"""
A collection of protocols for assigning force field parameters to molecular
systems.
"""
import abc
import io
import logging
import os
import re
import subprocess
import textwrap
from enum import Enum
import numpy as np
import requests
from simtk import openmm
from simtk.openmm import app
from openff.evaluator.attributes import UNDEFINED
from openff.evaluator.forcefield import (
ForceFieldSource,
LigParGenForceFieldSource,
SmirnoffForceFieldSource,
TLeapForceFieldSource,
)
from openff.evaluator.forcefield.system import ParameterizedSystem
from openff.evaluator.substances import Substance
from openff.evaluator.utils.openmm import pint_quantity_to_openmm
from openff.evaluator.utils.utils import (
get_data_filename,
has_openeye,
temporarily_change_directory,
)
from openff.evaluator.workflow import Protocol, workflow_protocol
from openff.evaluator.workflow.attributes import InputAttribute, OutputAttribute
logger = logging.getLogger(__name__)
[docs]@workflow_protocol()
class BaseBuildSystem(Protocol, abc.ABC):
"""The base class for any protocol whose role is to apply a set of
force field parameters to a given system.
"""
force_field_path = InputAttribute(
docstring="The file path to the force field parameters to assign to the system.",
type_hint=str,
default_value=UNDEFINED,
)
coordinate_file_path = InputAttribute(
docstring="The file path to the PDB coordinate file which defines the "
"topology of the system to which the force field parameters "
"will be assigned.",
type_hint=str,
default_value=UNDEFINED,
)
substance = InputAttribute(
docstring="The composition of the system.",
type_hint=Substance,
default_value=UNDEFINED,
)
parameterized_system = OutputAttribute(
docstring="The parameterized system object.", type_hint=ParameterizedSystem
)
@staticmethod
def _append_system(existing_system, system_to_append, index_map=None):
"""Appends a system object onto the end of an existing system.
Parameters
----------
existing_system: simtk.openmm.System, optional
The base system to extend.
system_to_append: simtk.openmm.System
The system to append.
index_map: dict of int and int, optional
A map to apply to the indices of atoms in the `system_to_append`.
This is predominantly to be used when the ordering of the atoms
in the `system_to_append` does not match the ordering in the full
topology.
"""
supported_force_types = [
openmm.HarmonicBondForce,
openmm.HarmonicAngleForce,
openmm.PeriodicTorsionForce,
openmm.NonbondedForce,
]
number_of_appended_forces = 0
index_offset = existing_system.getNumParticles()
# Create an index map if one is not provided.
if index_map is None:
index_map = {i: i for i in range(system_to_append.getNumParticles())}
# Append the particles.
for index in range(system_to_append.getNumParticles()):
index = index_map[index]
existing_system.addParticle(system_to_append.getParticleMass(index))
# Append the constraints
for index in range(system_to_append.getNumConstraints()):
index_a, index_b, distance = system_to_append.getConstraintParameters(index)
index_a = index_map[index_a]
index_b = index_map[index_b]
existing_system.addConstraint(
index_a + index_offset, index_b + index_offset, distance
)
# Validate the forces to append.
for force_to_append in system_to_append.getForces():
if type(force_to_append) in supported_force_types:
continue
raise ValueError(
f"The system contains an unsupported type of "
f"force: {type(force_to_append)}."
)
# Append the forces.
for force_to_append in system_to_append.getForces():
existing_force = None
for force in existing_system.getForces():
if type(force) not in supported_force_types:
raise ValueError(
f"The existing system contains an unsupported type "
f"of force: {type(force)}."
