def convert(self):
# Set OEMol
ifs = oemolistream()
ifs.SetFlavor(OEFormat_MOL2, OEIFlavor_MOL2_Forcefield)
ifs.open(self.mol2_file)
# Read in molecules
for i, mol in enumerate(ifs.GetOEMols()):
if i > 0:
raise Exception(
'Only single residue molecules are currently supported')
OETriposAtomNames(mol)
self.molecules.append(OEMol(mol))
# Set topology
self.mol2_topo = pmd.load_file(self.mol2_file, structure=True)
# Parameterize
ff = ForceField('forcefield/smirnoff99Frosst.offxml')
self.labels = ff.labelMolecules(self.molecules, verbose=False)
self.off_system = ff.createSystem(self.mol2_topo.topology,
self.molecules,
nonbondedCutoff=1.1 * unit.nanometer,
ewaldErrorTolerance=1e-4)
# Load into Parmed
self.pmd_system = pmd.openmm.topsystem.load_topology(
self.mol2_topo.topology, self.off_system, self.mol2_topo.positions)
# Convert to AmberParm
self.parm = pmd.amber.AmberParm.from_structure(self.pmd_system)
# HACKY PART!!
# Amber specifies that the third atom in an improper is the central
# atom, but smirnoff currently specifies the second atom. A check for
# impropers was conducted during pmd.openmm.topsystem.load_topology(),
# but that looked at the third atom, so we'll recheck the second atom.
for i, dihedral in enumerate(cnvs.parm.dihedrals):
a1 = dihedral.atom1
a2 = dihedral.atom2
a3 = dihedral.atom3
a4 = dihedral.atom4
if a1 in a2.bond_partners and a3 in a2.bond_partners and a4 in a2.bond_partners:
(dihedral.atom1, dihedral.atom2, dihedral.atom3,
dihedral.atom4) = (a3, a4, a2, a1)
dihedral.improper = True
# Create unique atom types
unique_types = aimtools.unique_types.create_unique_type_list(self.parm)
# Write AMBER mol2 and frcmod
aimtools.unique_types.write_unique_frcmod_mol2s(
self.parm, unique_types, names=self.output_prefix)
#!/bin/env python
from openforcefield.utils import *
from openforcefield.typing.engines.smirnoff import get_molecule_parameterIDs, ForceField
# Create an oemol
mol = OEMol()
OEParseSmiles(mol, 'CCC')
OEAddExplicitHydrogens(mol)
ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.ffxml'))
labels = ff.labelMolecules([mol], verbose=True)
print labels
for mol_entry in range(len(labels)):
for force in labels[mol_entry].keys():
print("\n%s:" % force)
for (atom_indices, pid, smirks) in labels[mol_entry][force]:
atomstr = ''
for idx in atom_indices:
atomstr += '%6s' % idx
print("%s : %s \t smirks %s" % (atomstr, pid, smirks))
#forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml'))
forcefield = ForceField(
get_data_filename('forcefield/smirnoff99Frosst.offxml'))
# Load molecule using OpenEye tools
mol = oechem.OEGraphMol()
ifs = oechem.oemolistream(mol_filename)
# LPW: I don't understand the meaning of these lines.
# flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield
# ifs.SetFlavor( oechem.OEFormat_MOL2, flavor)
oechem.OEReadMolecule(ifs, mol)
oechem.OETriposAtomNames(mol)
pdbatoms = list(pdb.topology.atoms())
labels = forcefield.labelMolecules([mol])[0]
for key, val in labels.items():
print(key)
for v in val:
anames = '-'.join([pdbatoms[i].name for i in v[0]])
anums = '-'.join([str(i) for i in v[0]])
print("%20s %20s %5s %-s" % (anames, anums, v[1], v[2]))
# The rest of this is not needed.
sys.exit()
# Create the OpenMM system
system = forcefield.createSystem(pdb.topology, [mol],
nonbondedMethod=PME,
nonbondedCutoff=1.0 * unit.nanometers,
rigidWater=True)
def get_molecule_parameterIDs(oemols, ffxml):
"""Process a list of oemols with a specified SMIRNOFF ffxml file and determine which parameters are used by which molecules, returning collated results.
Parameters
----------
oemols : list
List of OpenEye OEChem molecules to parse; must have explicit hydrogens.
Returns
-------
parameters_by_molecule : dict
Parameter IDs used in each molecule, keyed by isomeric SMILES
generated from provided OEMols. Each entry in the dict is a list
which does not necessarily have unique entries; i.e. parameter IDs
which are used more than once will occur multiple times.
parameters_by_ID : dict
Molecules in which each parameter ID occur, keyed by parameter ID.
Each entry in the dict is a set of isomeric SMILES for molecules
in which that parameter occurs. No frequency information is stored.
"""
# Create storage
parameters_by_molecule = {}
parameters_by_ID = {}
# Generate isomeric SMILES
isosmiles = list()
for mol in oemols:
smi = oechem.OECreateIsoSmiString(mol)
if not smi in isosmiles:
isosmiles.append(smi)
# If the molecule is already here, raise exception
else:
raise ValueError(
"Error: get_molecule_parameterIDs has been provided a list of oemols which contains the same molecule, having isomeric smiles %s, more than once."
% smi)
# Label molecules
ff = ForceField(ffxml)
labels = ff.labelMolecules(oemols)
# Organize labels into output dictionary by looping over all molecules/smiles
for idx in range(len(isosmiles)):
# Pull smiles, initialize storage
smi = isosmiles[idx]
parameters_by_molecule[smi] = []
# Organize data for this molecule
data = labels[idx]
for force_type in data.keys():
for (atom_indices, pid, smirks) in data[force_type]:
# Store pid to molecule
parameters_by_molecule[smi].append(pid)
# Store which molecule this pid occurred in
if pid not in parameters_by_ID:
parameters_by_ID[pid] = set()
parameters_by_ID[pid].add(smi)
else:
parameters_by_ID[pid].add(smi)
return parameters_by_molecule, parameters_by_ID
# Load a SMIRNOFF forcefield
#forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml'))
forcefield = ForceField(get_data_filename('forcefield/smirnoff99Frosst.offxml'))
# Load molecule using OpenEye tools
mol = oechem.OEGraphMol()
ifs = oechem.oemolistream(mol_filename)
# LPW: I don't understand the meaning of these lines.
# flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield
# ifs.SetFlavor( oechem.OEFormat_MOL2, flavor)
oechem.OEReadMolecule(ifs, mol)
oechem.OETriposAtomNames(mol)
pdbatoms = list(pdb.topology.atoms())
labels = forcefield.labelMolecules([mol])[0]
for key, val in labels.items():
print(key)
for v in val:
anames = '-'.join([pdbatoms[i].name for i in v[0]])
anums = '-'.join([str(i) for i in v[0]])
print("%20s %20s %5s %-s" % (anames, anums, v[1], v[2]))
# The rest of this is not needed.
sys.exit()
# Create the OpenMM system
system = forcefield.createSystem(pdb.topology, [mol], nonbondedMethod=PME, nonbondedCutoff=1.0*unit.nanometers, rigidWater=True)
# Set up an OpenMM simulation
integrator = openmm.LangevinIntegrator(temperature, friction, time_step)
