def min_ffxml(mol, ofs, ffxml):
"""
Minimize the mol with force field input from FFXML file.
Parameters
----------
mol : OpenEye single-conformer molecule
ofs : OpenEye output filestream
ffxml : string
name of FFXML file
"""
# make copy of the input mol
oe_mol = oechem.OEGraphMol(mol)
try:
# create openforcefield molecule ==> prone to triggering Exception
off_mol = Molecule.from_openeye(oe_mol)
# load in force field
ff = ForceField(ffxml)
# create components for OpenMM system
topology = Topology.from_molecules(molecules=[off_mol])
# create openmm system ==> prone to triggering Exception
#system = ff.create_openmm_system(topology, charge_from_molecules=[off_mol])
system = ff.create_openmm_system(topology)
except Exception as e:
smilabel = oechem.OEGetSDData(oe_mol, "SMILES QCArchive")
print( ' >>> openforcefield failed to create OpenMM system: '
f'{oe_mol.GetTitle()} {smilabel}: {e}')
return
positions = structure.extractPositionsFromOEMol(oe_mol)
# minimize structure with ffxml
newpos, energy = run_openmm(topology, system, positions)
# save geometry, save energy as tag, write mol to file
oe_mol.SetCoords(oechem.OEFloatArray(newpos))
oechem.OESetSDData(oe_mol, "Energy FFXML", str(energy))
oechem.OEWriteConstMolecule(ofs, oe_mol)
return
def test_merge_system():
"""Test merging of a system created from AMBER and another created from SMIRNOFF."""
from .utils import create_system_from_amber, get_amber_file_path, get_alkethoh_file_path
# Create System from AMBER
prmtop_filename, inpcrd_filename = get_amber_file_path(
'cyclohexane_ethanol_0.4_0.6')
system0, topology0, positions0 = create_system_from_amber(
prmtop_filename, inpcrd_filename)
# TODO:
from openeye import oechem
# Load simple OEMol
alkethoh_mol2_filepath = get_alkethoh_file_path('AlkEthOH_c100')[0]
ifs = oechem.oemolistream(alkethoh_mol2_filepath)
mol = oechem.OEMol()
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)
# Load forcefield file.
AlkEthOH_offxml_filename = utils.get_data_file_path(
'test_forcefields/Frosst_AlkEthOH.offxml')
forcefield = ForceField(AlkEthOH_offxml_filename)
# Create OpenMM System and Topology.
off_mol = Molecule.from_openeye(mol, allow_undefined_stereo=True)
off_top = Topology.from_molecules([off_mol])
system1 = forcefield.create_openmm_system(off_top)
topology1 = structure.generateTopologyFromOEMol(mol)
positions1 = structure.extractPositionsFromOEMol(mol)
structure.merge_system(topology0,
topology1,
system0,
system1,
positions0,
positions1,
verbose=True)
def test_positions(self):
"""Test ability to extract and set positions."""
molecules = structure.read_molecules('zinc-subset-tripos.mol2.gz',
verbose=False)
positions = structure.extractPositionsFromOEMol(molecules[0])
structure.setPositionsInOEMol(molecules[0], positions)