def test_rb_energy_round_trip(tmpdir):
"""
Make sure that no parameters are lost when reading in RBterms.
"""
with tmpdir.as_cwd():
# load the molecule and parameterise
mol = Ligand.from_file(file_name=get_data("cyclohexane.sdf"))
XML().run(molecule=mol, input_files=[get_data("cyclohexane.xml")])
# load the serialised system we extract the parameters from as our reference
ref_system = XmlSerializer.deserializeSystem(
open("serialised.xml").read())
parm_top = load_topology(mol.to_openmm_topology(),
system=ref_system,
xyz=mol.openmm_coordinates())
ref_energy = energy_decomposition_system(parm_top,
ref_system,
platform="Reference")
# now we need to build the system from our stored parameters
mol.write_parameters(file_name="test.xml")
ff = app.ForceField("test.xml")
qube_system = ff.createSystem(mol.to_openmm_topology())
with open("qube.xml", "w") as xml_out:
xml_out.write(XmlSerializer.serialize(qube_system))
qube_struc = load_topology(mol.to_openmm_topology(),
system=qube_system,
xyz=mol.openmm_coordinates())
qube_energy = energy_decomposition_system(qube_struc,
qube_system,
platform="Reference")
# compare the decomposed energies of the groups
for force_group, energy in ref_energy:
for qube_force, qube_e in qube_energy:
if force_group == qube_force:
assert energy == pytest.approx(qube_e, abs=2e-3)
def test_offxml_round_trip(tmpdir, openff, molecule):
"""
Test round tripping offxml parameters through qubekit
"""
with tmpdir.as_cwd():
mol = Ligand.from_file(get_data(molecule))
offmol = Molecule.from_file(get_data(molecule))
openff.run(mol)
mol.to_offxml("test.offxml")
# build another openmm system and serialise to compare with deepdiff
offxml = ForceField("test.offxml")
assert offxml.author == f"QUBEKit_version_{qubekit.__version__}"
qubekit_system = offxml.create_openmm_system(
topology=offmol.to_topology())
qubekit_xml = xmltodict.parse(
openmm.XmlSerializer.serialize(qubekit_system))
with open("qubekit_xml", "w") as output:
output.write(openmm.XmlSerializer.serialize(qubekit_system))
openff_system = xmltodict.parse(open("serialised.xml").read())
offxml_diff = DeepDiff(
qubekit_xml,
openff_system,
ignore_order=True,
significant_digits=6,
)
# the only difference should be in torsions with a 0 barrier height which are excluded from an offxml
for item in offxml_diff["iterable_item_removed"].values():
assert item["@k"] == "0"
# load both systems and compute the energy
qubekit_top = load_topology(
mol.to_openmm_topology(),
system=qubekit_system,
xyz=mol.openmm_coordinates(),
)
qubekit_energy = energy_decomposition_system(qubekit_top,
qubekit_system,
platform="Reference")
ref_system = XmlSerializer.deserializeSystem(
open("serialised.xml").read())
parm_top = load_topology(mol.to_openmm_topology(),
system=ref_system,
xyz=mol.openmm_coordinates())
ref_energy = energy_decomposition_system(parm_top,
ref_system,
platform="Reference")
# compare the decomposed energies of the groups
for force_group, energy in ref_energy:
for qube_force, qube_e in qubekit_energy:
if force_group == qube_force:
assert energy == pytest.approx(qube_e, abs=2e-3)
def test_round_trip_energy(tmpdir, molecule, method, openff, antechamber):
"""
Make sure that no terms are missing when storing parameters from source by comparing energies.
Note we relax the comparison to abs=2e-3 due to differences in nonbonded cutoffs, phase rounding and the ordering
improper torsions are applied.
