openforcefield.topology.FrozenMolecule¶

class openforcefield.topology.FrozenMolecule(other=None, file_format=None, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit, allow_undefined_stereo=False)[source]¶

Immutable chemical representation of a molecule, such as a small molecule or biopolymer.

Examples

Create a molecule from a sdf file

>>> from openforcefield.utils import get_data_file_path
>>> sdf_filepath = get_data_file_path('molecules/ethanol.sdf')
>>> molecule = FrozenMolecule.from_file(sdf_filepath)

Convert to OpenEye OEMol object

>>> oemol = molecule.to_openeye()

Create a molecule from an OpenEye molecule

>>> molecule = FrozenMolecule.from_openeye(oemol)

Convert to RDKit Mol object

>>> rdmol = molecule.to_rdkit()

Create a molecule from an RDKit molecule

>>> molecule = FrozenMolecule.from_rdkit(rdmol)

Create a molecule from IUPAC name (requires the OpenEye toolkit)

>>> molecule = FrozenMolecule.from_iupac('imatinib')

Create a molecule from SMILES

>>> molecule = FrozenMolecule.from_smiles('Cc1ccccc1')

Warning

This API is experimental and subject to change.

Attributes

angles: Get an iterator over all i-j-k angles.
atoms: Iterate over all Atom objects.
bonds: Iterate over all Bond objects.
conformers: Returns the list of conformers for this molecule.
has_unique_atom_names: True if the molecule has unique atom names, False otherwise.
hill_formula: Get the Hill formula of the molecule
impropers: Iterate over all proper torsions in the molecule
n_angles: int: number of angles in the Molecule.
n_atoms: The number of Atom objects.
n_bonds: The number of Bond objects.
n_conformers: Returns the number of conformers for this molecule.
n_impropers: int: number of improper torsions in the Molecule.
n_particles: The number of Particle objects, which corresponds to how many positions must be used.
n_propers: int: number of proper torsions in the Molecule.
n_rings: Return the number of rings found in the Molecule
n_virtual_particles: The number of VirtualParticle objects.
n_virtual_sites: The number of VirtualSite objects.
name: The name (or title) of the molecule
partial_charges: Returns the partial charges (if present) on the molecule.
particles: Iterate over all Particle objects.
propers: Iterate over all proper torsions in the molecule
properties: The properties dictionary of the molecule
rings: Return the number of rings in this molecule.
torsions: Get an iterator over all i-j-k-l torsions.
total_charge: Return the total charge on the molecule
virtual_sites: Iterate over all VirtualSite objects.

