openforcefield.utils.toolkits.RDKitToolkitWrapper

class openforcefield.utils.toolkits.RDKitToolkitWrapper[source]

RDKit toolkit wrapper

Warning

This API is experimental and subject to change.

Attributes:
toolkit_file_read_formats

List of file formats that this toolkit can read.

toolkit_file_write_formats

List of file formats that this toolkit can write.

toolkit_installation_instructions

classmethod(function) -> method

toolkit_name

The name of the toolkit wrapped by this class.

Methods

find_smarts_matches(molecule, smarts[, …]) Find all SMARTS matches for the specified molecule, using the specified aromaticity model.
from_file(filename, file_format[, …]) Create an openforcefield.topology.Molecule from a file using this toolkit.
from_file_obj(file_obj, file_format[, …]) Return an openforcefield.topology.Molecule from a file-like object (an object with a “.read()” method using this toolkit.
from_object(object) If given an rdchem.Mol (or rdchem.Mol-derived object), this function will load it into an openforcefield.topology.molecule.
from_rdkit(rdmol[, allow_undefined_stereo]) Create a Molecule from an RDKit molecule.
from_smiles(smiles[, hydrogens_are_explicit]) Create a Molecule from a SMILES string using the RDKit toolkit.
generate_conformers(molecule[, …]) Generate molecule conformers using RDKit.
is_available() Check whether toolkit is available for use.
requires_toolkit()
to_file(molecule, outfile, outfile_format) Writes an OpenFF Molecule to a file-like object
to_file_obj(molecule, file_obj, outfile_format) Writes an OpenFF Molecule to a file-like object
to_rdkit(molecule[, aromaticity_model]) Create an RDKit molecule
to_smiles(molecule) Uses the RDKit toolkit to convert a Molecule into a SMILES string.
toolkit_is_available() Check whether the RDKit toolkit can be imported
__init__($self, /, *args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

Methods

find_smarts_matches(molecule, smarts[, …]) Find all SMARTS matches for the specified molecule, using the specified aromaticity model.
from_file(filename, file_format[, …]) Create an openforcefield.topology.Molecule from a file using this toolkit.
from_file_obj(file_obj, file_format[, …]) Return an openforcefield.topology.Molecule from a file-like object (an object with a “.read()” method using this toolkit.
from_object(object) If given an rdchem.Mol (or rdchem.Mol-derived object), this function will load it into an openforcefield.topology.molecule.
from_rdkit(rdmol[, allow_undefined_stereo]) Create a Molecule from an RDKit molecule.
from_smiles(smiles[, hydrogens_are_explicit]) Create a Molecule from a SMILES string using the RDKit toolkit.
generate_conformers(molecule[, …]) Generate molecule conformers using RDKit.
is_available() Check whether toolkit is available for use.
requires_toolkit()
to_file(molecule, outfile, outfile_format) Writes an OpenFF Molecule to a file-like object
to_file_obj(molecule, file_obj, outfile_format) Writes an OpenFF Molecule to a file-like object
to_rdkit(molecule[, aromaticity_model]) Create an RDKit molecule
to_smiles(molecule) Uses the RDKit toolkit to convert a Molecule into a SMILES string.
toolkit_is_available() Check whether the RDKit toolkit can be imported

Attributes

toolkit_file_read_formats List of file formats that this toolkit can read.
toolkit_file_write_formats List of file formats that this toolkit can write.
toolkit_installation_instructions classmethod(function) -> method
toolkit_name The name of the toolkit wrapped by this class.
static toolkit_is_available()[source]

Check whether the RDKit toolkit can be imported

Returns:
is_installed : bool

True if RDKit is installed, False otherwise.

classmethod is_available()[source]

Check whether toolkit is available for use.

Parameters:
is_available : bool

True if toolkit is available for use, False otherwise

from_object(object)[source]

If given an rdchem.Mol (or rdchem.Mol-derived object), this function will load it into an openforcefield.topology.molecule. Otherwise, it will return False.

Parameters:
object : A rdchem.Mol-derived object

An object to be type-checked and converted into a Molecule, if possible.

Returns:
Molecule or False

An openforcefield.topology.molecule Molecule.

Raises:
NotImplementedError

If the object could not be converted into a Molecule.

from_file(filename, file_format, allow_undefined_stereo=False)[source]

Create an openforcefield.topology.Molecule from a file using this toolkit.

Parameters:
filename : str

The file to read the molecule from

file_format : str

Format specifier, usually file suffix (eg. ‘MOL2’, ‘SMI’) Note that not all toolkits support all formats. Check ToolkitWrapper.toolkit_file_read_formats for details.

allow_undefined_stereo : bool, default=False

If false, raises an exception if oemol contains undefined stereochemistry.

Returns:
molecules : iterable of Molecules

a list of Molecule objects is returned.

from_file_obj(file_obj, file_format, allow_undefined_stereo=False)[source]

Return an openforcefield.topology.Molecule from a file-like object (an object with a “.read()” method using this toolkit.