)
if type(force_to_append) != type(force):
continue
existing_force = force
break
if existing_force is None:
existing_force = type(force_to_append)()
existing_system.addForce(existing_force)
if isinstance(force_to_append, openmm.HarmonicBondForce):
# Add the bonds.
for index in range(force_to_append.getNumBonds()):
index_a, index_b, *parameters = force_to_append.getBondParameters(
index
)
index_a = index_map[index_a]
index_b = index_map[index_b]
existing_force.addBond(
index_a + index_offset, index_b + index_offset, *parameters
)
elif isinstance(force_to_append, openmm.HarmonicAngleForce):
# Add the angles.
for index in range(force_to_append.getNumAngles()):
(
index_a,
index_b,
index_c,
*parameters,
) = force_to_append.getAngleParameters(index)
index_a = index_map[index_a]
index_b = index_map[index_b]
index_c = index_map[index_c]
existing_force.addAngle(
index_a + index_offset,
index_b + index_offset,
index_c + index_offset,
*parameters,
)
elif isinstance(force_to_append, openmm.PeriodicTorsionForce):
# Add the torsions.
for index in range(force_to_append.getNumTorsions()):
(
index_a,
index_b,
index_c,
index_d,
*parameters,
) = force_to_append.getTorsionParameters(index)
index_a = index_map[index_a]
index_b = index_map[index_b]
index_c = index_map[index_c]
index_d = index_map[index_d]
existing_force.addTorsion(
index_a + index_offset,
index_b + index_offset,
index_c + index_offset,
index_d + index_offset,
*parameters,
)
elif isinstance(force_to_append, openmm.NonbondedForce):
# Add the vdW parameters
for index in range(force_to_append.getNumParticles()):
index = index_map[index]
existing_force.addParticle(
*force_to_append.getParticleParameters(index)
)
# Add the 1-2, 1-3 and 1-4 exceptions.
for index in range(force_to_append.getNumExceptions()):
(
index_a,
index_b,
*parameters,
) = force_to_append.getExceptionParameters(index)
index_a = index_map[index_a]
index_b = index_map[index_b]
existing_force.addException(
index_a + index_offset, index_b + index_offset, *parameters
)
number_of_appended_forces += 1
if number_of_appended_forces != system_to_append.getNumForces():
raise ValueError("Not all forces were appended.")
def _execute(self, directory, available_resources):
raise NotImplementedError()
@workflow_protocol()
class TemplateBuildSystem(BaseBuildSystem, abc.ABC):
"""A base protocol for any protocol which assign parameters to a system
by first assigning parameters to each individual component of the system,
and then replicating those templates for each instance of the component.
"""
class WaterModel(Enum):
"""An enum which describes which water model is being
used, so that correct charges can be applied.
Warnings
--------
This is only a temporary addition until full water model support
is introduced.
"""
TIP3P = "TIP3P"
water_model = InputAttribute(
docstring="The water model to apply, if any water molecules are present.",
type_hint=WaterModel,
default_value=WaterModel.TIP3P,
)
@staticmethod
def _build_tip3p_system(cutoff, cell_vectors):
"""Builds a `simtk.openmm.System` object containing a single water model
Parameters
----------
cutoff: openff.evaluator.unit.Quantity
The non-bonded cutoff.
cell_vectors: openff.evaluator.unit.Quantity
The full system's cell vectors.
Returns
-------
simtk.openmm.System
The created system.
"""
force_field_path = get_data_filename("forcefield/tip3p.xml")
water_pdb_path = get_data_filename("forcefield/tip3p.pdb")
component_pdb_file = app.PDBFile(water_pdb_path)
component_topology = component_pdb_file.topology
component_topology.setUnitCellDimensions(cell_vectors)
# Create the system object.
force_field_template = app.ForceField(force_field_path)
component_system = force_field_template.createSystem(
topology=component_topology,
nonbondedMethod=app.PME,
nonbondedCutoff=cutoff,
constraints=app.HBonds,
rigidWater=True,
removeCMMotion=False,
)
return component_system
@staticmethod
def _create_empty_system(cutoff):
"""Creates an empty system object with stub forces.
Parameters
----------
cutoff: simtk.unit
The non-bonded cutoff.
Returns
-------
simtk.openmm.System
The created system object.
"""
system = openmm.System()
system.addForce(openmm.HarmonicBondForce())
system.addForce(openmm.HarmonicAngleForce())
system.addForce(openmm.PeriodicTorsionForce())
nonbonded_force = openmm.NonbondedForce()
nonbonded_force.setCutoffDistance(cutoff)
nonbonded_force.setNonbondedMethod(openmm.NonbondedForce.PME)
system.addForce(nonbonded_force)
return system
@abc.abstractmethod
def _parameterize_molecule(self, molecule, force_field_source, cutoff):
"""Parameterize the specified molecule.