Methods

`are_isomorphic`(mol1, mol2[, …])	Determines whether the two molecules are isomorphic by comparing their graph representations and the chosen node/edge attributes.
`assign_fractional_bond_orders`([…])	Update and store list of bond orders this molecule.
`assign_partial_charges`(partial_charge_method)	Calculate partial atomic charges for this molecule using an underlying toolkit, and assign the new values to the partial_charges attribute.
`canonical_order_atoms`([toolkit_registry])	Canonical order the atoms in a copy of the molecule using a toolkit, returns a new copy.
`chemical_environment_matches`(query[, …])	Retrieve all matches for a given chemical environment query.
`compute_partial_charges_am1bcc`([…])	Calculate partial atomic charges for this molecule using AM1-BCC run by an underlying toolkit and assign them to this molecule’s partial_charges attribute.
`enumerate_protomers`([max_states])	Enumerate the formal charges of a molecule to generate different protomoers.
`enumerate_stereoisomers`([undefined_only, …])	Enumerate the stereocenters and bonds of the current molecule.
`enumerate_tautomers`([max_states, …])	Enumerate the possible tautomers of the current molecule
`find_rotatable_bonds`([…])	Find all bonds classed as rotatable ignoring any matched to the `ignore_functional_groups` list.
`from_bson`(serialized)	Instantiate an object from a BSON serialized representation.
`from_dict`(molecule_dict)	Create a new Molecule from a dictionary representation
`from_file`(file_path[, file_format, …])	Create one or more molecules from a file
`from_inchi`(inchi[, allow_undefined_stereo, …])	Construct a Molecule from a InChI representation
`from_iupac`(iupac_name[, toolkit_registry, …])	Generate a molecule from IUPAC or common name
`from_json`(serialized)	Instantiate an object from a JSON serialized representation.
`from_mapped_smiles`(mapped_smiles[, …])	Create an openforcefield.topology.molecule.Molecule from a mapped SMILES made with cmiles.
`from_messagepack`(serialized)	Instantiate an object from a MessagePack serialized representation.
`from_openeye`(args, *kwargs)	Create a Molecule from an OpenEye molecule.
`from_pdb_and_smiles`(file_path, smiles[, …])	Create a Molecule from a pdb file and a SMILES string using RDKit.
`from_pickle`(serialized)	Instantiate an object from a pickle serialized representation.
`from_qcschema`(qca_record[, client, …])	Create a Molecule from a QCArchive entry based on the cmiles information.
`from_rdkit`(args, *kwargs)	Create a Molecule from an RDKit molecule.
`from_smiles`(smiles[, …])	Construct a Molecule from a SMILES representation
`from_toml`(serialized)	Instantiate an object from a TOML serialized representation.
`from_topology`(topology)	Return a Molecule representation of an openforcefield Topology containing a single Molecule object.
`from_xml`(serialized)	Instantiate an object from an XML serialized representation.
`from_yaml`(serialized)	Instantiate from a YAML serialized representation.
`generate_conformers`([toolkit_registry, …])	Generate conformers for this molecule using an underlying toolkit.
`generate_unique_atom_names`()	Generate unique atom names using element name and number of times that element has occurred e.g.
`get_bond_between`(i, j)	Returns the bond between two atoms
`is_isomorphic_with`(other, **kwargs)	Check if the molecule is isomorphic with the other molecule which can be an openforcefield.topology.Molecule, or TopologyMolecule or nx.Graph().
`remap`(mapping_dict[, current_to_new])	Remap all of the indexes in the molecule to match the given mapping dict
`strip_atom_stereochemistry`(smarts[, …])	Delete stereochemistry information for certain atoms, if it is present.
`to_bson`()	Return a BSON serialized representation.
`to_dict`()	Return a dictionary representation of the molecule.
`to_file`(file_path, file_format[, …])	Write the current molecule to a file or file-like object
`to_hill_formula`(molecule)	Generate the Hill formula from either a FrozenMolecule, TopologyMolecule or nx.Graph() of the molecule
`to_inchi`([fixed_hydrogens, toolkit_registry])	Create an InChI string for the molecule using the requested toolkit backend.
`to_inchikey`([fixed_hydrogens, toolkit_registry])	Create an InChIKey for the molecule using the requested toolkit backend.
`to_iupac`([toolkit_registry])	Generate IUPAC name from Molecule
`to_json`([indent])	Return a JSON serialized representation.
`to_messagepack`()	Return a MessagePack representation.
`to_networkx`()	Generate a NetworkX undirected graph from the Molecule.
`to_openeye`([aromaticity_model])	Create an OpenEye molecule
`to_pickle`()	Return a pickle serialized representation.
`to_qcschema`([multiplicity, conformer, extras])	Generate the qschema input format used to submit jobs to archive or run qcengine calculations locally, spec can be found here <https://molssi-qc-schema.readthedocs.io/en/latest/index.html>
`to_rdkit`([aromaticity_model])	Create an RDKit molecule
`to_smiles`([isomeric, explicit_hydrogens, …])	Return a canonical isomeric SMILES representation of the current molecule.
`to_toml`()	Return a TOML serialized representation.
`to_topology`()	Return an openforcefield Topology representation containing one copy of this molecule
`to_xml`([indent])	Return an XML representation.
`to_yaml`()	Return a YAML serialized representation.

__init__(other=None, file_format=None, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit, allow_undefined_stereo=False)[source]¶

Create a new FrozenMolecule object

Parameters

otheroptional, default=None

If specified, attempt to construct a copy of the Molecule from the specified object. This can be any one of the following:

a Molecule object
a file that can be used to construct a Molecule object
an openeye.oechem.OEMol
an rdkit.Chem.rdchem.Mol
a serialized Molecule object

file_formatstr, optional, default=None

If providing a file-like object, you must specify the format of the data. If providing a file, the file format will attempt to be guessed from the suffix.

toolkit_registrya ToolkitRegistry or ToolkitWrapper object, optional, default=GLOBAL_TOOLKIT_REGISTRY

ToolkitRegistry or ToolkitWrapper to use for I/O operations

allow_undefined_stereobool, default=False

If loaded from a file and False, raises an exception if undefined stereochemistry is detected during the molecule’s construction.

