def test_generateResidueTemplate():
"""
Test GAFF residue template generation from OEMol molecules.
"""
from openeye import oechem, oeiupac
from pkg_resources import resource_filename
gaff_xml_filename = utils.get_data_filename("parameters/gaff.xml")
# Test independent ForceField instances.
for molecule_name in IUPAC_molecule_names:
mol = createOEMolFromIUPAC(molecule_name)
# Generate an ffxml residue template.
from openmoltools.forcefield_generators import generateResidueTemplate
[template, ffxml] = generateResidueTemplate(mol)
# Create a ForceField object.
forcefield = ForceField(gaff_xml_filename)
# Add the additional parameters and template to the forcefield.
forcefield.registerResidueTemplate(template)
forcefield.loadFile(StringIO(ffxml))
# Create a Topology from the molecule.
from openmoltools.forcefield_generators import generateTopologyFromOEMol
topology = generateTopologyFromOEMol(mol)
# Parameterize system.
system = forcefield.createSystem(topology, nonbondedMethod=NoCutoff)
# Check potential is finite.
positions = extractPositionsFromOEMOL(mol)
check_potential_is_finite(system, positions)
# Test adding multiple molecules to a single ForceField instance.
forcefield = ForceField(gaff_xml_filename)
for molecule_name in IUPAC_molecule_names:
mol = createOEMolFromIUPAC(molecule_name)
# Generate an ffxml residue template.
from openmoltools.forcefield_generators import generateResidueTemplate
[template, ffxml] = generateResidueTemplate(mol)
# Add the additional parameters and template to the forcefield.
forcefield.registerResidueTemplate(template)
forcefield.loadFile(StringIO(ffxml))
# Create a Topology from the molecule.
from openmoltools.forcefield_generators import generateTopologyFromOEMol
topology = generateTopologyFromOEMol(mol)
# Parameterize system.
system = forcefield.createSystem(topology, nonbondedMethod=NoCutoff)
# Check potential is finite.
positions = extractPositionsFromOEMOL(mol)
check_potential_is_finite(system, positions)
def test_generateResidueTemplate():
"""
Test GAFF residue template generation from OEMol molecules.
"""
from openeye import oechem, oeiupac
from pkg_resources import resource_filename
gaff_xml_filename = utils.get_data_filename("parameters/gaff.xml")
# Test independent ForceField instances.
for molecule_name in IUPAC_molecule_names:
mol = createOEMolFromIUPAC(molecule_name)
# Generate an ffxml residue template.
from openmoltools.forcefield_generators import generateResidueTemplate
[template, ffxml] = generateResidueTemplate(mol)
# Create a ForceField object.
forcefield = ForceField(gaff_xml_filename)
# Add the additional parameters and template to the forcefield.
forcefield.registerResidueTemplate(template)
forcefield.loadFile(StringIO(ffxml))
# Create a Topology from the molecule.
from openmoltools.forcefield_generators import generateTopologyFromOEMol
topology = generateTopologyFromOEMol(mol)
# Parameterize system.
system = forcefield.createSystem(topology, nonbondedMethod=NoCutoff)
# Check potential is finite.
positions = extractPositionsFromOEMOL(mol)
check_potential_is_finite(system, positions)
# Test adding multiple molecules to a single ForceField instance.
forcefield = ForceField(gaff_xml_filename)
for molecule_name in IUPAC_molecule_names:
mol = createOEMolFromIUPAC(molecule_name)
# Generate an ffxml residue template.
from openmoltools.forcefield_generators import generateResidueTemplate
[template, ffxml] = generateResidueTemplate(mol)
# Add the additional parameters and template to the forcefield.
forcefield.registerResidueTemplate(template)
forcefield.loadFile(StringIO(ffxml))
# Create a Topology from the molecule.
from openmoltools.forcefield_generators import generateTopologyFromOEMol
topology = generateTopologyFromOEMol(mol)
# Parameterize system.
system = forcefield.createSystem(topology, nonbondedMethod=NoCutoff)
# Check potential is finite.
positions = extractPositionsFromOEMOL(mol)
check_potential_is_finite(system, positions)
def createSystemFromIUPAC(iupac_name):
"""
Create an openmm system out of an oemol
Parameters
----------
iupac_name : str
IUPAC name
Returns
-------
molecule : openeye.OEMol
OEMol molecule
system : openmm.System object
OpenMM system
positions : [n,3] np.array of floats
Positions
topology : openmm.app.Topology object
Topology
"""
from perses.utils.data import get_data_filename
from perses.utils.openeye import extractPositionsFromOEMol
# Create OEMol
molecule = iupac_to_oemol(iupac_name)
# Generate a topology.
from openmoltools.forcefield_generators import generateTopologyFromOEMol
topology = generateTopologyFromOEMol(molecule)
# Initialize a forcefield with GAFF.
# TODO: Fix path for `gaff.xml` since it is not yet distributed with OpenMM
from simtk.openmm.app import ForceField
gaff_xml_filename = get_data_filename('data/gaff.xml')
forcefield = ForceField(gaff_xml_filename)
# Generate template and parameters.
from openmoltools.forcefield_generators import generateResidueTemplate
[template, ffxml] = generateResidueTemplate(molecule)
# Register the template.
forcefield.registerResidueTemplate(template)
# Add the parameters.
forcefield.loadFile(StringIO(ffxml))
# Create the system.
system = forcefield.createSystem(topology, removeCMMotion=False)
# Extract positions
positions = extractPositionsFromOEMol(molecule)
return (molecule, system, positions, topology)
def createSystemFromIUPAC(iupac_name):
"""
Create an openmm system out of an oemol
Parameters
----------
iupac_name : str
IUPAC name
Returns
-------
molecule : openeye.OEMol
OEMol molecule
system : openmm.System object
OpenMM system
positions : [n,3] np.array of floats
Positions
topology : openmm.app.Topology object
Topology
"""
# Create OEMol
molecule = createOEMolFromIUPAC(iupac_name)
# Generate a topology.
from openmoltools.forcefield_generators import generateTopologyFromOEMol
topology = generateTopologyFromOEMol(molecule)
# Initialize a forcefield with GAFF.
# TODO: Fix path for `gaff.xml` since it is not yet distributed with OpenMM
from simtk.openmm.app import ForceField
gaff_xml_filename = get_data_filename('data/gaff.xml')
forcefield = ForceField(gaff_xml_filename)
# Generate template and parameters.
from openmoltools.forcefield_generators import generateResidueTemplate
[template, ffxml] = generateResidueTemplate(molecule)
# Register the template.
forcefield.registerResidueTemplate(template)
# Add the parameters.
forcefield.loadFile(StringIO(ffxml))
# Create the system.
system = forcefield.createSystem(topology)
# Extract positions
positions = extractPositionsFromOEMOL(molecule)
return (molecule, system, positions, topology)