#!/usr/bin/env python
# =============================================================================================
# MODULE DOCSTRING
# =============================================================================================
"""
Parameter assignment tools for the SMIRNOFF (SMIRKS Native Open Force Field) format.
.. codeauthor:: John D. Chodera <john.chodera@choderalab.org>
.. codeauthor:: David L. Mobley <dmobley@mobleylab.org>
.. codeauthor:: Peter K. Eastman <peastman@stanford.edu>
.. todo ::
* Speed up overall import time by putting non-global imports only where they are needed
"""
__all__ = [
"get_available_force_fields",
"MAX_SUPPORTED_VERSION",
"ParameterHandlerRegistrationError",
"SMIRNOFFVersionError",
"SMIRNOFFAromaticityError",
"ParseError",
"ForceField",
]
# =============================================================================================
# GLOBAL IMPORTS
# =============================================================================================
import copy
import logging
import os
import pathlib
from collections import OrderedDict
from simtk import openmm, unit
from openforcefield.topology.molecule import DEFAULT_AROMATICITY_MODEL
from openforcefield.typing.engines.smirnoff.io import ParameterIOHandler
from openforcefield.typing.engines.smirnoff.parameters import ParameterHandler
from openforcefield.typing.engines.smirnoff.plugins import load_handler_plugins
from openforcefield.utils import (
MessageException,
all_subclasses,
convert_0_1_smirnoff_to_0_2,
convert_0_2_smirnoff_to_0_3,
convert_all_quantities_to_string,
convert_all_strings_to_quantity,
)
# =============================================================================================
# CONFIGURE LOGGER
# =============================================================================================
logger = logging.getLogger(__name__)
# =============================================================================================
# PRIVATE METHODS
# =============================================================================================
# Directory paths used by ForceField to discover offxml files.
_installed_offxml_dir_paths = []
def _get_installed_offxml_dir_paths():
"""Return the list of directory paths where to search for offxml files.
This function load the information by calling all the entry points
registered in the "openff.forcefielddirs" group. Each entry point
(i.e. a function) should return a list of paths to directories
containing the offxml files.
Returns
-------
installed_offxml_dir_paths : List[str]
All the installed directory paths where ``ForceField`` will
look for offxml files.
"""
global _installed_offxml_dir_paths
if len(_installed_offxml_dir_paths) == 0:
from pkg_resources import iter_entry_points
# Find all registered entry points that should return a list of
# paths to directories where to search for offxml files.
for entry_point in iter_entry_points(
group="openforcefield.smirnoff_forcefield_directory"
):
_installed_offxml_dir_paths.extend(entry_point.load()())
return _installed_offxml_dir_paths
[docs]def get_available_force_fields(full_paths=False):
"""
Get the filenames of all available .offxml force field files.
Availability is determined by what is discovered through the
`openforcefield.smirnoff_forcefield_directory` entry point. If the
`openforcefields` package is installed, this should include several
.offxml files such as `openff-1.0.0.offxml`.
Parameters
----------
full_paths : bool, default=False
If False, return the name of each available *.offxml file.
If True, return the full path to each available .offxml file.
Returns
-------
available_force_fields : List[str]
List of available force field files
"""
installed_paths = _get_installed_offxml_dir_paths()
available_force_fields = []
for installed_path in installed_paths:
for globbed in pathlib.Path(installed_path).rglob("*.offxml"):
if full_paths:
available_force_fields.append(globbed.as_posix())
else:
available_force_fields.append(globbed.name)
return available_force_fields
# TODO: Instead of having a global version number, alow each Force to have a separate version number
MAX_SUPPORTED_VERSION = (
"1.0" # maximum version of the SMIRNOFF spec supported by this SMIRNOFF forcefield
)
class ParameterHandlerRegistrationError(MessageException):
"""
Exception for errors in ParameterHandler registration
"""
pass
class SMIRNOFFVersionError(MessageException):
"""
Exception thrown when an incompatible SMIRNOFF version data structure in attempted to be read.
"""
pass
class SMIRNOFFAromaticityError(MessageException):
"""
Exception thrown when an incompatible SMIRNOFF aromaticity model is checked for compatibility.
"""
pass
class ParseError(MessageException):
"""
Error for when a SMIRNOFF data structure is not parseable by a ForceField
"""
pass
# =============================================================================================
# FORCEFIELD
# =============================================================================================
# QUESTION: How should we document private object fields?
# TODO: How do we serialize/deserialize `ForceField`'s object model? Can we rely on pickle?
[docs]class ForceField:
"""A factory that assigns SMIRNOFF parameters to a molecular system
:class:`ForceField` is a factory that constructs an OpenMM :class:`simtk.openmm.System` object from a
:class:`openforcefield.topology.Topology` object defining a (bio)molecular system containing one or more molecules.
When a :class:`ForceField` object is created from one or more specified SMIRNOFF serialized representations,
all :class:`ParameterHandler` subclasses currently imported are identified and registered to handle different
sections of the SMIRNOFF force field definition file(s).
All :class:`ParameterIOHandler` subclasses currently imported are identified and registered to handle different
serialization formats (such as XML).
The force field definition is processed by these handlers to populate the ``ForceField`` object model data
structures that can easily be manipulated via the API:
Processing a :class:`Topology` object defining a chemical system will then call all :class`ParameterHandler`
objects in an order guaranteed to satisfy the declared processing order constraints of each
:class`ParameterHandler`.
Attributes
----------
parameters : dict of str : list of ParameterType
``parameters[tagname]`` is the instantiated :class:`ParameterHandler` class that handles parameters associated
with the force ``tagname``.
This is the primary means of retrieving and modifying parameters, such as
``parameters['vdW'][0].sigma *= 1.1``
parameter_object_handlers : dict of str : ParameterHandler class
Registered list of :class:`ParameterHandler` classes that will handle different forcefield tags to create the parameter object model.
``parameter_object_handlers[tagname]`` is the :class:`ParameterHandler` that will be instantiated to process the force field definition section ``tagname``.
:class:`ParameterHandler` classes are registered when the ForceField object is created, but can be manipulated afterwards.
parameter_io_handlers : dict of str : ParameterIOHandler class
Registered list of :class:`ParameterIOHandler` classes that will handle serializing/deserializing the parameter object model to string or file representations, such as XML.
