def compute_hydration_energy(molecule, parameters, platform_name="Reference"):
"""
Compute hydration energy of a specified molecule given the specified GBVI parameter set.
ARGUMENTS
molecule (OEMol) - molecule with GBVI atom types
parameters (dict) - parameters for GBVI atom types
RETURNS
energy (float) - hydration energy in kcal/mol
"""
platform = openmm.Platform.getPlatformByName(platform_name)
# Create OpenMM System.
system = openmm.System()
for atom in molecule.GetAtoms():
mass = OEGetDefaultMass(atom.GetAtomicNum())
system.addParticle(mass * units.amu)
# Add GBVI term
# gbvi_force = openmm.GBVISoftcoreForce()
gbvi_force = openmm.GBVIForce()
gbvi_force.setNonbondedMethod(openmm.GBVIForce.NoCutoff) # set no cutoff
gbvi_force.setSoluteDielectric(1)
gbvi_force.setSolventDielectric(78)
# Use scaling method.
# gbvi_force.setBornRadiusScalingMethod(openmm.GBVISoftcoreForce.QuinticSpline)
# gbvi_force.setQuinticLowerLimitFactor(0.75)
# gbvi_force.setQuinticUpperBornRadiusLimit(50.0*units.nanometers)
# Build indexable list of atoms.
atoms = [atom for atom in molecule.GetAtoms()]
# Assign GB/VI parameters.
for atom in molecule.GetAtoms():
atomtype = atom.GetStringData("gbvi_type") # GBVI atomtype
charge = atom.GetPartialCharge() * units.elementary_charge
try:
radius = parameters['%s_%s' %
(atomtype, 'radius')] * units.angstroms
gamma = parameters['%s_%s' %
(atomtype,
'gamma')] * units.kilocalories_per_mole
except Exception, exception:
print "Cannot find parameters for atomtype '%s' in molecule '%s'" % (
atomtype, molecule.GetTitle())
print parameters.keys()
raise exception
# gamma *= -1.0 # DEBUG
lambda_ = 1.0 # fully interacting
# gbvi_force.addParticle(charge, radius, gamma, lambda_) # for GBVISoftcoreForce
gbvi_force.addParticle(charge, radius, gamma) # for GBVIForce
def hydration_energy_factory_cachesystem(molecule, default_parameters):
"""
A faster version of hydration_energy_factory that caches the system and coordinates.
"""
# Create OpenMM System.
system = openmm.System()
for atom in molecule.GetAtoms():
mass = OEGetDefaultMass(atom.GetAtomicNum())
system.addParticle(mass * units.amu)
# Add GBVI term
# gbvi_force = openmm.GBVISoftcoreForce()
gbvi_force = openmm.GBVIForce()
gbvi_force.setNonbondedMethod(openmm.GBVIForce.NoCutoff) # set no cutoff
gbvi_force.setSoluteDielectric(1)
gbvi_force.setSolventDielectric(78)
# Use scaling method.
# gbvi_force.setBornRadiusScalingMethod(openmm.GBVISoftcoreForce.QuinticSpline)
# gbvi_force.setQuinticLowerLimitFactor(0.75)
# gbvi_force.setQuinticUpperBornRadiusLimit(50.0*units.nanometers)
# Build indexable list of atoms.
atoms = [atom for atom in molecule.GetAtoms()]
# Assign GB/VI parameters.
for atom in molecule.GetAtoms():
atomtype = atom.GetStringData("gbvi_type") # GBVI atomtype
charge = atom.GetPartialCharge() * units.elementary_charge
try:
radius = parameters['%s_%s' %
(atomtype, 'radius')] * units.angstroms
gamma = parameters['%s_%s' %
(atomtype,
'gamma')] * units.kilocalories_per_mole
except Exception, exception:
print "Cannot find parameters for atomtype '%s' in molecule '%s'" % (
atomtype, molecule.GetTitle())
print parameters.keys()
raise exception
# gamma *= -1.0 # DEBUG
lambda_ = 1.0 # fully interacting
# gbvi_force.addParticle(charge, radius, gamma, lambda_) # for GBVISoftcoreForce
gbvi_force.addParticle(charge, radius, gamma) # for GBVIForce
def compute_hydration_energies(molecules, parameters):
"""
Compute solvation energies of all specified molecules using given parameter set.
ARGUMENTS
molecules (list of OEMol) - molecules with atom types
parameters (dict) - parameters for atom types
RETURNS
energies (dict) - energies[molecule] is the computed solvation energy of given molecule
"""
energies = dict(
) # energies[index] is the computed solvation energy of molecules[index]
platform = openmm.Platform.getPlatformByName("Reference")
for molecule in molecules:
# Create OpenMM System.
system = openmm.System()
for atom in molecule.GetAtoms():
mass = OEGetDefaultMass(atom.GetAtomicNum())
system.addParticle(mass * units.amu)
# Add nonbonded term.
# nonbonded_force = openmm.NonbondedSoftcoreForce()
# nonbonded_force.setNonbondedMethod(openmm.NonbondedForce.NoCutoff)
# for atom in molecule.GetAtoms():
# charge = 0.0 * units.elementary_charge
# sigma = 1.0 * units.angstrom
# epsilon = 0.0 * units.kilocalories_per_mole
# nonbonded_force.addParticle(charge, sigma, epsilon)
# system.addForce(nonbonded_force)
# Add GBVI term
# gbvi_force = openmm.GBVISoftcoreForce()
gbvi_force = openmm.GBVIForce()
gbvi_force.setNonbondedMethod(
openmm.GBVIForce.NoCutoff) # set no cutoff
gbvi_force.setSoluteDielectric(1)
gbvi_force.setSolventDielectric(78)