Parameters
----------
molecule: openff.toolkit.topology.Molecule
The molecule to parameterize.
force_field_source: ForceFieldSource
The tleap source which describes which parameters to apply.
cutoff: simtk.unit
The non-bonded cutoff.
Returns
-------
simtk.openmm.System
The parameterized system.
"""
raise NotImplementedError()
def _execute(self, directory, available_resources):
from openff.toolkit.topology import Molecule, Topology
force_field_source = ForceFieldSource.from_json(self.force_field_path)
cutoff = pint_quantity_to_openmm(force_field_source.cutoff)
# Load in the systems topology
openmm_pdb_file = app.PDBFile(self.coordinate_file_path)
# Create an OFF topology for better insight into the layout of the system
# topology.
unique_molecules = {}
for component in self.substance:
unique_molecule = Molecule.from_smiles(component.smiles)
unique_molecules[unique_molecule.to_smiles()] = unique_molecule
# Parameterize each component in the system.
system_templates = {}
for index, (smiles, unique_molecule) in enumerate(unique_molecules.items()):
if smiles in ["O", "[H]O[H]", "[H][O][H]"]:
component_system = self._build_tip3p_system(
cutoff,
openmm_pdb_file.topology.getUnitCellDimensions(),
)
else:
component_directory = os.path.join(directory, str(index))
os.makedirs(component_directory, exist_ok=True)
with temporarily_change_directory(component_directory):
component_system = self._parameterize_molecule(
unique_molecule, force_field_source, cutoff
)
system_templates[smiles] = component_system
# Apply the parameters to the topology.
topology = Topology.from_openmm(
openmm_pdb_file.topology, unique_molecules.values()
)
# Create the full system object from the component templates.
system = self._create_empty_system(cutoff)
for topology_molecule in topology.topology_molecules:
smiles = topology_molecule.reference_molecule.to_smiles()
system_template = system_templates[smiles]
index_map = {}
for index, topology_atom in enumerate(topology_molecule.atoms):
index_map[topology_atom.atom.molecule_particle_index] = index
# Append the component template to the full system.
self._append_system(system, system_template, index_map)
if openmm_pdb_file.topology.getPeriodicBoxVectors() is not None:
system.setDefaultPeriodicBoxVectors(
*openmm_pdb_file.topology.getPeriodicBoxVectors()
)
# Serialize the system object.
system_path = os.path.join(directory, "system.xml")
with open(system_path, "w") as file:
file.write(openmm.XmlSerializer.serialize(system))
self.parameterized_system = ParameterizedSystem(
substance=self.substance,
force_field=force_field_source,
topology_path=self.coordinate_file_path,
system_path=system_path,
)
[docs]@workflow_protocol()
class BuildSmirnoffSystem(BaseBuildSystem):
"""Parametrise a set of molecules with a given smirnoff force field
using the `OpenFF toolkit <https://github.com/openforcefield/openff-toolkit>`_.
"""
def _execute(self, directory, available_resources):
from openff.toolkit.topology import Molecule, Topology
pdb_file = app.PDBFile(self.coordinate_file_path)
force_field_source = ForceFieldSource.from_json(self.force_field_path)
if not isinstance(force_field_source, SmirnoffForceFieldSource):
raise ValueError(
"Only SMIRNOFF force fields are supported by this protocol."
)
force_field = force_field_source.to_force_field()
# Create the molecules to parameterize from the input substance.
unique_molecules = []
for component in self.substance.components:
molecule = Molecule.from_smiles(smiles=component.smiles)
if molecule is None:
raise ValueError(f"{component} could not be converted to a Molecule")
unique_molecules.append(molecule)
# Create the topology to parameterize from the input coordinates and the
# expected molecule species.
topology = Topology.from_openmm(
pdb_file.topology, unique_molecules=unique_molecules
)
system = force_field.create_openmm_system(topology)
if system is None:
raise RuntimeError(
"Failed to create a system from the specified topology and molecules."