``parameter_io_handlers[iotype]`` is the :class:`ParameterHandler` that will be instantiated to process the serialization scheme ``iotype``.
:class:`ParameterIOHandler` classes are registered when the ForceField object is created, but can be manipulated afterwards.
Examples
--------
Create a new ForceField containing the smirnoff99Frosst parameter set:
>>> from openforcefield.typing.engines.smirnoff import ForceField
>>> forcefield = ForceField('test_forcefields/smirnoff99Frosst.offxml')
Create an OpenMM system from a :class:`openforcefield.topology.Topology` object:
>>> from openforcefield.topology import Molecule, Topology
>>> ethanol = Molecule.from_smiles('CCO')
>>> topology = Topology.from_molecules(molecules=[ethanol])
>>> system = forcefield.create_openmm_system(topology)
Modify the long-range electrostatics method:
>>> forcefield.get_parameter_handler('Electrostatics').method = 'PME'
Inspect the first few vdW parameters:
>>> low_precedence_parameters = forcefield.get_parameter_handler('vdW').parameters[0:3]
Retrieve the vdW parameters by SMIRKS string and manipulate it:
>>> parameter = forcefield.get_parameter_handler('vdW').parameters['[#1:1]-[#7]']
>>> parameter.rmin_half += 0.1 * unit.angstroms
>>> parameter.epsilon *= 1.02
Make a child vdW type more specific (checking modified SMIRKS for validity):
>>> forcefield.get_parameter_handler('vdW').parameters[-1].smirks += '~[#53]'
.. warning ::
While we check whether the modified SMIRKS is still valid and has the appropriate valence type,
we currently don't check whether the typing remains hierarchical, which could result in some types
no longer being assignable because more general types now come *below* them and preferentially match.
Delete a parameter:
>>> del forcefield.get_parameter_handler('vdW').parameters['[#1:1]-[#6X4]']
Insert a parameter at a specific point in the parameter tree:
>>> from openforcefield.typing.engines.smirnoff import vdWHandler
>>> new_parameter = vdWHandler.vdWType(smirks='[*:1]', epsilon=0.0157*unit.kilocalories_per_mole, rmin_half=0.6000*unit.angstroms)
>>> forcefield.get_parameter_handler('vdW').parameters.insert(0, new_parameter)
.. warning ::
We currently don't check whether removing a parameter could accidentally remove the root type, so it's possible to no longer type all molecules this way.
"""
[docs] def __init__(
self,
*sources,
aromaticity_model=DEFAULT_AROMATICITY_MODEL,
parameter_handler_classes=None,
parameter_io_handler_classes=None,
disable_version_check=False,
allow_cosmetic_attributes=False,
load_plugins=False,
):
"""Create a new :class:`ForceField` object from one or more SMIRNOFF parameter definition files.
Parameters
----------
sources : string or file-like object or open file handle or URL (or iterable of these)
A list of files defining the SMIRNOFF force field to be loaded.
Currently, only `the SMIRNOFF XML format <https://github.com/openforcefield/openforcefield/blob/master/The-SMIRNOFF-force-field-format.md>`_ is supported.
Each entry may be an absolute file path, a path relative to the current working directory, a path relative to this module's data subdirectory
(for built in force fields), or an open file-like object with a ``read()`` method from which the forcefield XML data can be loaded.
If multiple files are specified, any top-level tags that are repeated will be merged if they are compatible,
with files appearing later in the sequence resulting in parameters that have higher precedence.
Support for multiple files is primarily intended to allow solvent parameters to be specified by listing them last in the sequence.
aromaticity_model : string, default='OEAroModel_MDL'
The aromaticity model used by the force field. Currently, only 'OEAroModel_MDL' is supported
parameter_handler_classes : iterable of ParameterHandler classes, optional, default=None
If not None, the specified set of ParameterHandler classes will be instantiated to create the parameter object model.
By default, all imported subclasses of ParameterHandler are automatically registered.
parameter_io_handler_classes : iterable of ParameterIOHandler classes
If not None, the specified set of ParameterIOHandler classes will be used to parse/generate serialized parameter sets.
By default, all imported subclasses of ParameterIOHandler are automatically registered.
disable_version_check : bool, optional, default=False
If True, will disable checks against the current highest supported forcefield version.
This option is primarily intended for forcefield development.
allow_cosmetic_attributes : bool, optional. Default = False
Whether to retain non-spec kwargs from data sources.
load_plugins: bool, optional. Default = False
Whether to load ``ParameterHandler`` classes which have been registered
by installed plugins.
Examples
--------
Load one SMIRNOFF parameter set in XML format (searching the package data directory by default, which includes some standard parameter sets):
>>> forcefield = ForceField('test_forcefields/smirnoff99Frosst.offxml')
Load multiple SMIRNOFF parameter sets:
forcefield = ForceField('test_forcefields/smirnoff99Frosst.offxml', 'test_forcefields/tip3p.offxml')
Load a parameter set from a string:
>>> offxml = '<SMIRNOFF version="0.2" aromaticity_model="OEAroModel_MDL"/>'
>>> forcefield = ForceField(offxml)
"""
# Clear all object fields
self._initialize()
self.aromaticity_model = aromaticity_model
# Store initialization options
self.disable_version_check = disable_version_check
# if True, we won't check which SMIRNOFF version number we're parsing
# Register all ParameterHandler objects that will process SMIRNOFF force definitions
# TODO: We need to change this to just find all ParameterHandler objects in this file;
# otherwise, we can't define two different ParameterHandler subclasses to compare for a new type of energy term
# since both will try to register themselves for the same XML tag and an Exception will be raised.
if parameter_handler_classes is None:
parameter_handler_classes = all_subclasses(ParameterHandler)
if load_plugins:
registered_handlers = load_handler_plugins()
# Make sure the same handlers aren't added twice.
parameter_handler_classes += [
handler
for handler in registered_handlers
if handler not in parameter_handler_classes
]
self._register_parameter_handler_classes(parameter_handler_classes)
# Register all ParameterIOHandler objects that will process serialized parameter representations
if parameter_io_handler_classes is None:
parameter_io_handler_classes = all_subclasses(ParameterIOHandler)
self._register_parameter_io_handler_classes(parameter_io_handler_classes)
# Parse all sources containing SMIRNOFF parameter definitions
self.parse_sources(sources, allow_cosmetic_attributes=allow_cosmetic_attributes)
def _initialize(self):
"""
Initialize all object fields.