"""
if method == "openff":
engine = openff
else:
engine = antechamber
with tmpdir.as_cwd():
mol = Ligand.from_file(get_data(molecule))
# parametrise the system
engine.run(mol)
# this will make a serialised system in the folder so get the reference energy
ref_system = XmlSerializer.deserializeSystem(
open("serialised.xml").read())
parm_top = load_topology(mol.to_openmm_topology(),
system=ref_system,
xyz=mol.openmm_coordinates())
ref_energy = energy_decomposition_system(parm_top,
ref_system,
platform="Reference")
# now we need to build the system from our stored parameters
mol.write_parameters(file_name="test.xml")
ff = app.ForceField("test.xml")
qube_system = ff.createSystem(mol.to_openmm_topology())
with open("qube.xml", "w") as xml_out:
xml_out.write(XmlSerializer.serialize(qube_system))
qube_struc = load_topology(mol.to_openmm_topology(),
system=qube_system,
xyz=mol.openmm_coordinates())
qube_energy = energy_decomposition_system(qube_struc,
qube_system,
platform="Reference")
# compare the decomposed energies of the groups
for force_group, energy in ref_energy:
for qube_force, qube_e in qube_energy:
if force_group == qube_force:
assert energy == pytest.approx(qube_e, abs=2e-3)
def init_openmm(self, integrator_params=None, create_system_params=None):
"""
Method that initiates OpenMM by creating
Parameters
----------
integrator_params : dict
Keyword arguments passed to the simtk.openmm.openmm.LangevinIntegrator
create_system_params : dict
Keyword arguments passed to simtk.openmm.app.amberprmtopfile.createSystem
Returns
-------
system : simtk.openmm.openmm.System
OpenMM system created.
"""
from simtk.openmm import XmlSerializer
assert self.topology_format is not None, "No topology format was provided."
assert self.crd_format is not None, "No coordinate format was provided."
if self.topology_format.upper() in ["AMBER", "GROMACS", "CHARMM"]:
assert self.top_file is not None, "Topology format is {} but no topology file was provided.".format(
self.topology_format)
else:
raise NotImplementedError(
"Topology format {} is not known.".format(
self.topology_format))
assert self.crd_file is not None, "create_system flag is True but no crd_file was provided."
if self.platform_name is None:
logging.info("No platform set. Will use reference.")
self.platform_name = "Reference"
else:
assert self.platform_name in [
"Reference", "CPU", "OpenCL", "CUDA"
], """create_system flag is True but no
correct platform was provided."""
# Read topology
if self.topology_format.upper() == "AMBER":
if self.topology is None:
top = app.AmberPrmtopFile(self.top_file)
self.topology = top.topology
elif self.topology_format.upper() == "GROMACS":
if self.topology is None:
top = app.GromacsTopFile(self.top_file)
self.topology = top.topology
elif self.topology_format.upper() == "CHARMM":
if self.topology is None:
top = app.CharmmPsfFile(self.top_file)
self.topology = top.topology
charmm_params = app.CharmmParameterSet('charmm.rtf',
self.charmm_param_file)
else:
raise NotImplementedError(
"Topology format {} is not currently supported.".format(
self.topology_format))
# Read coordinate file
if self.crd_format.upper() == "AMBER":
crd = app.AmberInpcrdFile(self.crd_file)
elif self.crd_format.upper() == "GROMACS":
crd = app.GromacsGroFile(self.crd_file)
elif self.crd_format.upper() == "CHARMM":
crd = app.CharmmCrdFile(self.crd_file)
elif self.crd_format.upper() == "PDB":
crd = app.PDBFile(self.crd_file)
else:
raise NotImplementedError(
"Coordinate format {} is not currently supported.".format(
self.crd_format))
if self.system is None:
if self.xml_file is None:
assert create_system_params is not None, "No settings to create the system were provided."
logging.info("Creating OpenMM System from {} file.".format(
self.topology_format))
if self.topology_format.upper() == "CHARMM":
self.system = top.createSystem(charmm_params,
**create_system_params)
else:
self.system = top.createSystem(**create_system_params)
else:
logging.info("Creating OpenMM System from XML file.")
xml_file = open(self.xml_file)
self.system = XmlSerializer.deserializeSystem(xml_file.read())
xml_file.close()
if self.integrator is None:
assert integrator_params is not None, "No settings to create the integrator were provided."
self.integrator = openmm.LangevinIntegrator(
integrator_params['temperature'],
integrator_params["frictionCoeff"],
integrator_params["stepSize"])
logging.info("Creating OpenMM integrator.")
if self.platform is None:
self.platform = openmm.Platform.getPlatformByName(
self.platform_name)
logging.info("Creating OpenMM platform.")
if self.context is None:
self.context = openmm.Context(self.system, self.integrator,
self.platform)
logging.info("Creating OpenMM Context.")
# Set positions in context
self.context.setPositions(crd.positions)
return self.system
