def test_generate_ffxml_from_molecules():
"""
Test generation of single ffxml file from a list of molecules
"""
# Create a test set of molecules.
molecules = [createOEMolFromIUPAC(name) for name in IUPAC_molecule_names]
# Create an ffxml file.
from openmoltools.forcefield_generators import generateForceFieldFromMolecules
ffxml = generateForceFieldFromMolecules(molecules)
# Create a ForceField.
gaff_xml_filename = utils.get_data_filename("parameters/gaff.xml")
forcefield = ForceField(gaff_xml_filename)
try:
forcefield.loadFile(StringIO(ffxml))
except Exception as e:
msg = str(e)
msg += "ffxml contents:\n"
for (index, line) in enumerate(ffxml.split('\n')):
msg += 'line %8d : %s\n' % (index, line)
raise Exception(msg)
# Parameterize the molecules.
from openmoltools.forcefield_generators import generateTopologyFromOEMol
for molecule in molecules:
# Create topology from molecule.
topology = generateTopologyFromOEMol(molecule)
# Create system with forcefield.
system = forcefield.createSystem(topology)
# Check potential is finite.
positions = extractPositionsFromOEMOL(molecule)
check_potential_is_finite(system, positions)
def test_generate_ffxml_from_molecules():
"""
Test generation of single ffxml file from a list of molecules
"""
# Create a test set of molecules.
molecules = [createOEMolFromIUPAC(name) for name in IUPAC_molecule_names]
# Create an ffxml file.
from openmoltools.forcefield_generators import generateForceFieldFromMolecules
ffxml = generateForceFieldFromMolecules(molecules)
# Create a ForceField.
gaff_xml_filename = utils.get_data_filename("parameters/gaff.xml")
forcefield = ForceField(gaff_xml_filename)
try:
forcefield.loadFile(StringIO(ffxml))
except Exception as e:
msg = str(e)
msg += "ffxml contents:\n"
for (index, line) in enumerate(ffxml.split("\n")):
msg += "line %8d : %s\n" % (index, line)
raise Exception(msg)
# Parameterize the molecules.
from openmoltools.forcefield_generators import generateTopologyFromOEMol
for molecule in molecules:
# Create topology from molecule.
topology = generateTopologyFromOEMol(molecule)
# Create system with forcefield.
system = forcefield.createSystem(topology)
# Check potential is finite.
positions = extractPositionsFromOEMOL(molecule)
check_potential_is_finite(system, positions)
def test_debug_ffxml(self):
"""Test that debug ffxml file is created when requested"""
with tempfile.TemporaryDirectory() as tmpdirname:
debug_ffxml_filename = os.path.join(tmpdirname, 'molecule.ffxml')
cache = os.path.join(tmpdirname, 'db.json')
# Create a generator that only knows about one molecule
molecule = self.molecules[0]
generator = self.TEMPLATE_GENERATOR(molecules=molecule, cache=cache)
# Create a ForceField
from simtk.openmm.app import ForceField
forcefield = ForceField()
# Register the template generator
forcefield.registerTemplateGenerator(generator.generator)
# Ensure no file is created
from simtk.openmm.app import NoCutoff
openmm_topology = molecule.to_topology().to_openmm()
system = forcefield.createSystem(openmm_topology, nonbondedMethod=NoCutoff)
assert not os.path.exists(debug_ffxml_filename)
# Enable debug file output creation
forcefield = ForceField()
forcefield.registerTemplateGenerator(generator.generator)
generator.debug_ffxml_filename = debug_ffxml_filename
# Ensure that an ffxml file is created
system = forcefield.createSystem(openmm_topology, nonbondedMethod=NoCutoff)
assert os.path.exists(debug_ffxml_filename)
# Ensure we can use that file to create a new force field
forcefield_from_ffxml = ForceField()
if hasattr(generator, 'gaff_xml_filename'):
forcefield_from_ffxml.loadFile(generator.gaff_xml_filename)
forcefield_from_ffxml.loadFile(debug_ffxml_filename)
system2 = forcefield_from_ffxml.createSystem(openmm_topology, nonbondedMethod=NoCutoff)
# TODO: Test that systems are equivalent
assert system.getNumParticles() == system2.getNumParticles()
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)
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)