Examples

Create an empty molecule:

>>> empty_molecule = FrozenMolecule()

Create a molecule from a file that can be used to construct a molecule, using either a filename or file-like object:

>>> from openforcefield.utils import get_data_file_path
>>> sdf_filepath = get_data_file_path('molecules/ethanol.sdf')
>>> molecule = FrozenMolecule(sdf_filepath)
>>> molecule = FrozenMolecule(open(sdf_filepath, 'r'), file_format='sdf')

>>> import gzip
>>> mol2_gz_filepath = get_data_file_path('molecules/toluene.mol2.gz')
>>> molecule = FrozenMolecule(gzip.GzipFile(mol2_gz_filepath, 'r'), file_format='mol2')

Create a molecule from another molecule:

>>> molecule_copy = FrozenMolecule(molecule)

Convert to OpenEye OEMol object

>>> oemol = molecule.to_openeye()

Create a molecule from an OpenEye molecule:

>>> molecule = FrozenMolecule(oemol)

Convert to RDKit Mol object

>>> rdmol = molecule.to_rdkit()

Create a molecule from an RDKit molecule:

>>> molecule = FrozenMolecule(rdmol)

Create a molecule from a serialized molecule object:

>>> serialized_molecule = molecule.__getstate__()
>>> molecule_copy = Molecule(serialized_molecule)

Methods

`__init__`([other, file_format, …])	Create a new FrozenMolecule object
`are_isomorphic`(mol1, mol2[, …])	Determines whether the two molecules are isomorphic by comparing their graph representations and the chosen node/edge attributes.
`assign_fractional_bond_orders`([…])	Update and store list of bond orders this molecule.
`assign_partial_charges`(partial_charge_method)	Calculate partial atomic charges for this molecule using an underlying toolkit, and assign the new values to the partial_charges attribute.
`canonical_order_atoms`([toolkit_registry])	Canonical order the atoms in a copy of the molecule using a toolkit, returns a new copy.
`chemical_environment_matches`(query[, …])	Retrieve all matches for a given chemical environment query.
`compute_partial_charges_am1bcc`([…])	Calculate partial atomic charges for this molecule using AM1-BCC run by an underlying toolkit and assign them to this molecule’s partial_charges attribute.
`enumerate_protomers`([max_states])	Enumerate the formal charges of a molecule to generate different protomoers.
`enumerate_stereoisomers`([undefined_only, …])	Enumerate the stereocenters and bonds of the current molecule.
`enumerate_tautomers`([max_states, …])	Enumerate the possible tautomers of the current molecule
`find_rotatable_bonds`([…])	Find all bonds classed as rotatable ignoring any matched to the `ignore_functional_groups` list.
`from_bson`(serialized)	Instantiate an object from a BSON serialized representation.
`from_dict`(molecule_dict)	Create a new Molecule from a dictionary representation
`from_file`(file_path[, file_format, …])	Create one or more molecules from a file
`from_inchi`(inchi[, allow_undefined_stereo, …])	Construct a Molecule from a InChI representation
`from_iupac`(iupac_name[, toolkit_registry, …])	Generate a molecule from IUPAC or common name
`from_json`(serialized)	Instantiate an object from a JSON serialized representation.
`from_mapped_smiles`(mapped_smiles[, …])	Create an openforcefield.topology.molecule.Molecule from a mapped SMILES made with cmiles.
`from_messagepack`(serialized)	Instantiate an object from a MessagePack serialized representation.
`from_openeye`(args, *kwargs)	Create a Molecule from an OpenEye molecule.
`from_pdb_and_smiles`(file_path, smiles[, …])	Create a Molecule from a pdb file and a SMILES string using RDKit.
`from_pickle`(serialized)	Instantiate an object from a pickle serialized representation.
`from_qcschema`(qca_record[, client, …])	Create a Molecule from a QCArchive entry based on the cmiles information.
`from_rdkit`(args, *kwargs)	Create a Molecule from an RDKit molecule.
`from_smiles`(smiles[, …])	Construct a Molecule from a SMILES representation
`from_toml`(serialized)	Instantiate an object from a TOML serialized representation.
`from_topology`(topology)	Return a Molecule representation of an openforcefield Topology containing a single Molecule object.
`from_xml`(serialized)	Instantiate an object from an XML serialized representation.
`from_yaml`(serialized)	Instantiate from a YAML serialized representation.
`generate_conformers`([toolkit_registry, …])	Generate conformers for this molecule using an underlying toolkit.
`generate_unique_atom_names`()	Generate unique atom names using element name and number of times that element has occurred e.g.
`get_bond_between`(i, j)	Returns the bond between two atoms
`is_isomorphic_with`(other, **kwargs)	Check if the molecule is isomorphic with the other molecule which can be an openforcefield.topology.Molecule, or TopologyMolecule or nx.Graph().
`remap`(mapping_dict[, current_to_new])	Remap all of the indexes in the molecule to match the given mapping dict
`strip_atom_stereochemistry`(smarts[, …])	Delete stereochemistry information for certain atoms, if it is present.
`to_bson`()	Return a BSON serialized representation.
`to_dict`()	Return a dictionary representation of the molecule.
`to_file`(file_path, file_format[, …])	Write the current molecule to a file or file-like object
`to_hill_formula`(molecule)	Generate the Hill formula from either a FrozenMolecule, TopologyMolecule or nx.Graph() of the molecule
`to_inchi`([fixed_hydrogens, toolkit_registry])	Create an InChI string for the molecule using the requested toolkit backend.
`to_inchikey`([fixed_hydrogens, toolkit_registry])	Create an InChIKey for the molecule using the requested toolkit backend.
`to_iupac`([toolkit_registry])	Generate IUPAC name from Molecule
`to_json`([indent])	Return a JSON serialized representation.
`to_messagepack`()	Return a MessagePack representation.
`to_networkx`()	Generate a NetworkX undirected graph from the Molecule.
`to_openeye`([aromaticity_model])	Create an OpenEye molecule
`to_pickle`()	Return a pickle serialized representation.
`to_qcschema`([multiplicity, conformer, extras])	Generate the qschema input format used to submit jobs to archive or run qcengine calculations locally, spec can be found here <https://molssi-qc-schema.readthedocs.io/en/latest/index.html>
`to_rdkit`([aromaticity_model])	Create an RDKit molecule
`to_smiles`([isomeric, explicit_hydrogens, …])	Return a canonical isomeric SMILES representation of the current molecule.
`to_toml`()	Return a TOML serialized representation.
`to_topology`()	Return an openforcefield Topology representation containing one copy of this molecule
`to_xml`([indent])	Return an XML representation.
`to_yaml`()	Return a YAML serialized representation.