"""
self._MIN_SUPPORTED_SMIRNOFF_VERSION = 0.1
self._MAX_SUPPORTED_SMIRNOFF_VERSION = 0.3
self._disable_version_check = (
False # if True, will disable checking compatibility version
)
self._aromaticity_model = None
self._parameter_handler_classes = (
OrderedDict()
) # Parameter handler classes that _can_ be initialized if needed
self._parameter_handlers = (
OrderedDict()
) # ParameterHandler classes to be instantiated for each parameter type
self._parameter_io_handler_classes = (
OrderedDict()
) # ParameterIOHandler classes that _can_ be initialiazed if needed
self._parameter_io_handlers = (
OrderedDict()
) # ParameterIO classes to be used for each file type
self._author = None
self._date = None
def _check_smirnoff_version_compatibility(self, version):
"""
Raise a parsing exception if the given file version is incompatible with this ForceField class.
Parameters
----------
version : str
The SMIRNOFF version being read.
Raises
------
SMIRNOFFVersionError if an incompatible version is passed in.
"""
import packaging.version
# Use PEP-440 compliant version number comparison, if requested
if (not self.disable_version_check) and (
(
packaging.version.parse(str(version))
> packaging.version.parse(str(self._MAX_SUPPORTED_SMIRNOFF_VERSION))
)
or (
packaging.version.parse(str(version))
< packaging.version.parse(str(self._MIN_SUPPORTED_SMIRNOFF_VERSION))
)
):
raise SMIRNOFFVersionError(
"SMIRNOFF offxml file was written with version {}, but this version of ForceField only supports "
"version {} to version {}".format(
version,
self._MIN_SUPPORTED_SMIRNOFF_VERSION,
self._MAX_SUPPORTED_SMIRNOFF_VERSION,
)
)
@property
def aromaticity_model(self):
"""Returns the aromaticity model for this ForceField object.
Returns
-------
aromaticity_model
The aromaticity model for this force field.
"""
return self._aromaticity_model
@aromaticity_model.setter
def aromaticity_model(self, aromaticity_model):
"""
Register that this forcefield is using an aromaticity model. Will check for
compatibility with other aromaticity model(s) already in use.
Parameters
----------
aromaticity_model : str
The aromaticity model to register.
Raises
------
SMIRNOFFAromaticityError if an incompatible aromaticity model is passed in.
.. notes ::
* Currently, the only supported aromaticity model is 'OEAroModel_MDL'.
"""
# Implement better logic here if we ever support another aromaticity model
if aromaticity_model != "OEAroModel_MDL":
raise SMIRNOFFAromaticityError(
"Read aromaticity model {}. Currently only "
"OEAroModel_MDL is supported.".format(aromaticity_model)
)
self._aromaticity_model = aromaticity_model
def _add_author(self, author):
"""
Add an author to this forcefield. If this functional is called multiple times, all provided authors
will be concatenated with the string " AND ". No redundancy checking is performed by this function.
Parameters
----------
author : str
The author to add to this ForceField object
"""
if self._author is None:
self._author = author
else:
self._author += " AND " + author
def _add_date(self, date):
"""
Add an date to this forcefield. If this functional is called multiple times, all provided dates
will be concatenated with the string " AND ". No redundancy checking is performed by this function.
Parameters
----------
date : str
The author to add to this ForceField object
"""
if self._date is None:
self._date = date
else:
self._date += " AND " + date
@property
def author(self):
"""Returns the author data for this ForceField object. If not defined in any loaded files, this will be None.
Returns
-------
author : str
The author data for this forcefield.
"""
return self._author
@author.setter
def author(self, author):
"""Set the author data for this ForceField object. If not defined in any loaded files, this will be None.
Parameters
----------
author : str
The author data to set for this forcefield.
"""
self._author = author
@property
def date(self):
"""Returns the date data for this ForceField object. If not defined in any loaded files, this will be None.
Returns
-------
date : str
The date data for this forcefield.
"""
return self._date
@date.setter
def date(self, date):
"""Set the author data for this ForceField object. If not defined in any loaded files, this will be None.
Parameters
----------
date : str
The date data to set for this forcefield.
"""
self._date = date
def _register_parameter_handler_classes(self, parameter_handler_classes):
"""
Register multiple ParameterHandler classes, ensuring they specify unique tags to process
.. warning :: This API is experimental and subject to change.
Parameters
----------
parameter_handler_classes : iterable of ParameterHandler subclasses
List of ParameterHandler classes to register for this ForceField.
"""
for parameter_handler_class in parameter_handler_classes:
tagname = parameter_handler_class._TAGNAME
if tagname is not None:
if tagname in self._parameter_handler_classes:
raise Exception(
"Attempting to register ParameterHandler {}, which provides a parser for tag"
" '{}', but ParameterHandler {} has already been registered to handle that tag.".format(
parameter_handler_class,
tagname,
self._parameter_handler_classes[tagname],
)
)
self._parameter_handler_classes[tagname] = parameter_handler_class
def _register_parameter_io_handler_classes(self, parameter_io_handler_classes):
"""
Register multiple ParameterIOHandler classes, ensuring they specify unique suffixes
.. warning :: This API is experimental and subject to change.
Parameters
----------
parameter_io_handler_classes : iterable of ParameterIOHandler subclasses
All specified ParameterIOHandler classes will be registered as ways to translate to/from the object model
to serialized parameter sets.
Raises
------
Exception if two ParameterIOHandlers are attempted to be registered for the same file format.
"""
for parameter_io_handler_class in parameter_io_handler_classes:
serialization_format = parameter_io_handler_class._FORMAT
if serialization_format is not None:
if serialization_format in self._parameter_io_handler_classes.keys():
raise Exception(
"Attempting to register ParameterIOHandler {}, which provides a IO parser for format "
"'{}', but ParameterIOHandler {} has already been registered to handle that tag.".format(
parameter_io_handler_class,
serialization_format,
self._parameter_io_handler_classes[serialization_format],
)
)
self._parameter_io_handler_classes[
serialization_format
] = parameter_io_handler_class
[docs] def register_parameter_handler(self, parameter_handler):
"""
Register a new ParameterHandler for a specific tag, making it
available for lookup in the ForceField.
