def deepCopyForce(self, ff):
p = ff.params
if (ff.charmm):
ff2 = self.forces.makeForceField(self.phys, "charmm")
else:
ff2 = self.forces.makeForceField(self.phys)
for ii in ff.forcetypes:
ff2.forcetypes.append(ii)
ff2.params = p
ff2.build()
#self.forces.removeForceField(ff)
import ForceGroup
ForceGroup._swig_setattr_nondynamic(ff2, ForceGroup.ForceGroup, "thisown", 0)
return ff2
def deepCopyForce(self, ff):
p = ff.params
if ff.charmm:
ff2 = self.forces.makeForceField(self.phys, "charmm")
else:
ff2 = self.forces.makeForceField(self.phys)
for ii in ff.forcetypes:
ff2.forcetypes.append(ii)
ff2.params = p
ff2.build()
# self.forces.removeForceField(ff)
import ForceGroup
ForceGroup._swig_setattr_nondynamic(ff2, ForceGroup.ForceGroup, "thisown", 0)
return ff2
def build(self):
"""
Using an MDL force factory, instantiate all force objects stored in the forcetypes data member of each force field. These will be SWIG-wrapped objects and are appended to the forcearray data member of each force field.
"""
# TMC 1-13-08: I think this can be improved. Future:
# 1. Have a build() member of the ForceField class.
# 2. Make the ForceFactory a singleton.
# 3. Give the ForceFactory a method which maps force characters to creation functions. In this way there are multiple mapping levels.
self.forceFactory.hd = 0
if (self.params['LennardJones'] !=
self.params['Coulomb']):
self.breakLennardJonesCoulombForce()
self.dirty = 0
self.forcearray = []
bornflag=-1
for forcetype in self.forcetypes:
if (forcetype == 'b'):
self.forcearray.append(self.forceFactory.createBondForce(self.bc))
elif (forcetype == 'a'):
self.forcearray.append(self.forceFactory.createAngleForce(self.bc))
elif (forcetype == 'd'):
self.forcearray.append(self.forceFactory.createDihedralForce(self.bc))
elif (forcetype == 'i'):
self.forcearray.append(self.forceFactory.createImproperForce(self.bc))
elif (forcetype == 'l'):
self.forcearray.append(self.forceFactory.createLennardJonesForce(self.bc, self.params['LennardJones']))
elif (forcetype == 'c'):
if (self.params['Coulomb']['algorithm'] == 'SCPISM'):
self.phys.myTop.doSCPISM = 1
self.phys.build()
#if (not self.params['Coulomb'].has_key('NoBorn')):
# print "CREATING BORN FORCE"
# self.forcearray.append(self.forceFactory.createBornForce(self.bc, self.params['Coulomb']))
# bornflag = len(self.forcearray)-1
#else:
# print "NOT CREATING BORN FORCE"
if (self.params['Coulomb']['algorithm'] == 'GB' or
self.params['Coulomb']['algorithm'] == 'GBACE'):
self.forcearray.append(self.forceFactory.createBornBurial())
self.addForce(self.forcearray[len(self.forcearray)-1])
self.forcearray.append(self.forceFactory.createBornRadii())
self.addForce(self.forcearray[len(self.forcearray)-1])
if (not self.params['Coulomb'].has_key('OnlyBorn')):
self.forcearray.append(self.forceFactory.createCoulombForce(self.bc, self.params['Coulomb']))
elif (forcetype == 'e'):
self.forcearray.append(self.forceFactory.createCoulombDiElecForce(self.bc, self.params['CoulombDiElec']))
elif (forcetype == 'lc'):
self.forcearray.append(self.forceFactory.createLennardJonesCoulombForce(self.bc, self.params['LennardJonesCoulomb']))
elif (forcetype == 'h'):
self.forcearray.append(self.forceFactory.createHarmDihedralForce(self.bc, self.params['HarmonicDihedral']))
self.addForce(self.forcearray[len(self.forcearray)-1])
import ForceGroup
ForceGroup._swig_setattr_nondynamic(self.forcearray[len(self.forcearray)-1], ForceGroup.Force, "thisown", 0)
if (bornflag != -1): self.forcetypes.insert(bornflag, 'c')
for pyforce in self.pythonforces:
self.forcearray.append(PySystemForce.PySystemForce(pyforce))
PySystemForce._swig_setattr_nondynamic(self.forcearray[len(self.forcearray)-1], PySystemForce.PySystemForce, "thisown", 0)
self.addSystemForce(self.forcearray[len(self.forcearray)-1])
def build(self):
"""
Using an MDL force factory, instantiate all force objects stored in the forcetypes data member of each force field. These will be SWIG-wrapped objects and are appended to the forcearray data member of each force field.