Attributes

`angles`	Get an iterator over all i-j-k angles.
`atoms`	Iterate over all Atom objects.
`bonds`	Iterate over all Bond objects.
`conformers`	Returns the list of conformers for this molecule.
`has_unique_atom_names`	True if the molecule has unique atom names, False otherwise.
`hill_formula`	Get the Hill formula of the molecule
`impropers`	Iterate over all proper torsions in the molecule
`n_angles`	int: number of angles in the Molecule.
`n_atoms`	The number of Atom objects.
`n_bonds`	The number of Bond objects.
`n_conformers`	Returns the number of conformers for this molecule.
`n_impropers`	int: number of improper torsions in the Molecule.
`n_particles`	The number of Particle objects, which corresponds to how many positions must be used.
`n_propers`	int: number of proper torsions in the Molecule.
`n_rings`	Return the number of rings found in the Molecule
`n_virtual_particles`	The number of VirtualParticle objects.
`n_virtual_sites`	The number of VirtualSite objects.
`name`	The name (or title) of the molecule
`partial_charges`	Returns the partial charges (if present) on the molecule.
`particles`	Iterate over all Particle objects.
`propers`	Iterate over all proper torsions in the molecule
`properties`	The properties dictionary of the molecule
`rings`	Return the number of rings in this molecule.
`torsions`	Get an iterator over all i-j-k-l torsions.
`total_charge`	Return the total charge on the molecule
`virtual_sites`	Iterate over all VirtualSite objects.

property has_unique_atom_names¶: True if the molecule has unique atom names, False otherwise.

generate_unique_atom_names()[source]¶: Generate unique atom names using element name and number of times that element has occurred e.g. ‘C1’, ‘H1’, ‘O1’, ‘C2’, …

strip_atom_stereochemistry(smarts, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit)[source]¶

Delete stereochemistry information for certain atoms, if it is present. This method can be used to “normalize” molecules imported from different cheminformatics toolkits, which differ in which atom centers are considered stereogenic.

Parameters

smarts: str or ChemicalEnvironment: Tagged SMARTS with a single atom with index 1. Any matches for this atom will have any assigned stereocheistry information removed.
toolkit_registrya ToolkitRegistry or ToolkitWrapper object, optional, default=GLOBAL_TOOLKIT_REGISTRY: ToolkitRegistry or ToolkitWrapper to use for I/O operations

to_dict()[source]¶

Return a dictionary representation of the molecule.

Returns

molecule_dictOrderedDict: A dictionary representation of the molecule.

classmethod from_dict(molecule_dict)[source]¶

Create a new Molecule from a dictionary representation

Parameters

molecule_dictOrderedDict: A dictionary representation of the molecule.

Returns

moleculeMolecule: A Molecule created from the dictionary representation

to_smiles(isomeric=True, explicit_hydrogens=True, mapped=False, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit)[source]¶

Return a canonical isomeric SMILES representation of the current molecule. A partially mapped smiles can also be generated for atoms of interest by supplying an atom_map to the properties dictionary.