.. warning :: This API is experimental and subject to change.
Parameters
----------
parameter_handler : A ParameterHandler object
The ParameterHandler to register. The TAGNAME attribute of this object will be used as the key for
registration.
"""
tagname = parameter_handler._TAGNAME
if tagname in self._parameter_handlers.keys():
raise ParameterHandlerRegistrationError(
"Tried to register parameter handler '{}' for tag '{}', but "
"tag is already registered to {}".format(
parameter_handler, tagname, self._parameter_handlers[tagname]
)
)
self._parameter_handlers[parameter_handler._TAGNAME] = parameter_handler
[docs] def register_parameter_io_handler(self, parameter_io_handler):
"""
Register a new ParameterIOHandler, making it available for lookup in the ForceField.
.. warning :: This API is experimental and subject to change.
Parameters
----------
parameter_io_handler : A ParameterIOHandler object
The ParameterIOHandler to register. The FORMAT attribute of this object will be used
to associate it to a file format/suffix.
"""
io_format = parameter_io_handler._FORMAT
if io_format in self._parameter_io_handlers.keys():
raise ParameterHandlerRegistrationError(
"Tried to register parameter IO handler '{}' for tag '{}', but "
"tag is already registered to {}".format(
parameter_io_handler,
io_format,
self._parameter_io_handlers[io_format],
)
)
self._parameter_io_handlers[io_format] = parameter_io_handler
@property
def registered_parameter_handlers(self):
"""
Return the list of registered parameter handlers by name
.. warning :: This API is experimental and subject to change.
Returns
-------
registered_parameter_handlers: iterable of names of ParameterHandler objects in this ForceField
"""
return [*self._parameter_handlers.keys()]
# TODO: Do we want to make this optional?
@staticmethod
def _check_for_missing_valence_terms(
name, topology, assigned_terms, topological_terms
):
"""
Check to ensure there are no missing valence terms in the given topology, identifying potential gaps in
parameter coverage.
.. warning :: This API is experimental and subject to change.
Parameters
----------
name : str
Name of the calling force Handler
topology : openforcefield.topology.Topology
The Topology object
assigned_terms : iterable of ints or int tuples
Atom index tuples defining added valence terms
topological_terms : iterable of atoms or atom tuples
Atom tuples defining topological valence atomsets to which forces should be assigned
"""
# Convert assigned terms and topological terms to lists
assigned_terms = [item for item in assigned_terms]
topological_terms = [item for item in topological_terms]
def ordered_tuple(atoms):
atoms = list(atoms)
if atoms[0] < atoms[-1]:
return tuple(atoms)
else:
return tuple(reversed(atoms))
try:
topology_set = set(
[
ordered_tuple(atom.index for atom in atomset)
for atomset in topological_terms
]
)
assigned_set = set(
[
ordered_tuple(index for index in atomset)
for atomset in assigned_terms
]
)
except TypeError as te:
topology_set = set([atom.index for atom in topological_terms])
assigned_set = set([atomset[0] for atomset in assigned_terms])
def render_atoms(atomsets):
msg = ""
for atomset in atomsets:
msg += f"{atomset:30} :"
try:
for atom_index in atomset:
atom = atoms[atom_index]
msg += f" {atom.residue.index:5} {atom.residue.name:3} {atom.name:3}"
except TypeError as te:
atom = atoms[atomset]
msg += (
f" {atom.residue.index:5} {atom.residue.name:3} {atom.name:3}"
)
msg += "\n"
return msg
if set(assigned_set) != set(topology_set):
# Form informative error message
msg = f"{name}: Mismatch between valence terms added and topological terms expected.\n"
atoms = [atom for atom in topology.topology_atoms]
if len(assigned_set.difference(topology_set)) > 0:
msg += "Valence terms created that are not present in Topology:\n"
msg += render_atoms(assigned_set.difference(topology_set))
if len(topology_set.difference(assigned_set)) > 0:
msg += "Topological atom sets not assigned parameters:\n"
msg += render_atoms(topology_set.difference(assigned_set))
msg += "topology_set:\n"
msg += str(topology_set) + "\n"
msg += "assigned_set:\n"
msg += str(assigned_set) + "\n"
raise Exception(
msg
) # TODO: Should we raise a more specific exception here?
[docs] def get_parameter_handler(
self, tagname, handler_kwargs=None, allow_cosmetic_attributes=False
):
"""Retrieve the parameter handlers associated with the provided tagname.
If the parameter handler has not yet been instantiated, it will be created and returned.
If a parameter handler object already exists, it will be checked for compatibility
and an Exception raised if it is incompatible with the provided kwargs. If compatible, the
existing ParameterHandler will be returned.
Parameters
----------
tagname : str
The name of the parameter to be handled.
handler_kwargs : dict, optional. Default = None
Dict to be passed to the handler for construction or checking compatibility. If this is None and no
existing ParameterHandler exists for the desired tag, a handler will be initialized with all default
values. If this is None and a handler for the desired tag exists, the existing ParameterHandler will
be returned.
allow_cosmetic_attributes : bool, optional. Default = False
Whether to permit non-spec kwargs in smirnoff_data.
Returns
-------
handler : An openforcefield.engines.typing.smirnoff.ParameterHandler
Raises
------
KeyError if there is no ParameterHandler for the given tagname
"""
# If there are no kwargs for the handler, initialize handler_kwargs as an empty dict
skip_version_check = False
if handler_kwargs is None:
handler_kwargs = dict()
skip_version_check = True
# Ensure that the ForceField has a ParameterHandler class registered that can handle this tag
ph_class = self._get_parameter_handler_class(tagname)
if tagname in self._parameter_handlers:
# If a handler of this class already exists, ensure that the two handlers encode compatible science
old_handler = self._parameter_handlers[tagname]
# If no handler kwargs were provided, skip the compatibility check
if handler_kwargs != {}:
# Initialize a new instance of this parameter handler class with the given kwargs
new_handler = ph_class(
**handler_kwargs,
allow_cosmetic_attributes=allow_cosmetic_attributes,
skip_version_check=skip_version_check,
)
old_handler.check_handler_compatibility(new_handler)
return_handler = old_handler
elif tagname in self._parameter_handler_classes:
# Otherwise, register this handler in the forcefield
# Initialize a new instance of this parameter handler class with the given kwargs
new_handler = ph_class(
**handler_kwargs,
allow_cosmetic_attributes=allow_cosmetic_attributes,
skip_version_check=skip_version_check,
)
self.register_parameter_handler(new_handler)
return_handler = new_handler
return return_handler
[docs] def get_parameter_io_handler(self, io_format):
"""Retrieve the parameter handlers associated with the provided tagname.