)
system_xml = openmm.XmlSerializer.serialize(system)
system_path = os.path.join(directory, "system.xml")
with open(system_path, "w") as file:
file.write(system_xml)
self.parameterized_system = ParameterizedSystem(
substance=self.substance,
force_field=force_field_source,
topology_path=self.coordinate_file_path,
system_path=system_path,
)
[docs]@workflow_protocol()
class BuildLigParGenSystem(TemplateBuildSystem):
"""Parametrise a set of molecules with the OPLS-AA/M force field.
using a `LigParGen server <http://zarbi.chem.yale.edu/ligpargen/>`_.
Notes
-----
This protocol is currently a work in progress and as such has limited
functionality compared to the more established `BuildSmirnoffSystem` protocol.
References
----------
[1] Potential energy functions for atomic-level simulations of water and organic and
biomolecular systems. Jorgensen, W. L.; Tirado-Rives, J. Proc. Nat. Acad. Sci.
USA 2005, 102, 6665-6670
[2] 1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase
Simulations. Dodda, L. S.; Vilseck, J. Z.; Tirado-Rives, J.; Jorgensen, W. L.
J. Phys. Chem. B, 2017, 121 (15), pp 3864-3870
[3] LigParGen web server: An automatic OPLS-AA parameter generator for organic ligands.
Dodda, L. S.;Cabeza de Vaca, I.; Tirado-Rives, J.; Jorgensen, W. L.
Nucleic Acids Research, Volume 45, Issue W1, 3 July 2017, Pages W331-W336
"""
@staticmethod
def _built_template(molecule, force_field_source):
"""Builds a force field template object.
Parameters
----------
molecule: openff.toolkit.topology.Molecule
The molecule to templatize.
force_field_source: LigParGenForceFieldSource
The tleap source which describes which parameters to apply.
Returns
-------
simtk.openmm.app.ForceField
The force field template.
"""
from simtk import unit as simtk_unit
initial_request_url = force_field_source.request_url
empty_stream = io.BytesIO(b"\r\n")
total_charge = molecule.total_charge
if isinstance(total_charge, simtk_unit.Quantity):
total_charge = total_charge.value_in_unit(simtk_unit.elementary_charge)
charge_model = "cm1abcc"
if (
force_field_source.preferred_charge_model
== LigParGenForceFieldSource.ChargeModel.CM1A_1_14
or not np.isclose(total_charge, 0.0)
):
charge_model = "cm1a"
if (
force_field_source.preferred_charge_model
!= LigParGenForceFieldSource.ChargeModel.CM1A_1_14
):
logger.warning(
f"The preferred charge model is {str(force_field_source.preferred_charge_model)}, "
f"however the system is charged and so the "
f"{str(LigParGenForceFieldSource.ChargeModel.CM1A_1_14)} model will be used in its "
f"place."
)
data_body = {
"smiData": (None, molecule.to_smiles()),
"molpdbfile": ("", empty_stream),
"checkopt": (None, 0),
"chargetype": (None, charge_model),
"dropcharge": (None, str(total_charge)),
}
# Perform the initial request for LigParGen to parameterize the molecule.
request = requests.post(url=initial_request_url, files=data_body)
# Cleanup the empty stream
empty_stream.close()
if request.status_code != requests.codes.ok:
return f"The request failed with return code {request.status_code}."
response_content = request.content
# Retrieve the server file name.
force_field_file_name = re.search(
r"value=\"/tmp/(.*?).xml\"", response_content.decode()
)
if force_field_file_name is None:
return "The request could not successfully be completed."
force_field_file_name = force_field_file_name.group(1)
# Download the force field xml file.
download_request_url = force_field_source.download_url
download_force_field_body = {
"go": (None, "XML"),
"fileout": (None, f"/tmp/{force_field_file_name}.xml"),
}
request = requests.post(
url=download_request_url, files=download_force_field_body
)
if request.status_code != requests.codes.ok:
return f"The request to download the system xml file failed with return code {request.status_code}."
force_field_response = request.content
force_field_path = "template.xml"
with open(force_field_path, "wb") as file:
file.write(force_field_response)
return app.ForceField(force_field_path)
def _parameterize_molecule(self, molecule, force_field_source, cutoff):
"""Parameterize the specified molecule.