Note

RDKit and OpenEye versions will not necessarily return the same representation.

Parameters

isomeric: bool optional, default= True: return an isomeric smiles
explicit_hydrogens: bool optional, default=True: return a smiles string containing all hydrogens explicitly
mapped: bool optional, default=False: return a explicit hydrogen mapped smiles, the atoms to be mapped can be controlled by supplying an atom map into the properties dictionary. If no mapping is passed all atoms will be mapped in order, else an atom map dictionary from the current atom index to the map id should be supplied with no duplicates. The map ids (values) should start from 0 or 1.
toolkit_registryopenforcefield.utils.toolkits.ToolkitRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for SMILES conversion

Returns

smilesstr: Canonical isomeric explicit-hydrogen SMILES

Examples

>>> from openforcefield.utils import get_data_file_path
>>> sdf_filepath = get_data_file_path('molecules/ethanol.sdf')
>>> molecule = Molecule(sdf_filepath)
>>> smiles = molecule.to_smiles()

static from_inchi(inchi, allow_undefined_stereo=False, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit)[source]¶

Construct a Molecule from a InChI representation

Parameters

inchistr: The InChI representation of the molecule.
allow_undefined_stereobool, default=False: Whether to accept InChI with undefined stereochemistry. If False, an exception will be raised if a InChI with undefined stereochemistry is passed into this function.
toolkit_registryopenforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for InChI-to-molecule conversion

Returns

moleculeopenforcefield.topology.Molecule

Examples

make cis-1,2-Dichloroethene >>> molecule = Molecule.from_inchi(‘InChI=1S/C2H2Cl2/c3-1-2-4/h1-2H/b2-1-‘)

to_inchi(fixed_hydrogens=False, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit)[source]¶

Create an InChI string for the molecule using the requested toolkit backend. InChI is a standardised representation that does not capture tautomers unless specified using the fixed hydrogen layer.

For information on InChi see here https://iupac.org/who-we-are/divisions/division-details/inchi/

Parameters

fixed_hydrogens: bool, default=False: If a fixed hydrogen layer should be added to the InChI, if True this will produce a non standard specific InChI string of the molecule.
toolkit_registryopenforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for molecule-to-InChI conversion

Returns

inchi: str: The InChI string of the molecule.

Raises

InvalidToolkitRegistryError: If an invalid object is passed as the toolkit_registry parameter

to_inchikey(fixed_hydrogens=False, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit)[source]¶

Create an InChIKey for the molecule using the requested toolkit backend. InChIKey is a standardised representation that does not capture tautomers unless specified using the fixed hydrogen layer.

For information on InChi see here https://iupac.org/who-we-are/divisions/division-details/inchi/

Parameters

fixed_hydrogens: bool, default=False: If a fixed hydrogen layer should be added to the InChI, if True this will produce a non standard specific InChI string of the molecule.
toolkit_registryopenforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for molecule-to-InChIKey conversion

Returns

inchi_key: str: The InChIKey representation of the molecule.

Raises

InvalidToolkitRegistryError: If an invalid object is passed as the toolkit_registry parameter

static from_smiles(smiles, hydrogens_are_explicit=False, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit, allow_undefined_stereo=False)[source]¶

Construct a Molecule from a SMILES representation

Parameters

smilesstr: The SMILES representation of the molecule.
hydrogens_are_explicitbool, default = False: If False, the cheminformatics toolkit will perform hydrogen addition
toolkit_registryopenforcefield.utils.toolkits.ToolkitRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for SMILES-to-molecule conversion
allow_undefined_stereobool, default=False: Whether to accept SMILES with undefined stereochemistry. If False, an exception will be raised if a SMILES with undefined stereochemistry is passed into this function.

Returns

moleculeopenforcefield.topology.Molecule

Examples

>>> molecule = Molecule.from_smiles('Cc1ccccc1')

static are_isomorphic(mol1, mol2, return_atom_map=False, aromatic_matching=True, formal_charge_matching=True, bond_order_matching=True, atom_stereochemistry_matching=True, bond_stereochemistry_matching=True, strip_pyrimidal_n_atom_stereo=True, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit)[source]¶

Determines whether the two molecules are isomorphic by comparing their graph representations and the chosen node/edge attributes. Minimally connections and atomic_number are checked.

If nx.Graphs() are given they must at least have atomic_number attributes on nodes. other optional attributes for nodes are: is_aromatic, formal_charge and stereochemistry. optional attributes for edges are: is_aromatic, bond_order and stereochemistry.

Warning

This API is experimental and subject to change.