"""
# TMC 1-13-08: I think this can be improved. Future:
# 1. Have a build() member of the ForceField class.
# 2. Make the ForceFactory a singleton.
# 3. Give the ForceFactory a method which maps force characters to creation functions. In this way there are multiple mapping levels.
self.forceFactory.hd = 0
if (self.params['LennardJones'] != self.params['Coulomb']):
self.breakLennardJonesCoulombForce()
self.dirty = 0
self.forcearray = []
bornflag = -1
for forcetype in self.forcetypes:
if (forcetype == 'b'):
self.forcearray.append(
self.forceFactory.createBondForce(self.bc))
elif (forcetype == 'a'):
self.forcearray.append(
self.forceFactory.createAngleForce(self.bc))
elif (forcetype == 'd'):
self.forcearray.append(
self.forceFactory.createDihedralForce(self.bc))
elif (forcetype == 'i'):
self.forcearray.append(
self.forceFactory.createImproperForce(self.bc))
elif (forcetype == 'l'):
self.forcearray.append(
self.forceFactory.createLennardJonesForce(
self.bc, self.params['LennardJones']))
elif (forcetype == 'c'):
if (self.params['Coulomb']['algorithm'] == 'SCPISM'):
self.phys.myTop.doSCPISM = 1
self.phys.build()
#if (not self.params['Coulomb'].has_key('NoBorn')):
# print "CREATING BORN FORCE"
# self.forcearray.append(self.forceFactory.createBornForce(self.bc, self.params['Coulomb']))
# bornflag = len(self.forcearray)-1
#else:
# print "NOT CREATING BORN FORCE"
if (self.params['Coulomb']['algorithm'] == 'GB'
or self.params['Coulomb']['algorithm'] == 'GBACE'):
self.forcearray.append(
self.forceFactory.createBornBurial())
self.addForce(self.forcearray[len(self.forcearray) - 1])
self.forcearray.append(self.forceFactory.createBornRadii())
self.addForce(self.forcearray[len(self.forcearray) - 1])
if (not self.params['Coulomb'].has_key('OnlyBorn')):
self.forcearray.append(
self.forceFactory.createCoulombForce(
self.bc, self.params['Coulomb']))
elif (forcetype == 'e'):
self.forcearray.append(
self.forceFactory.createCoulombDiElecForce(
self.bc, self.params['CoulombDiElec']))
elif (forcetype == 'lc'):
self.forcearray.append(
self.forceFactory.createLennardJonesCoulombForce(
self.bc, self.params['LennardJonesCoulomb']))
elif (forcetype == 'h'):
self.forcearray.append(
self.forceFactory.createHarmDihedralForce(
self.bc, self.params['HarmonicDihedral']))
self.addForce(self.forcearray[len(self.forcearray) - 1])
import ForceGroup
ForceGroup._swig_setattr_nondynamic(
self.forcearray[len(self.forcearray) - 1], ForceGroup.Force,
"thisown", 0)
if (bornflag != -1): self.forcetypes.insert(bornflag, 'c')
for pyforce in self.pythonforces:
self.forcearray.append(PySystemForce.PySystemForce(pyforce))
PySystemForce._swig_setattr_nondynamic(
self.forcearray[len(self.forcearray) - 1],
PySystemForce.PySystemForce, "thisown", 0)
self.addSystemForce(self.forcearray[len(self.forcearray) - 1])