If the parameter IO handler has not yet been instantiated, it will be created.
Parameters
----------
io_format : str
The name of the io format to be handled.
Returns
-------
io_handler : An openforcefield.engines.typing.smirnoff.ParameterIOHandler
Raises
------
KeyError if there is no ParameterIOHandler for the given tagname
"""
# Uppercase the format string to avoid case mismatches
io_format = io_format.upper()
# Remove "." (ParameterIOHandler tags do not include it)
io_format = io_format.strip(".")
# Find or initialize ParameterIOHandler for this format
io_handler = None
if io_format in self._parameter_io_handlers.keys():
io_handler = self._parameter_io_handlers[io_format]
elif io_format in self._parameter_io_handler_classes.keys():
new_handler_class = self._parameter_io_handler_classes[io_format]
io_handler = new_handler_class()
self.register_parameter_io_handler(io_handler)
if io_handler is None:
msg = "Cannot find a registered parameter IO handler for format '{}'\n".format(
io_format
)
msg += "Registered parameter IO handlers: {}\n".format(
self._parameter_io_handlers.keys()
)
raise KeyError(msg)
return io_handler
[docs] def parse_sources(self, sources, allow_cosmetic_attributes=True):
"""Parse a SMIRNOFF force field definition.
Parameters
----------
sources : string or file-like object or open file handle or URL (or iterable of these)
A list of files defining the SMIRNOFF force field to be loaded.
Currently, only `the SMIRNOFF XML format <https://github.com/openforcefield/openforcefield/blob/master/The-SMIRNOFF-force-field-format.md>`_ is supported.
Each entry may be an absolute file path, a path relative to the current working directory, a path relative to this module's data subdirectory
(for built in force fields), or an open file-like object with a ``read()`` method from which the forcefield XML data can be loaded.
If multiple files are specified, any top-level tags that are repeated will be merged if they are compatible,
with files appearing later in the sequence resulting in parameters that have higher precedence.
Support for multiple files is primarily intended to allow solvent parameters to be specified by listing them last in the sequence.
allow_cosmetic_attributes : bool, optional. Default = False
Whether to permit non-spec kwargs present in the source.
.. notes ::
* New SMIRNOFF sections are handled independently, as if they were specified in the same file.
* If a SMIRNOFF section that has already been read appears again, its definitions are appended to the end of the previously-read
definitions if the sections are configured with compatible attributes; otherwise, an ``IncompatibleTagException`` is raised.
"""
# Ensure that we are working with an iterable
try:
sources = iter(sources)
except TypeError as te:
# Make iterable object
sources = [sources]
# TODO: If a non-first source fails here, the forcefield might be partially modified
for source in sources:
smirnoff_data = self.parse_smirnoff_from_source(source)
self._load_smirnoff_data(
smirnoff_data, allow_cosmetic_attributes=allow_cosmetic_attributes
)
def _to_smirnoff_data(self, discard_cosmetic_attributes=False):
"""
Convert this ForceField and all related ParameterHandlers to an OrderedDict representing a SMIRNOFF
data object.
Returns
-------
smirnoff_dict : OrderedDict
A nested OrderedDict representing this ForceField as a SMIRNOFF data object.
discard_cosmetic_attributes : bool, optional. Default=False
Whether to discard any non-spec attributes stored in the ForceField.
"""
l1_dict = OrderedDict()
# Assume we will write out SMIRNOFF data in compliance with the max supported spec version
l1_dict["version"] = self._MAX_SUPPORTED_SMIRNOFF_VERSION
# Write out the aromaticity model used
l1_dict["aromaticity_model"] = self._aromaticity_model
# Write out author and date (if they have been set)
if not (self._author is None):
l1_dict["Author"] = self._author
# Write out author and date (if they have been set)
if not (self._date is None):
l1_dict["Date"] = self._date
for handler_format, parameter_handler in self._parameter_handlers.items():
handler_tag = parameter_handler._TAGNAME
l1_dict[handler_tag] = parameter_handler.to_dict(
discard_cosmetic_attributes=discard_cosmetic_attributes
)
smirnoff_dict = OrderedDict()
smirnoff_dict["SMIRNOFF"] = l1_dict
smirnoff_dict = convert_all_quantities_to_string(smirnoff_dict)
return smirnoff_dict
# TODO: Should we call this "from_dict"?
def _load_smirnoff_data(self, smirnoff_data, allow_cosmetic_attributes=False):
"""
Add parameters from a SMIRNOFF-format data structure to this ForceField.
Parameters
----------
smirnoff_data : OrderedDict
A representation of a SMIRNOFF-format data structure. Begins at top-level 'SMIRNOFF' key.
allow_cosmetic_attributes : bool, optional. Default = False
Whether to permit non-spec kwargs in smirnoff_data.
"""
from collections import defaultdict
import packaging.version
# Check that the SMIRNOFF version of this data structure is supported by this ForceField implementation
if "SMIRNOFF" in smirnoff_data:
version = smirnoff_data["SMIRNOFF"]["version"]
elif "SMIRFF" in smirnoff_data:
version = smirnoff_data["SMIRFF"]["version"]
else:
raise ParseError("'version' attribute must be specified in SMIRNOFF tag")
self._check_smirnoff_version_compatibility(str(version))
# Convert 0.1 spec files to 0.3 SMIRNOFF data format by converting
# from 0.1 spec to 0.2, then 0.2 to 0.3
if packaging.version.parse(str(version)) == packaging.version.parse("0.1"):
# NOTE: This will convert the top-level "SMIRFF" tag to "SMIRNOFF"
smirnoff_data = convert_0_1_smirnoff_to_0_2(smirnoff_data)
smirnoff_data = convert_0_2_smirnoff_to_0_3(smirnoff_data)