Parameters

mol1an openforcefield.topology.molecule.FrozenMolecule or TopologyMolecule or nx.Graph()
mol2an openforcefield.topology.molecule.FrozenMolecule or TopologyMolecule or nx.Graph(): The molecule to test for isomorphism.
return_atom_map: bool, default=False, optional: will return an optional dict containing the atomic mapping.
aromatic_matching: bool, default=True, optional: compare the aromatic attributes of bonds and atoms.
formal_charge_matching: bool, default=True, optional: compare the formal charges attributes of the atoms.
bond_order_matching: bool, deafult=True, optional: compare the bond order on attributes of the bonds.
atom_stereochemistry_matchingbool, default=True, optional: If False, atoms’ stereochemistry is ignored for the purpose of determining equality.
bond_stereochemistry_matchingbool, default=True, optional: If False, bonds’ stereochemistry is ignored for the purpose of determining equality.
strip_pyrimidal_n_atom_stereo: bool, default=True, optional: If True, any stereochemistry defined around pyrimidal nitrogen stereocenters will be disregarded in the isomorphism check.
toolkit_registryopenforcefield.utils.toolkits.ToolkitRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for removing stereochemistry from pyrimidal nitrogens.

Returns

molecules_are_isomorphicbool
atom_mapdefault=None, Optional,: [Dict[int,int]] ordered by mol1 indexing {mol1_index: mol2_index} If molecules are not isomorphic given input arguments, will return None instead of dict.

is_isomorphic_with(other, **kwargs)[source]¶

Check if the molecule is isomorphic with the other molecule which can be an openforcefield.topology.Molecule, or TopologyMolecule or nx.Graph(). Full matching is done using the options described bellow.

Warning

This API is experimental and subject to change.

Parameters

other: openforcefield.topology.Molecule or TopologyMolecule or nx.Graph()
return_atom_map: bool, default=False, optional: will return an optional dict containing the atomic mapping.
aromatic_matching: bool, default=True, optional
compare the aromatic attributes of bonds and atoms.
formal_charge_matching: bool, default=True, optional
compare the formal charges attributes of the atoms.
bond_order_matching: bool, deafult=True, optional
compare the bond order on attributes of the bonds.
atom_stereochemistry_matchingbool, default=True, optional: If False, atoms’ stereochemistry is ignored for the purpose of determining equality.
bond_stereochemistry_matchingbool, default=True, optional: If False, bonds’ stereochemistry is ignored for the purpose of determining equality.
strip_pyrimidal_n_atom_stereo: bool, default=True, optional: If True, any stereochemistry defined around pyrimidal nitrogen stereocenters will be disregarded in the isomorphism check.
toolkit_registryopenforcefield.utils.toolkits.ToolkitRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for removing stereochemistry from pyrimidal nitrogens.

Returns

isomorphicbool

generate_conformers(toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit, n_conformers=10, rms_cutoff=None, clear_existing=True)[source]¶

Generate conformers for this molecule using an underlying toolkit. If n_conformers=0, no toolkit wrapper will be called. If n_conformers=0 and clear_existing=True, molecule.conformers will be set to None.

Parameters

toolkit_registryopenforcefield.utils.toolkits.ToolkitRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for SMILES-to-molecule conversion
n_conformersint, default=1: The maximum number of conformers to produce
rms_cutoffsimtk.Quantity-wrapped float, in units of distance, optional, default=None: The minimum RMS value at which two conformers are considered redundant and one is deleted. Precise implementation of this cutoff may be toolkit-dependent. If None, the cutoff is set to be the default value for each ToolkitWrapper (generally 1 Angstrom).
clear_existingbool, default=True: Whether to overwrite existing conformers for the molecule

Raises

InvalidToolkitRegistryError: If an invalid object is passed as the toolkit_registry parameter

Examples

>>> molecule = Molecule.from_smiles('CCCCCC')
>>> molecule.generate_conformers()

compute_partial_charges_am1bcc(use_conformers=None, strict_n_conformers=False, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit)[source]¶

Calculate partial atomic charges for this molecule using AM1-BCC run by an underlying toolkit and assign them to this molecule’s partial_charges attribute.

Parameters

strict_n_conformersbool, default=False: Whether to raise an exception if an invalid number of conformers is provided for the given charge method. If this is False and an invalid number of conformers is found, a warning will be raised.
use_conformersiterable of simtk.unit.Quantity-wrapped numpy arrays, each with shape (n_atoms, 3) and dimension of distance. Optional, default=None: Coordinates to use for partial charge calculation. If None, an appropriate number of conformers for the given charge method will be generated.
toolkit_registryopenforcefield.utils.toolkits.ToolkitRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for the calculation

Raises

InvalidToolkitRegistryError: If an invalid object is passed as the toolkit_registry parameter

Examples

>>> molecule = Molecule.from_smiles('CCCCCC')
>>> molecule.generate_conformers()
>>> molecule.compute_partial_charges_am1bcc()

assign_partial_charges(partial_charge_method, strict_n_conformers=False, use_conformers=None, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit)[source]¶

Calculate partial atomic charges for this molecule using an underlying toolkit, and assign the new values to the partial_charges attribute.

