def calculate_eng(self, oe_mol):
# Extract starting MD data from OEMol
mdData = utils.MDData(oe_mol)
topology = mdData.topology
positions = mdData.positions
structure = mdData.structure
box = mdData.box
# OpenMM system
system = structure.createSystem(nonbondedMethod=eval("app.%s" % self.cube.args.nonbondedMethod),
nonbondedCutoff=self.cube.args.nonbondedCutoff * unit.angstroms,
constraints=eval("app.%s" % self.cube.args.constraints))
# OpenMM Integrator
integrator = openmm.LangevinIntegrator(self.cube.args.temperature * unit.kelvin,
1.0 / unit.picoseconds, 0.002 * unit.picoseconds)
# Set Simulation
simulation = app.Simulation(topology, system, integrator)
# Set Positions
simulation.context.setPositions(positions)
# Set Box dimensions
simulation.context.setPeriodicBoxVectors(box[0], box[1], box[2])
# Collect the OpenMM state energy info
state = simulation.context.getState(getEnergy=True)
# Potential Energy
peng = state.getPotentialEnergy()
return peng
def process(self, mol, port):
try:
# The copy of the dictionary option as local variable
# is necessary to avoid filename collisions due to
# the parallel cube processes
opt = dict(self.opt)
if utils.PackageOEMol.checkTags(mol, ['Structure']):
gd = utils.PackageOEMol.unpack(mol)
opt['outfname'] = '{}-{}'.format(gd['IDTag'],
self.opt['outfname'])
mdData = utils.MDData(mol)
opt['molecule'] = mol
self.log.info('START NPT SIMULATION %s' % gd['IDTag'])
simtools.simulation(mdData, **opt)
packedmol = mdData.packMDData(mol)
self.success.emit(packedmol)
except Exception as e:
# Attach error message to the molecule that failed
self.log.error(traceback.format_exc())
mol.SetData('error', str(e))
# Return failed mol
self.failure.emit(mol)
return
def calculate_VT(self, oe_mol):
# Extract starting MD data from OEMol
mdData = utils.MDData(oe_mol)
structure = mdData.structure
topology = mdData.topology
positions = mdData.positions
velocities = mdData.velocities
box = mdData.box
volume = box[0][0] * box[1][1] * box[2][2]
# OpenMM system
system = structure.createSystem(nonbondedMethod=eval("app.%s" % self.cube.args.nonbondedMethod),
nonbondedCutoff=self.cube.args.nonbondedCutoff * unit.angstroms,
constraints=eval("app.%s" % self.cube.args.constraints))
# OpenMM Integrator
integrator = openmm.LangevinIntegrator(self.cube.args.temperature * unit.kelvin,
1.0 / unit.picoseconds, 0.002 * unit.picoseconds)
# Add Force Barostat to the system
system.addForce(openmm.MonteCarloBarostat(self.cube.args.pressure * unit.atmospheres,
self.cube.args.temperature*unit.kelvin, 25))
# Set Simulation
simulation = app.Simulation(topology, system, integrator)
# Set Positions
simulation.context.setPositions(positions)
# Set Velocities
simulation.context.setVelocities(velocities)
# Set Box dimensions
simulation.context.setPeriodicBoxVectors(box[0], box[1], box[2])
# Collect the OpenMM state energy info
state = simulation.context.getState(getEnergy=True)
# Kinetic Energy
keng = state.getKineticEnergy()
# Calculate system degrees of freedom:
dof = 0
for i in range(system.getNumParticles()):
if system.getParticleMass(i) > 0 * unit.dalton:
dof += 3
dof -= system.getNumConstraints()
if any(type(system.getForce(i)) == openmm.CMMotionRemover for i in range(system.getNumForces())):
dof -= 3
# Calculate the temperature from the equipartition theorem
temperature = ((2*keng)/(dof*unit.MOLAR_GAS_CONSTANT_R))
return volume, temperature
def process(self, mol, port):
try:
# The copy of the dictionary option as local variable
# is necessary to avoid filename collisions due to
# the parallel cube processes
opt = dict(self.opt)
# Update cube simulation parameters with the eventually molecule SD tags
new_args = {
dp.GetTag(): dp.GetValue()
for dp in oechem.OEGetSDDataPairs(mol)
if dp.GetTag() in ["temperature", "pressure"]
}
if new_args:
for k in new_args:
try:
new_args[k] = float(new_args[k])
except:
pass
self.log.info(
"Updating parameters for molecule: {}\n{}".format(
mol.GetTitle(), new_args))
opt.update(new_args)
if utils.PackageOEMol.checkTags(mol, ['Structure']):
gd = utils.PackageOEMol.unpack(mol)
opt['outfname'] = '{}-{}'.format(gd['IDTag'],
self.opt['outfname'])
mdData = utils.MDData(mol)
opt['molecule'] = mol
self.log.info('START NPT SIMULATION %s' % gd['IDTag'])
simtools.simulation(mdData, **opt)
packedmol = mdData.packMDData(mol)
self.success.emit(packedmol)
except Exception as e:
# Attach error message to the molecule that failed
self.log.error(traceback.format_exc())
mol.SetData('error', str(e))
# Return failed mol
self.failure.emit(mol)
return