]] type2 = data.atomType[data.atoms[angle[1]]]
type3 = data.atomType[data.atoms[angle[2]]] type3 = data.atomType[data.atoms[angle[2]]]
hit = 0
for i in range(len(self.types1)): for i in range(len(self.types1)):
types1 = self.types1[i] types1 = self.types1[i]
...@@ -2177,7 +2160,6 @@ class AmoebaAngleGenerator: ...@@ -2177,7 +2160,6 @@ class AmoebaAngleGenerator:
types3 = self.types3[i] types3 = self.types3[i]
if (type1 in types1 and type2 in types2 and type3 in types3) or (type1 in types3 and type2 in types2 and type3 in types1): if (type1 in types1 and type2 in types2 and type3 in types3) or (type1 in types3 and type2 in types2 and type3 in types1):
hit = 1
angleDict['idealAngle'] = self.angle[i][0] angleDict['idealAngle'] = self.angle[i][0]
if (isConstrained and self.k[i] != 0.0): if (isConstrained and self.k[i] != 0.0):
addAngleConstraint(angle, self.angle[i][0]*math.pi/180.0, data, sys) addAngleConstraint(angle, self.angle[i][0]*math.pi/180.0, data, sys)
...@@ -2185,14 +2167,6 @@ class AmoebaAngleGenerator: ...@@ -2185,14 +2167,6 @@ class AmoebaAngleGenerator:
force.addAngle(angle[0], angle[1], angle[2], angle[3], self.angle[i][0], self.k[i]) force.addAngle(angle[0], angle[1], angle[2], angle[3], self.angle[i][0], self.k[i])
break break
if (hit == 0):
outputString = "AmoebaInPlaneAngleGenerator missing types: [%s %s %s] atoms: " % (type1, type2, type3)
outputString += getAtomPrint( data, angle[0] ) + ' '
outputString += getAtomPrint( data, angle[1] ) + ' '
outputString += getAtomPrint( data, angle[2] )
outputString += " indices: [%6d %6d %6d]" % (angle[0], angle[1], angle[2])
raise ValueError(outputString)
parsers["AmoebaAngleForce"] = AmoebaAngleGenerator.parseElement parsers["AmoebaAngleForce"] = AmoebaAngleGenerator.parseElement
#============================================================================================= #=============================================================================================
...@@ -2562,7 +2536,6 @@ class AmoebaTorsionGenerator: ...@@ -2562,7 +2536,6 @@ class AmoebaTorsionGenerator:
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]]]
hit = 0
for i in range(len(self.types1)): for i in range(len(self.types1)):
types1 = self.types1[i] types1 = self.types1[i]
...@@ -2573,7 +2546,6 @@ class AmoebaTorsionGenerator: ...@@ -2573,7 +2546,6 @@ class AmoebaTorsionGenerator:
# match types in forward or reverse direction # match types in forward or reverse direction
if (type1 in types1 and type2 in types2 and type3 in types3 and type4 in types4) or (type4 in types1 and type3 in types2 and type2 in types3 and type1 in types4): if (type1 in types1 and type2 in types2 and type3 in types3 and type4 in types4) or (type4 in types1 and type3 in types2 and type2 in types3 and type1 in types4):
hit = 1
if self.t1[i][0] != 0: if self.t1[i][0] != 0:
force.addTorsion(torsion[0], torsion[1], torsion[2], torsion[3], 1, self.t1[i][1], self.t1[i][0]) force.addTorsion(torsion[0], torsion[1], torsion[2], torsion[3], 1, self.t1[i][1], self.t1[i][0])
if self.t2[i][0] != 0: if self.t2[i][0] != 0:
...@@ -2582,15 +2554,6 @@ class AmoebaTorsionGenerator: ...@@ -2582,15 +2554,6 @@ class AmoebaTorsionGenerator:
force.addTorsion(torsion[0], torsion[1], torsion[2], torsion[3], 3, self.t3[i][1], self.t3[i][0]) force.addTorsion(torsion[0], torsion[1], torsion[2], torsion[3], 3, self.t3[i][1], self.t3[i][0])
break break
if (hit == 0):
outputString = "AmoebaTorsionGenerator missing type: [%s %s %s %s] atoms: " % (type1, type2, type3, type4)
outputString += getAtomPrint( data, torsion[0] ) + ' '
outputString += getAtomPrint( data, torsion[1] ) + ' '
outputString += getAtomPrint( data, torsion[2] ) + ' '
outputString += getAtomPrint( data, torsion[3] )
outputString += " indices: [%6d %6d %6d %6d]" % (torsion[0], torsion[1], torsion[2], torsion[3])
raise ValueError(outputString)
parsers["AmoebaTorsionForce"] = AmoebaTorsionGenerator.parseElement parsers["AmoebaTorsionForce"] = AmoebaTorsionGenerator.parseElement
#============================================================================================= #=============================================================================================
......
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