Parameters

partial_charge_methodstring: The partial charge calculation method to use for partial charge calculation.
strict_n_conformersbool, default=False: Whether to raise an exception if an invalid number of conformers is provided for the given charge method. If this is False and an invalid number of conformers is found, a warning will be raised.
use_conformersiterable of simtk.unit.Quantity-wrapped numpy arrays, each with shape (n_atoms, 3) and dimension of distance. Optional, default=None: Coordinates to use for partial charge calculation. If None, an appropriate number of conformers will be generated.
toolkit_registryopenforcefield.utils.toolkits.ToolkitRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for the calculation.

Raises

InvalidToolkitRegistryError: If an invalid object is passed as the toolkit_registry parameter

Examples

>>> molecule = Molecule.from_smiles('CCCCCC')
>>> molecule.assign_partial_charges('am1-mulliken')

assign_fractional_bond_orders(bond_order_model=None, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit, use_conformers=None)[source]¶

Update and store list of bond orders this molecule. Bond orders are stored on each bond, in the bond.fractional_bond_order attribute.

Warning

This API is experimental and subject to change.

Parameters

toolkit_registryopenforcefield.utils.toolkits.ToolkitRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for SMILES-to-molecule conversion
bond_order_modelstring, optional. Default=None: The bond order model to use for fractional bond order calculation. If None, “am1-wiberg” will be used.
use_conformersiterable of simtk.unit.Quantity(np.array) with shape (n_atoms, 3) and dimension of distance, optional, default=None: The conformers to use for fractional bond order calculation. If None, an appropriate number of conformers will be generated by an available ToolkitWrapper.

Raises

InvalidToolkitRegistryError: If an invalid object is passed as the toolkit_registry parameter

Examples

>>> molecule = Molecule.from_smiles('CCCCCC')
>>> molecule.assign_fractional_bond_orders()

to_networkx()[source]¶

Generate a NetworkX undirected graph from the Molecule.

Nodes are Atoms labeled with particle indices and atomic elements (via the element node atrribute). Edges denote chemical bonds between Atoms. Virtual sites are not included, since they lack a concept of chemical connectivity.

Returns

graphnetworkx.Graph: The resulting graph, with nodes (atoms) labeled with atom indices, elements, stereochemistry and aromaticity flags and bonds with two atom indices, bond order, stereochemistry, and aromaticity flags

Examples

Retrieve the bond graph for imatinib (OpenEye toolkit required)

>>> molecule = Molecule.from_iupac('imatinib')
>>> nxgraph = molecule.to_networkx()

find_rotatable_bonds(ignore_functional_groups=None, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit)[source]¶

Find all bonds classed as rotatable ignoring any matched to the ignore_functional_groups list.

Parameters

ignore_functional_groups: optional, List[str], default=None,: A list of bond SMARTS patterns to be ignored when finding rotatable bonds.
toolkit_registry: openforcefield.utils.toolkits.ToolkitRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for SMARTS matching

Returns

bonds: List[openforcefield.topology.molecule.Bond]: The list of openforcefield.topology.molecule.Bond instances which are rotatable.

property partial_charges¶

Returns the partial charges (if present) on the molecule.

Returns

partial_chargesa simtk.unit.Quantity - wrapped numpy array [1 x n_atoms] or None: The partial charges on this Molecule’s atoms. Returns None if no charges have been specified.

property n_particles¶: The number of Particle objects, which corresponds to how many positions must be used.

property n_atoms¶: The number of Atom objects.

property n_virtual_sites¶: The number of VirtualSite objects.

property n_virtual_particles¶: The number of VirtualParticle objects.

property n_bonds¶: The number of Bond objects.

property n_angles¶: int: number of angles in the Molecule.

property n_propers¶: int: number of proper torsions in the Molecule.

property n_impropers¶: int: number of improper torsions in the Molecule.

property n_rings¶

Return the number of rings found in the Molecule

Requires the RDKit to be installed.

