def test_from_rdkit():
"""
Make sure we can create a molecule directly from an rdkit object.
"""
# load a molecule with openff
offmol = OFFMolecule.from_file(file_path=get_data("bace0.sdf"))
# make a ligand from the openff object
mol = Ligand.from_rdkit(rdkit_mol=offmol.to_rdkit())
# make sure we have the same molecule
mol2 = Ligand.from_file(get_data("bace0.sdf"))
for i in range(mol.n_atoms):
atom1 = mol.atoms[i]
atom2 = mol2.atoms[i]
assert atom1.dict() == atom2.dict()
for i in range(mol.n_bonds):
bond1 = mol.bonds[i]
bon2 = mol2.bonds[i]
assert bond1.dict() == bon2.dict()
assert np.allclose(mol.coordinates, mol2.coordinates)
def create_force(self, system, topology, **kwargs):
"""over write the force creation to use qubekit"""
# Get the OpenMM Nonbonded force or add if missing
existing = [system.getForce(i) for i in range(system.getNumForces())]
existing = [f for f in existing if type(f) == self._OPENMMTYPE]
# if not present make one and add the particles
if len(existing) == 0:
force = self._OPENMMTYPE()
system.addForce(force)
# add all atom particles, Vsites are added later
for _ in topology.topology_atoms:
force.addParticle(0.0, 1.0, 0.0)
else:
force = existing[0]
# If we're using PME, then the only possible openMM Nonbonded type is LJPME
if self.method == "PME":
# If we're given a nonperiodic box, we always set NoCutoff. Later we'll add support for CutoffNonPeriodic
if topology.box_vectors is None:
force.setNonbondedMethod(openmm.NonbondedForce.NoCutoff)
# if (topology.box_vectors is None):
# raise SMIRNOFFSpecError("If vdW method is PME, a periodic Topology "
# "must be provided")
else:
force.setNonbondedMethod(openmm.NonbondedForce.LJPME)
force.setCutoffDistance(self.cutoff)
force.setEwaldErrorTolerance(1.0e-4)
# If method is cutoff, then we currently support openMM's PME for periodic system and NoCutoff for nonperiodic
elif self.method == "cutoff":
# If we're given a nonperiodic box, we always set NoCutoff. Later we'll add support for CutoffNonPeriodic
if topology.box_vectors is None:
force.setNonbondedMethod(openmm.NonbondedForce.NoCutoff)
else:
force.setNonbondedMethod(openmm.NonbondedForce.PME)
force.setUseDispersionCorrection(True)
force.setCutoffDistance(self.cutoff)
lj = LennardJones612(
free_parameters={
"H": h_base(r_free=self.hfree.value_in_unit(unit.angstroms)),
"C": c_base(r_free=self.cfree.value_in_unit(unit.angstroms)),
"X": h_base(r_free=self.xfree.value_in_unit(unit.angstroms)),
"O": o_base(r_free=self.ofree.value_in_unit(unit.angstroms)),
"N": n_base(r_free=self.nfree.value_in_unit(unit.angstroms)),
"Cl": cl_base(r_free=self.clfree.value_in_unit(unit.angstroms)),
"S": s_base(r_free=self.sfree.value_in_unit(unit.angstroms)),
"F": f_base(r_free=self.ffree.value_in_unit(unit.angstroms)),
"Br": br_base(r_free=self.brfree.value_in_unit(unit.angstroms)),
"I": i_base(r_free=self.ifree.value_in_unit(unit.angstroms)),
"P": p_base(r_free=self.ifree.value_in_unit(unit.angstroms)),
"B": b_base(r_free=self.bfree.value_in_unit(unit.angstroms)),
"Si": si_base(r_free=self.sifree.value_in_unit(unit.angstroms)),
},
alpha=self.alpha,
beta=self.beta,
)
water = Molecule.from_smiles("O")
for ref_mol in topology.reference_molecules:
# skip any waters
if ref_mol == water:
continue
# if the molecule has no conformer generate one
if ref_mol.n_conformers == 0:
ref_mol.generate_conformers(n_conformers=1)
qb_mol = Ligand.from_rdkit(ref_mol.to_rdkit())
for parameter in self.parameters:
matches = ref_mol.chemical_environment_matches(
parameter.smirks, unique=False
)
for match in matches:
qb_mol.atoms[match[0]].aim.volume = parameter.volume.value_in_unit(
unit.angstroms**3
)
# make sure all atoms in the molecule have volumes, assign dummy values
for i in range(qb_mol.n_atoms):
atom = qb_mol.atoms[i]
assert atom.aim.volume is not None
qb_mol.NonbondedForce.create_parameter(
atoms=(i,), charge=0, sigma=0, epsilon=0
)
# calculate the nonbonded terms
lj.run(qb_mol)
# assign to all copies in the system
for topology_molecule in topology._reference_molecule_to_topology_molecules[
ref_mol
]:
for topology_particle in topology_molecule.atoms:
if type(topology_particle) is TopologyAtom:
ref_mol_particle_index = (
topology_particle.atom.molecule_particle_index
)
elif type(topology_particle) is TopologyVirtualSite:
ref_mol_particle_index = (
topology_particle.virtual_site.molecule_particle_index
)
else:
raise ValueError(
f"Particles of type {type(topology_particle)} are not supported"
)
topology_particle_index = topology_particle.topology_particle_index
particle_parameters = qb_mol.NonbondedForce[
(ref_mol_particle_index,)
]
# Set the nonbonded force parameters
force.setParticleParameters(
topology_particle_index,
particle_parameters.charge, # this is a dummy charge which needs to be corrected
particle_parameters.sigma,
particle_parameters.epsilon,
)