Parameters
----------
force_field_source: LigParGenForceFieldSource
The tleap source which describes which parameters to apply.
Returns
-------
simtk.openmm.System
The parameterized system.
"""
from simtk import unit as simtk_unit
template = self._built_template(molecule, force_field_source)
off_topology = molecule.to_topology()
box_vectors = np.eye(3) * 10.0
openmm_topology = off_topology.to_openmm()
openmm_topology.setPeriodicBoxVectors(box_vectors * simtk_unit.nanometer)
system = template.createSystem(
topology=openmm_topology,
nonbondedMethod=app.PME,
nonbondedCutoff=cutoff,
constraints=app.HBonds,
rigidWater=True,
removeCMMotion=False,
)
with open("component.xml", "w") as file:
file.write(openmm.XmlSerializer.serialize(system))
return system
@staticmethod
def _apply_opls_mixing_rules(system):
"""Applies the OPLS mixing rules to the system.
Notes
-----
This method is based upon that found in the `LigParGen tutorial
<http://zarbi.chem.yale.edu/ligpargen/openMM_tutorial.html>`_.
Parameters
----------
system: simtk.openmm.System
The system object to apply the OPLS mixing rules to.
"""
from simtk import unit as simtk_unit
forces = [system.getForce(index) for index in range(system.getNumForces())]
forces = [force for force in forces if isinstance(force, openmm.NonbondedForce)]
for original_force in forces:
# Define a custom force with the OPLS mixing rules.
custom_force = openmm.CustomNonbondedForce(
"4*epsilon*((sigma/r)^12-(sigma/r)^6); "
"sigma=sqrt(sigma1*sigma2); "
"epsilon=sqrt(epsilon1*epsilon2)"
)
if original_force.getNonbondedMethod() == 4: # Check for PME
custom_force.setNonbondedMethod(
openmm.CustomNonbondedForce.CutoffPeriodic
)
else:
custom_force.setNonbondedMethod(original_force.getNonbondedMethod())
custom_force.addPerParticleParameter("sigma")
custom_force.addPerParticleParameter("epsilon")
custom_force.setCutoffDistance(original_force.getCutoffDistance())
system.addForce(custom_force)
lennard_jones_parameters = {}
for index in range(original_force.getNumParticles()):
charge, sigma, epsilon = original_force.getParticleParameters(index)
# Copy the original vdW parameters over to the new custom force.
lennard_jones_parameters[index] = (sigma, epsilon)
custom_force.addParticle([sigma, epsilon])
# Disable the original vdW interactions, but leave the charged interactions
# turned on.
original_force.setParticleParameters(index, charge, sigma, epsilon * 0)
# Update the 1-4 exceptions.
for exception_index in range(original_force.getNumExceptions()):
(
index_a,
index_b,
charge,
sigma,
epsilon,
) = original_force.getExceptionParameters(exception_index)
# Disable any 1-2, 1-3, 1-4 exceptions on the custom force, and instead let the
# original force handle it.
custom_force.addExclusion(index_a, index_b)
if not np.isclose(
epsilon.value_in_unit(simtk_unit.kilojoule_per_mole), 0.0
):
sigma_14 = np.sqrt(
lennard_jones_parameters[index_a][0]
* lennard_jones_parameters[index_b][0]
)
epsilon_14 = np.sqrt(
lennard_jones_parameters[index_a][1]
* lennard_jones_parameters[index_b][1]
)
original_force.setExceptionParameters(
exception_index, index_a, index_b, charge, sigma_14, epsilon_14
)
def _execute(self, directory, available_resources):
with open(self.force_field_path) as file:
force_field_source = ForceFieldSource.parse_json(file.read())
if not isinstance(force_field_source, LigParGenForceFieldSource):
raise ValueError(
"Only LigParGen force field sources are supported by this protocol."