Warning

This API is experimental and subject to change.

Parameters:
file_obj : file-like object

The file-like object to read the molecule from

file_format : str

Format specifier, usually file suffix (eg. ‘MOL2’, ‘SMI’) Note that not all toolkits support all formats. Check ToolkitWrapper.toolkit_file_read_formats for details.

allow_undefined_stereo : bool, default=False

If false, raises an exception if oemol contains undefined stereochemistry.

Returns:
molecules : Molecule or list of Molecules

a list of Molecule objects is returned.

to_file_obj(molecule, file_obj, outfile_format)[source]

Writes an OpenFF Molecule to a file-like object

Parameters:
molecule : an OpenFF Molecule

The molecule to write

file_obj

The file-like object to write to

outfile_format

The format for writing the molecule data

to_file(molecule, outfile, outfile_format)[source]

Writes an OpenFF Molecule to a file-like object

Parameters:
molecule : an OpenFF Molecule

The molecule to write

outfile

The filename to write to

outfile_format

The format for writing the molecule data

Returns
——
classmethod to_smiles(molecule)[source]

Uses the RDKit toolkit to convert a Molecule into a SMILES string.

Parameters:
molecule : An openforcefield.topology.Molecule

The molecule to convert into a SMILES.

Returns:
smiles : str

The SMILES of the input molecule.

from_smiles(smiles, hydrogens_are_explicit=False)[source]

Create a Molecule from a SMILES string using the RDKit toolkit.

Warning

This API is experimental and subject to change.

Parameters:
smiles : str

The SMILES string to turn into a molecule

hydrogens_are_explicit : bool, default=False

If False, RDKit will perform hydrogen addition using Chem.AddHs

Returns:
molecule : openforcefield.topology.Molecule

An openforcefield-style molecule.

generate_conformers(molecule, num_conformers=1, clear_existing=True)[source]

Generate molecule conformers using RDKit.

Warning

This API is experimental and subject to change.

molecule : a Molecule
The molecule to generate conformers for.
num_conformers : int, default=1
Maximum number of conformers to generate.
clear_existing : bool, default=True
Whether to overwrite existing conformers for the molecule.
from_rdkit(rdmol, allow_undefined_stereo=False)[source]

Create a Molecule from an RDKit molecule.

Requires the RDKit to be installed.

Warning

This API is experimental and subject to change.

Parameters:
rdmol : rkit.RDMol

An RDKit molecule

allow_undefined_stereo : bool, default=False

If false, raises an exception if rdmol contains undefined stereochemistry.

Returns:
molecule : openforcefield.Molecule

An openforcefield molecule

Examples

Create a molecule from an RDKit molecule

>>> from rdkit import Chem
>>> from openforcefield.tests.utils import get_data_filename
>>> rdmol = Chem.MolFromMolFile(get_data_filename('systems/monomers/ethanol.sdf'))
>>> toolkit_wrapper = RDKitToolkitWrapper()
>>> molecule = toolkit_wrapper.from_rdkit(rdmol)
classmethod to_rdkit(molecule, aromaticity_model='OEAroModel_MDL')[source]

Create an RDKit molecule

Requires the RDKit to be installed.

Warning

This API is experimental and subject to change.

Parameters:
aromaticity_model : str, optional, default=DEFAULT_AROMATICITY_MODEL

The aromaticity model to use

Returns:
rdmol : rkit.RDMol

An RDKit molecule

Examples

Convert a molecule to RDKit

>>> from openforcefield.topology import Molecule
>>> ethanol = Molecule.from_smiles('CCO')
>>> rdmol = ethanol.to_rdkit()
find_smarts_matches(molecule, smarts, aromaticity_model='OEAroModel_MDL')[source]

Find all SMARTS matches for the specified molecule, using the specified aromaticity model.

Warning

This API is experimental and subject to change.

Parameters:
molecule : openforcefield.topology.Molecule

The molecule for which all specified SMARTS matches are to be located

smarts : str

SMARTS string with optional SMIRKS-style atom tagging

aromaticity_model : str, optional, default=’OEAroModel_MDL’

Aromaticity model to use during matching

.. note :: Currently, the only supported ``aromaticity_model`` is ``OEAroModel_MDL``
toolkit_file_read_formats

List of file formats that this toolkit can read.

toolkit_file_write_formats

List of file formats that this toolkit can write.

toolkit_installation_instructions

classmethod(function) -> method

Convert a function to be a class method.

A class method receives the class as implicit first argument, just like an instance method receives the instance. To declare a class method, use this idiom:

class C:

@classmethod def f(cls, arg1, arg2, …):

It can be called either on the class (e.g. C.f()) or on an instance (e.g. C().f()). The instance is ignored except for its class. If a class method is called for a derived class, the derived class object is passed as the implied first argument.

Class methods are different than C++ or Java static methods. If you want those, see the staticmethod builtin.

toolkit_name

The name of the toolkit wrapped by this class.