# Convert 0.2 spec files to 0.3 SMIRNOFF data format by removing units
# from section headers and adding them to quantity strings at all levels.
elif packaging.version.parse(str(version)) == packaging.version.parse("0.2"):
smirnoff_data = convert_0_2_smirnoff_to_0_3(smirnoff_data)
# Ensure that SMIRNOFF is a top-level key of the dict
if not ("SMIRNOFF" in smirnoff_data):
raise ParseError(
"'SMIRNOFF' must be a top-level key in the SMIRNOFF object model"
)
# Check that the aromaticity model required by this parameter set is compatible with
# others loaded by this ForceField
if "aromaticity_model" in smirnoff_data["SMIRNOFF"]:
aromaticity_model = smirnoff_data["SMIRNOFF"]["aromaticity_model"]
self.aromaticity_model = aromaticity_model
elif self._aromaticity_model is None:
raise ParseError(
"'aromaticity_model' attribute must be specified in SMIRNOFF "
"tag, or contained in a previously-loaded SMIRNOFF data source"
)
if "Author" in smirnoff_data["SMIRNOFF"]:
self._add_author(smirnoff_data["SMIRNOFF"]["Author"])
if "Date" in smirnoff_data["SMIRNOFF"]:
self._add_date(smirnoff_data["SMIRNOFF"]["Date"])
# Go through the whole SMIRNOFF data structure, trying to convert all strings to Quantity
smirnoff_data = convert_all_strings_to_quantity(smirnoff_data)
# Go through the subsections, delegating each to the proper ParameterHandler
# Define keys which are expected from the spec, but are not parameter sections
l1_spec_keys = ["Author", "Date", "version", "aromaticity_model"]
# TODO: Throw SMIRNOFFSpecError for unrecognized keywords
for parameter_name in smirnoff_data["SMIRNOFF"]:
# Skip (for now) cosmetic l1 items. They're handled above
if parameter_name in l1_spec_keys:
continue
# Handle cases where a parameter name has no info (eg. ToolkitAM1BCC)
if smirnoff_data["SMIRNOFF"][parameter_name] is None:
# "get"ting the parameter handler here will also initialize it.
_ = self.get_parameter_handler(parameter_name, {})
continue
# Otherwise, we expect this l1_key to correspond to a ParameterHandler
section_dict = smirnoff_data["SMIRNOFF"][parameter_name]
# TODO: Implement a ParameterHandler.from_dict() that knows how to deserialize itself for extensibility.
# We could let it load the ParameterTypes from the dict and append them to the existing handler
# after verifying that they are compatible.
# Get the parameter types serialization that is not passed to the ParameterHandler constructor.
ph_class = self._get_parameter_handler_class(parameter_name)
try:
infotype = ph_class._INFOTYPE
parameter_list_tagname = infotype._ELEMENT_NAME
except AttributeError:
# The ParameterHandler doesn't have ParameterTypes (e.g. ToolkitAM1BCCHandler).
parameter_list_dict = {}
else:
parameter_list_dict = section_dict.pop(parameter_list_tagname, {})
# Must be wrapped into its own tag.
# Assumes that parameter_list_dict is always a list
# If the parameter list isn't empty, it must be transferred into its own tag.
# This is necessary for deserializing SMIRNOFF force field sections which may or may
# not have any smirks-based elements (like an empty ChargeIncrementModel section)
if parameter_list_dict != {}:
parameter_list_dict = {parameter_list_tagname: parameter_list_dict}
# Retrieve or create parameter handler, passing in section_dict to check for
# compatibility if a handler for this parameter name already exists
handler = self.get_parameter_handler(
parameter_name,
section_dict,
allow_cosmetic_attributes=allow_cosmetic_attributes,
)
handler._add_parameters(
parameter_list_dict, allow_cosmetic_attributes=allow_cosmetic_attributes
)
[docs] def parse_smirnoff_from_source(self, source):
"""
Reads a SMIRNOFF data structure from a source, which can be one of many types.
Parameters
----------
source : str or bytes
sources : string or file-like object or open file handle or URL (or iterable of these)
A list of files defining the SMIRNOFF force field to be loaded
Currently, only `the SMIRNOFF XML format <https://github.com/openforcefield/openforcefield/blob/master/The-SMIRNOFF-force-field-format.md>`_ is supported.
Each entry may be an absolute file path, a path relative to the current working directory, a path relative to this module's data subdirectory
(for built in force fields), or an open file-like object with a ``read()`` method from which the forcefield XML data can be loaded.
Returns
-------
smirnoff_data : OrderedDict
A representation of a SMIRNOFF-format data structure. Begins at top-level 'SMIRNOFF' key.
"""
from openforcefield.utils import get_data_file_path
# Check whether this could be a file path. It could also be a
# file handler or a simple XML string.
if isinstance(source, str):
# Try first the simple path.
searched_dirs_paths = [""]
# Then try a relative file path w.r.t. an installed directory.
searched_dirs_paths.extend(_get_installed_offxml_dir_paths())
# Finally, search in openforcefield/data/.
# TODO: Remove this when smirnoff99Frosst 1.0.9 will be released.
searched_dirs_paths.append(get_data_file_path(""))
# Determine the actual path of the file.
# TODO: What is desired toolkit behavior if two files with the desired name are available?
for dir_path in searched_dirs_paths:
file_path = os.path.join(dir_path, source)
if os.path.isfile(file_path):
source = file_path
break
# Process all SMIRNOFF definition files or objects
# QUESTION: Allow users to specify forcefield URLs so they can pull forcefield definitions from the web too?
io_formats_to_try = self._parameter_io_handler_classes.keys()
# Parse content depending on type
for parameter_io_format in io_formats_to_try:
parameter_io_handler = self.get_parameter_io_handler(parameter_io_format)
# Try parsing as a forcefield file or file-like object
try:
smirnoff_data = parameter_io_handler.parse_file(source)
return smirnoff_data
except ParseError as e:
exception_msg = e.msg
except (FileNotFoundError, OSError):
# If this is not a file path or a file handle, attempt parsing as a string.
try:
smirnoff_data = parameter_io_handler.parse_string(source)
return smirnoff_data
except ParseError as e:
exception_msg = e.msg
# If we haven't returned by now, the parsing was unsuccessful
valid_formats = [
input_format for input_format in self._parameter_io_handlers.keys()
]
msg = f"Source {source} could not be read. If this is a file, ensure that the path is correct.\n"
msg += "If the file is present, ensure it is in a known SMIRNOFF encoding.\n"
msg += f"Valid formats are: {valid_formats}\n"
msg += f"Parsing failed with the following error:\n{exception_msg}\n"
raise IOError(msg)
[docs] def to_string(self, io_format="XML", discard_cosmetic_attributes=False):
"""
Write this Forcefield and all its associated parameters to a string in a given format which
complies with the SMIRNOFF spec.