)
super(BuildLigParGenSystem, self)._execute(directory, available_resources)
with open(self.parameterized_system.system_path) as file:
system = openmm.XmlSerializer.deserialize(file.read())
# Apply the OPLS mixing rules.
self._apply_opls_mixing_rules(system)
with open(self.parameterized_system.system_path, "w") as file:
file.write(openmm.XmlSerializer.serialize(system))
[docs]@workflow_protocol()
class BuildTLeapSystem(TemplateBuildSystem):
"""Parametrise a set of molecules with an Amber based force field.
using the `tleap package <http://ambermd.org/AmberTools.php>`_.
Notes
-----
* This protocol is currently a work in progress and as such has limited
functionality compared to the more established `BuildSmirnoffSystem` protocol.
* This protocol requires the optional `ambertools >=19.0` dependency to be installed.
"""
[docs] class ChargeBackend(Enum):
"""The framework to use to assign partial charges."""
OpenEye = "OpenEye"
AmberTools = "AmberTools"
charge_backend = InputAttribute(
docstring="The backend framework to use to assign partial charges.",
type_hint=ChargeBackend,
default_value=lambda: BuildTLeapSystem.ChargeBackend.OpenEye
if has_openeye()
else BuildTLeapSystem.ChargeBackend.AmberTools,
)
@staticmethod
def _run_tleap(molecule, force_field_source, directory):
"""Uses tleap to apply parameters to a particular molecule,
generating a `.prmtop` and a `.rst7` file with the applied parameters.
Parameters
----------
molecule: openff.toolkit.topology.Molecule
The molecule to parameterize.
force_field_source: TLeapForceFieldSource
The tleap source which describes which parameters to apply.
directory: str
The directory to store and temporary files / the final
parameters in.
Returns
-------
str
The file path to the `prmtop` file.
str
The file path to the `rst7` file.
"""
from simtk import unit as simtk_unit
# Change into the working directory.
with temporarily_change_directory(directory):
initial_file_path = "initial.sdf"
molecule.to_file(initial_file_path, file_format="SDF")
# Save the molecule charges to a file.
charges = [
x.value_in_unit(simtk_unit.elementary_charge)
for x in molecule.partial_charges
]
with open("charges.txt", "w") as file:
file.write(textwrap.fill(" ".join(map(str, charges)), width=70))
if force_field_source.leap_source == "leaprc.gaff2":
amber_type = "gaff2"
elif force_field_source.leap_source == "leaprc.gaff":
amber_type = "gaff"
else:
raise ValueError(
f"The {force_field_source.leap_source} source is currently "
f"unsupported. Only the 'leaprc.gaff2' and 'leaprc.gaff' "
f" sources are supported."
)
# Run antechamber to find the correct atom types.
processed_mol2_path = "antechamber.mol2"
antechamber_process = subprocess.Popen(
[
"antechamber",
"-i",
initial_file_path,
"-fi",
"sdf",
"-o",
processed_mol2_path,
"-fo",
"mol2",
"-at",
amber_type,
"-rn",
"MOL",
"-an",
"no",
"-pf",
"yes",
"-c",
"rc",
"-cf",
"charges.txt",
],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
)
antechamber_output, antechamber_error = antechamber_process.communicate()
antechamber_exit_code = antechamber_process.returncode
with open("antechamber_output.log", "w") as file:
file.write(f"error code: {antechamber_exit_code}\nstdout:\n\n")
file.write("stdout:\n\n")
file.write(antechamber_output.decode())
file.write("\nstderr:\n\n")
file.write(antechamber_error.decode())
if not os.path.isfile(processed_mol2_path):
raise RuntimeError(
f"antechamber failed to assign atom types to the input mol2 file "
f"({initial_file_path})"
)
frcmod_path = None
if amber_type == "gaff" or amber_type == "gaff2":
# Optionally run parmchk to find any missing parameters.
frcmod_path = "parmck2.frcmod"
prmchk2_process = subprocess.Popen(
[
"parmchk2",
"-i",
processed_mol2_path,
"-f",
"mol2",
"-o",
frcmod_path,
"-s",
amber_type,
],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
)
prmchk2_output, prmchk2_error = prmchk2_process.communicate()
prmchk2_exit_code = prmchk2_process.returncode
with open("prmchk2_output.log", "w") as file:
file.write(f"error code: {prmchk2_exit_code}\nstdout:\n\n")
file.write(prmchk2_output.decode())
file.write("\nstderr:\n\n")
file.write(prmchk2_error.decode())
if not os.path.isfile(frcmod_path):
raise RuntimeError(
f"parmchk2 failed to assign missing {amber_type} parameters "
f"to the antechamber created mol2 file ({processed_mol2_path})",
)