# Use scaling method.
# gbvi_force.setBornRadiusScalingMethod(openmm.GBVISoftcoreForce.QuinticSpline)
# gbvi_force.setQuinticLowerLimitFactor(0.75)
# gbvi_force.setQuinticUpperBornRadiusLimit(50.0*units.nanometers)
# Build indexable list of atoms.
atoms = [atom for atom in molecule.GetAtoms()]
# Assign GB/VI parameters.
for atom in molecule.GetAtoms():
atomtype = atom.GetStringData("gbvi_type") # GBVI atomtype
charge = atom.GetPartialCharge() * units.elementary_charge
radius = parameters['%s_%s' %
(atomtype, 'radius')] * units.angstroms
gamma = parameters['%s_%s' %
(atomtype,
'gamma')] * units.kilocalories_per_mole
# gamma *= -1.0 # DEBUG
lambda_ = 1.0 # fully interacting
# gbvi_force.addParticle(charge, radius, gamma, lambda_) # for GBVISoftcoreForce
gbvi_force.addParticle(charge, radius, gamma) # for GBVIForce
# Add bonds.
for bond in molecule.GetBonds():
# Get atom indices.
iatom = bond.GetBgnIdx()
jatom = bond.GetEndIdx()
# Get bond length.
(xi, yi, zi) = molecule.GetCoords(atoms[iatom])
(xj, yj, zj) = molecule.GetCoords(atoms[jatom])
distance = math.sqrt((xi - xj)**2 + (yi - yj)**2 +
(zi - zj)**2) * units.angstroms
# Identify bonded atoms to GBVI.
gbvi_force.addBond(iatom, jatom, distance)
# Add the force to the system.
system.addForce(gbvi_force)
# Build coordinate array.
natoms = len(atoms)
coordinates = units.Quantity(numpy.zeros([natoms, 3]), units.angstroms)
for (index, atom) in enumerate(atoms):
(x, y, z) = molecule.GetCoords(atom)
coordinates[index, :] = units.Quantity(numpy.array([x, y, z]),
units.angstroms)
# Create OpenMM Context.
timestep = 1.0 * units.femtosecond # arbitrary
integrator = openmm.VerletIntegrator(timestep)
context = openmm.Context(system, integrator, platform)
# Set the coordinates.
context.setPositions(coordinates)
# Get the energy
state = context.getState(getEnergy=True)
energies[molecule] = state.getPotentialEnergy()
return energies
def __init__(self, molecule):
# Create OpenMM System.
system = openmm.System()
for atom in molecule.GetAtoms():
mass = OEGetDefaultMass(atom.GetAtomicNum())
system.addParticle(mass * units.amu)
# Add GBVI term
# gbvi_force = openmm.GBVISoftcoreForce()
gbvi_force = openmm.GBVIForce()
gbvi_force.setNonbondedMethod(
openmm.GBVIForce.NoCutoff) # set no cutoff
gbvi_force.setSoluteDielectric(1)
gbvi_force.setSolventDielectric(78)
# Use scaling method.
# gbvi_force.setBornRadiusScalingMethod(openmm.GBVISoftcoreForce.QuinticSpline)
# gbvi_force.setQuinticLowerLimitFactor(0.75)
# gbvi_force.setQuinticUpperBornRadiusLimit(50.0*units.nanometers)
# Build indexable list of atoms.
atoms = [atom for atom in molecule.GetAtoms()]
# Assign GB/VI parameters.
for atom in molecule.GetAtoms():
atomtype = atom.GetStringData("gbvi_type") # GBVI atomtype
charge = atom.GetPartialCharge() * units.elementary_charge
radius = parameters['%s_%s' %
(atomtype, 'radius')] * units.angstroms
gamma = parameters['%s_%s' %
(atomtype,
'gamma')] * units.kilocalories_per_mole
# gamma *= -1.0 # DEBUG
lambda_ = 1.0 # fully interacting
# gbvi_force.addParticle(charge, radius, gamma, lambda_) # for GBVISoftcoreForce
gbvi_force.addParticle(charge, radius, gamma) # for GBVIForce
# Add bonds.
for bond in molecule.GetBonds():
# Get atom indices.
iatom = bond.GetBgnIdx()
jatom = bond.GetEndIdx()
# Get bond length.
(xi, yi, zi) = molecule.GetCoords(atoms[iatom])
(xj, yj, zj) = molecule.GetCoords(atoms[jatom])
distance = math.sqrt((xi - xj)**2 + (yi - yj)**2 +
(zi - zj)**2) * units.angstroms
# Identify bonded atoms to GBVI.
gbvi_force.addBond(iatom, jatom, distance)
# Add the force to the system.
system.addForce(gbvi_force)
# Serialize the system.
serializer = openmm.XmlSerializer()
self.serialized_system = serializer.serialize(system)
# Build coordinate array.
natoms = len(atoms)
coordinates = units.Quantity(numpy.zeros([natoms, 3]), units.angstroms)
for (index, atom) in enumerate(atoms):
(x, y, z) = molecule.GetCoords(atom)
coordinates[index, :] = units.Quantity(numpy.array([x, y, z]),
units.angstroms)
self.coordinates = coordinates
return