Parameters
----------
io_format : str or ParameterIOHandler, optional. Default='XML'
The serialization format to write to
discard_cosmetic_attributes : bool, default=False
Whether to discard any non-spec attributes stored in the ForceField.
Returns
-------
forcefield_string : str
The string representation of the serialized forcefield
"""
# Resolve which IO handler to use
if isinstance(io_format, ParameterIOHandler):
io_handler = io_format
else:
io_handler = self.get_parameter_io_handler(io_format)
smirnoff_data = self._to_smirnoff_data(
discard_cosmetic_attributes=discard_cosmetic_attributes
)
string_data = io_handler.to_string(smirnoff_data)
return string_data
[docs] def to_file(self, filename, io_format=None, discard_cosmetic_attributes=False):
"""
Write this Forcefield and all its associated parameters to a string in a given format which
complies with the SMIRNOFF spec.
Parameters
----------
filename : str
The filename to write to
io_format : str or ParameterIOHandler, optional. Default=None
The serialization format to write out. If None, will attempt to be inferred from the filename.
discard_cosmetic_attributes : bool, default=False
Whether to discard any non-spec attributes stored in the ForceField.
Returns
-------
forcefield_string : str
The string representation of the serialized forcefield
"""
if io_format is None:
basename, io_format = os.path.splitext(filename)
# Resolve which IO handler to use
if isinstance(io_format, ParameterIOHandler):
io_handler = io_format
else:
# Handle the fact that .offxml is the same as .xml
if io_format.lower() == "offxml" or io_format.lower() == ".offxml":
io_format = "xml"
io_handler = self.get_parameter_io_handler(io_format)
# Write out the SMIRNOFF data to the IOHandler
smirnoff_data = self._to_smirnoff_data(
discard_cosmetic_attributes=discard_cosmetic_attributes
)
io_handler.to_file(filename, smirnoff_data)
def _resolve_parameter_handler_order(self):
"""Resolve the order in which ParameterHandler objects should execute to satisfy constraints.
Returns
-------
Iterable of ParameterHandlers
The ParameterHandlers in this ForceField, in the order that they should be called to satisfy constraints.
"""
# Create a DAG expressing dependencies
import networkx as nx
G = nx.DiGraph()
for tagname, parameter_handler in self._parameter_handlers.items():
G.add_node(tagname)
for tagname, parameter_handler in self._parameter_handlers.items():
if parameter_handler._DEPENDENCIES is not None:
for dependency in parameter_handler._DEPENDENCIES:
G.add_edge(dependency._TAGNAME, parameter_handler._TAGNAME)
# Ensure there are no loops in handler order
if not (nx.is_directed_acyclic_graph(G)):
raise RuntimeError(
"Unable to resolve order in which to run ParameterHandlers. Dependencies do not form "
"a directed acyclic graph."
)
# Resolve order
ordered_parameter_handlers = list()
for tagname in nx.topological_sort(G):
if tagname in self._parameter_handlers:
ordered_parameter_handlers.append(self._parameter_handlers[tagname])
return ordered_parameter_handlers
# TODO: Should we add convenience methods to parameterize a Topology and export directly to AMBER, gromacs, CHARMM, etc.?
# Or should we create an "enhanced" openforcefield System object that knows how to convert to all of these formats?
# We could even create a universal applyParameters(format='AMBER') method that allows us to export to whatever system we want.
# TODO: Should the Topology contain the default box vectors? Or should we require they be specified externally?
# TODO: How do we know if the system is periodic or not?
# TODO: Should we also accept a Molecule as an alternative to a Topology?
[docs] def create_openmm_system(self, topology, **kwargs):
"""Create an OpenMM System representing the interactions for the specified Topology with the current force field
Parameters
----------
topology : openforcefield.topology.Topology
The ``Topology`` corresponding to the system to be parameterized
charge_from_molecules : List[openforcefield.molecule.Molecule], optional. default =[]
If specified, partial charges will be taken from the given molecules
instead of being determined by the force field.
partial_bond_orders_from_molecules : List[openforcefield.molecule.Molecule], optional. default=[]
If specified, partial bond orders will be taken from the given molecules
instead of being determined by the force field.
**All** bonds on each molecule given must have ``fractional_bond_order`` specified.
A `ValueError` will be raised if any bonds have ``fractional_bond_order=None``.
Molecules in the topology not represented in this list will have fractional
bond orders calculated using underlying toolkits as needed.
return_topology : bool, optional. default=False
If ``True``, return tuple of ``(system, topology)``, where
``topology`` is the processed topology. Default ``False``. This topology will have the
final partial charges assigned on its reference_molecules attribute, as well as partial
bond orders (if they were calculated).
Returns
-------
system : simtk.openmm.System
The newly created OpenMM System corresponding to the specified ``topology``
topology : openforcefield.topology.Topology, optional.
If the `return_topology` keyword argument is used, this method will also return a Topology. This
can be used to inspect the partial charges and partial bond orders assigned to the molecules
during parameterization.