# Build the tleap input file.
template_lines = [f"source {force_field_source.leap_source}"]
if frcmod_path is not None:
template_lines.append(
f"loadamberparams {frcmod_path}",
)
prmtop_file_name = "structure.prmtop"
rst7_file_name = "structure.rst7"
template_lines.extend(
[
f"MOL = loadmol2 {processed_mol2_path}",
'setBox MOL "centers"',
"check MOL",
f"saveamberparm MOL {prmtop_file_name} {rst7_file_name}",
]
)
input_file_path = "tleap.in"
with open(input_file_path, "w") as file:
file.write("\n".join(template_lines))
# Run tleap.
tleap_process = subprocess.Popen(
["tleap", "-s ", "-f ", input_file_path], stdout=subprocess.PIPE
)
tleap_output, _ = tleap_process.communicate()
tleap_exit_code = tleap_process.returncode
with open("tleap_output.log", "w") as file:
file.write(f"error code: {tleap_exit_code}\nstdout:\n\n")
file.write(tleap_output.decode())
if not os.path.isfile(prmtop_file_name) or not os.path.isfile(
rst7_file_name
):
raise RuntimeError("tleap failed to execute.")
with open("leap.log", "r") as file:
if re.search(
"ERROR|WARNING|Warning|duplicate|FATAL|Could|Fatal|Error",
file.read(),
):
raise RuntimeError("tleap failed to execute.")
return (
os.path.join(directory, prmtop_file_name),
os.path.join(directory, rst7_file_name),
)
def _generate_charges(self, molecule):
"""Generates a set of partial charges for a molecule using
the specified charge backend.
Parameters
----------
molecule: openff.toolkit.topology.Molecule
The molecule to assign charges to.
"""
if self.charge_backend == BuildTLeapSystem.ChargeBackend.OpenEye:
from openff.toolkit.utils.toolkits import OpenEyeToolkitWrapper
toolkit_wrapper = OpenEyeToolkitWrapper()
elif self.charge_backend == BuildTLeapSystem.ChargeBackend.AmberTools:
from openff.toolkit.utils.toolkits import (
AmberToolsToolkitWrapper,
RDKitToolkitWrapper,
ToolkitRegistry,
)
toolkit_wrapper = ToolkitRegistry(
toolkit_precedence=[RDKitToolkitWrapper, AmberToolsToolkitWrapper]
)
else:
raise ValueError("Invalid toolkit specification.")
molecule.generate_conformers(toolkit_registry=toolkit_wrapper)
molecule.compute_partial_charges_am1bcc(toolkit_registry=toolkit_wrapper)
def _parameterize_molecule(self, molecule, force_field_source, cutoff):
"""Parameterize the specified molecule.
Parameters
----------
molecule: openff.toolkit.topology.Molecule
The molecule to parameterize.
force_field_source: TLeapForceFieldSource
The tleap source which describes which parameters to apply.
Returns
-------
simtk.openmm.System
The parameterized system.
"""
self._generate_charges(molecule)
prmtop_path, _ = BuildTLeapSystem._run_tleap(molecule, force_field_source, "")
prmtop_file = openmm.app.AmberPrmtopFile(prmtop_path)
system = prmtop_file.createSystem(
nonbondedMethod=app.PME,
nonbondedCutoff=cutoff,
constraints=app.HBonds,
rigidWater=True,
removeCMMotion=False,
)
with open("component.xml", "w") as file:
file.write(openmm.XmlSerializer.serialize(system))
return system
def _execute(self, directory, available_resources):
force_field_source = ForceFieldSource.from_json(self.force_field_path)
if not isinstance(force_field_source, TLeapForceFieldSource):
raise ValueError(
"Only TLeap force field sources are supported by this protocol."
)
super(BuildTLeapSystem, self)._execute(directory, available_resources)