"""
return_topology = kwargs.pop("return_topology", False)
# Make a deep copy of the topology so we don't accidentally modify it
topology = copy.deepcopy(topology)
# set all fractional_bond_orders in topology to None
for ref_mol in topology.reference_molecules:
for bond in ref_mol.bonds:
bond.fractional_bond_order = None
# Set the topology aromaticity model to that used by the current forcefield
# TODO: See openforcefield issue #206 for proposed implementation of aromaticity
# topology.set_aromaticity_model(self._aromaticity_model)
# Create an empty OpenMM System
system = openmm.System()
# Set periodic boundary conditions if specified
if topology.box_vectors is not None:
system.setDefaultPeriodicBoxVectors(*topology.box_vectors)
# Add particles (both atoms and virtual sites) with appropriate masses
for atom in topology.topology_particles:
system.addParticle(atom.atom.mass)
# Determine the order in which to process ParameterHandler objects in order to satisfy dependencies
parameter_handlers = self._resolve_parameter_handler_order()
# Check if any kwargs have been provided that aren't handled by force Handlers
# TODO: Delete this and kwargs from arguments above?
known_kwargs = set()
for parameter_handler in parameter_handlers:
known_kwargs.update(parameter_handler.known_kwargs)
unknown_kwargs = set(kwargs.keys()).difference(known_kwargs)
if len(unknown_kwargs) > 0:
msg = "The following keyword arguments to create_openmm_system() are not used by any registered force Handler: {}\n".format(
unknown_kwargs
)
msg += "Known keyword arguments: {}".format(known_kwargs)
raise ValueError(msg)
# Add forces and parameters to the System
for parameter_handler in parameter_handlers:
parameter_handler.create_force(system, topology, **kwargs)
# Let force Handlers do postprocessing
for parameter_handler in parameter_handlers:
parameter_handler.postprocess_system(system, topology, **kwargs)
if return_topology:
return (system, topology)
else:
return system
[docs] def create_parmed_structure(self, topology, positions, **kwargs):
"""Create a ParmEd Structure object representing the interactions for the specified Topology with the current force field
This method creates a `ParmEd <http://github.com/parmed/parmed>`_ ``Structure`` object containing a topology, positions, and parameters.
Parameters
----------
topology : openforcefield.topology.Topology
The ``Topology`` corresponding to the ``System`` object to be created.
positions : simtk.unit.Quantity of dimension (natoms,3) with units compatible with angstroms
The positions corresponding to the ``System`` object to be created
Returns
-------
structure : parmed.Structure
The newly created ``parmed.Structure`` object
"""
raise NotImplementedError
# import parmed
# TODO: Automagically handle expansion of virtual sites? Or is Topology supposed to do that?
# Create OpenMM System
# system = self.create_openmm_system(
# topology, **kwargs)
# Create a ParmEd Structure object
# structure = parmed.openmm.topsystem.load_topology(
# topology.to_openmm(), system, positions)
#
# return structure
[docs] def label_molecules(self, topology):
"""Return labels for a list of molecules corresponding to parameters from this force field.
For each molecule, a dictionary of force types is returned, and for each force type,
each force term is provided with the atoms involved, the parameter id assigned, and the corresponding SMIRKS.
Parameters
----------
topology : openforcefield.topology.Topology
A Topology object containing one or more unique molecules to be labeled
Returns
-------
molecule_labels : list
List of labels for unique molecules. Each entry in the list corresponds to
one unique molecule in the Topology and is a dictionary keyed by force type,
i.e., ``molecule_labels[0]['HarmonicBondForce']`` gives details for the harmonic
bond parameters for the first molecule. Each element is a list of the form:
``[ ( [ atom1, ..., atomN], parameter_id, SMIRKS), ... ]``.
.. todo ::
What is the most useful API for this method?
Should we instead accept :class:`Molecule` objects as input and individually return labels?
Should we attach the labels to the :class:`Molecule` object?
Or should we label all interactions in a :class:`Topology` instead of just labeling its ``unique_molecules``?
"""
from openforcefield.topology import Topology
from openforcefield.typing.engines.smirnoff.parameters import VirtualSiteHandler
# Loop over molecules and label
molecule_labels = list()
for molecule_idx, molecule in enumerate(topology.reference_molecules):
top_mol = Topology.from_molecules([molecule])
current_molecule_labels = dict()
param_is_list = False
for tag, parameter_handler in self._parameter_handlers.items():
if type(parameter_handler) == VirtualSiteHandler:
param_is_list = True
matches = parameter_handler.find_matches(top_mol)
# Remove the chemical environment matches from the
# matched results.
# Because we sometimes need to enforce atom ordering,
# `matches` here is not a normal `dict`, but rather
# one that transforms keys in arbitrary ways. Thus,
# we need to make a copy of its specific class here.
parameter_matches = matches.__class__()
# Now make parameter_matches into a dict mapping
# match objects to ParameterTypes
if param_is_list:
for match in matches:
parameter_matches[match] = [
m.parameter_type for m in matches[match]
]
else:
for match in matches:
parameter_matches[match] = matches[match].parameter_type
current_molecule_labels[tag] = parameter_matches
molecule_labels.append(current_molecule_labels)
return molecule_labels
def _get_parameter_handler_class(self, tagname):
"""Retrieve the ParameterHandler class associated to the tagname and throw a custom error if not found."""
try:
ph_class = self._parameter_handler_classes[tagname]
except KeyError:
msg = "Cannot find a registered parameter handler class for tag '{}'\n".format(
tagname
)
msg += "Known parameter handler class tags are {}".format(
self._parameter_handler_classes.keys()
)
raise KeyError(msg)
return ph_class
def __getitem__(self, val):
"""
Syntax sugar for lookikng up a ParameterHandler. Note that only
string-based lookups are currently supported.
"""
if isinstance(val, str):
if val in self._parameter_handlers:
return self.get_parameter_handler(val)
else:
raise KeyError(f"Parameter handler with name '{val}' not found.")
elif isinstance(val, ParameterHandler) or issubclass(val, ParameterHandler):
raise NotImplementedError
def __hash__(self):
"""Deterministically hash a ForceField object
Notable behavior:
* `author` and `date` are stripped from the ForceField
* `id` and `parent_id` are stripped from each ParameterType"""
# Completely re-constructing the force field may be overkill
# compared to deepcopying and modifying, but is not currently slow
ff_copy = ForceField()
ff_copy.date = None
ff_copy.author = None
param_attrs_to_strip = ["_id", "_parent_id"]
for handler_name in self.registered_parameter_handlers:
handler = copy.deepcopy(self.get_parameter_handler(handler_name))
for param in handler._parameters:
for attr in param_attrs_to_strip:
# param.__dict__.pop(attr, None) may be faster
# https://stackoverflow.com/a/42303681/4248961
if hasattr(param, attr):
delattr(param, attr)
ff_copy.register_parameter_handler(handler)
return hash(ff_copy.to_string(discard_cosmetic_attributes=True))