Note

For systems containing some special cases of connected rings, this function may not be well-behaved and may report a different number rings than expected. Some problematic cases include networks of many (5+) rings or bicyclic moieties (i.e. norbornane).

property particles¶: Iterate over all Particle objects.

property atoms¶: Iterate over all Atom objects.

property conformers¶: Returns the list of conformers for this molecule. This returns a list of simtk.unit.Quantity-wrapped numpy arrays, of shape (3 x n_atoms) and with dimensions of distance. The return value is the actual list of conformers, and changes to the contents affect the original FrozenMolecule.

property n_conformers¶: Returns the number of conformers for this molecule.

property virtual_sites¶: Iterate over all VirtualSite objects.

property bonds¶: Iterate over all Bond objects.

property angles¶: Get an iterator over all i-j-k angles.

property torsions¶

Get an iterator over all i-j-k-l torsions. Note that i-j-k-i torsions (cycles) are excluded.

Returns

torsionsiterable of 4-Atom tuples

property propers¶: Iterate over all proper torsions in the molecule

property impropers¶: Iterate over all proper torsions in the molecule

property total_charge¶: Return the total charge on the molecule

property name¶: The name (or title) of the molecule

property properties¶: The properties dictionary of the molecule

property hill_formula¶: Get the Hill formula of the molecule

static to_hill_formula(molecule)[source]¶

Generate the Hill formula from either a FrozenMolecule, TopologyMolecule or nx.Graph() of the molecule

Parameters

moleculeFrozenMolecule, TopologyMolecule or nx.Graph()

Returns

formulathe Hill formula of the molecule

Raises

NotImplementedErrorif the molecule is not of one of the specified types.

chemical_environment_matches(query, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit)[source]¶

Retrieve all matches for a given chemical environment query.

Parameters

querystr or ChemicalEnvironment: SMARTS string (with one or more tagged atoms) or ChemicalEnvironment query Query will internally be resolved to SMIRKS using query.asSMIRKS() if it has an .asSMIRKS method.
toolkit_registryopenforcefield.utils.toolkits.ToolkitRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=GLOBAL_TOOLKIT_REGISTRY: ToolkitRegistry or ToolkitWrapper to use for chemical environment matches

Returns

matcheslist of atom index tuples: A list of tuples, containing the indices of the matching atoms.

Examples

Retrieve all the carbon-carbon bond matches in a molecule

>>> molecule = Molecule.from_iupac('imatinib')
>>> matches = molecule.chemical_environment_matches('[#6X3:1]~[#6X3:2]')

classmethod from_iupac(iupac_name, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit, allow_undefined_stereo=False, **kwargs)[source]¶

Generate a molecule from IUPAC or common name

Parameters

iupac_namestr: IUPAC name of molecule to be generated
toolkit_registryopenforcefield.utils.toolkits.ToolkitRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=GLOBAL_TOOLKIT_REGISTRY: ToolkitRegistry or ToolkitWrapper to use for chemical environment matches
allow_undefined_stereobool, default=False: If false, raises an exception if molecule contains undefined stereochemistry.

Returns

moleculeMolecule: The resulting molecule with position

Note

This method requires the OpenEye toolkit to be installed. ..

Examples

Create a molecule from an IUPAC name

>>> molecule = Molecule.from_iupac('4-[(4-methylpiperazin-1-yl)methyl]-N-(4-methyl-3-{[4-(pyridin-3-yl)pyrimidin-2-yl]amino}phenyl)benzamide')

Create a molecule from a common name

>>> molecule = Molecule.from_iupac('imatinib')

to_iupac(toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit)[source]¶

Generate IUPAC name from Molecule

Returns

iupac_namestr: IUPAC name of the molecule

Note

This method requires the OpenEye toolkit to be installed. ..

Examples

>>> from openforcefield.utils import get_data_file_path
>>> sdf_filepath = get_data_file_path('molecules/ethanol.sdf')
>>> molecule = Molecule(sdf_filepath)
>>> iupac_name = molecule.to_iupac()

static from_topology(topology)[source]¶

Return a Molecule representation of an openforcefield Topology containing a single Molecule object.

Parameters

topologyopenforcefield.topology.Topology: The Topology object containing a single Molecule object. Note that OpenMM and MDTraj Topology objects are not supported.

Returns

moleculeopenforcefield.topology.Molecule: The Molecule object in the topology

Raises

ValueError: If the topology does not contain exactly one molecule.

Examples

Create a molecule from a Topology object that contains exactly one molecule

>>> molecule = Molecule.from_topology(topology)  

to_topology()[source]¶

Return an openforcefield Topology representation containing one copy of this molecule

Returns

topologyopenforcefield.topology.Topology: A Topology representation of this molecule

Examples

>>> molecule = Molecule.from_iupac('imatinib')
>>> topology = molecule.to_topology()

static from_file(file_path, file_format=None, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit, allow_undefined_stereo=False)[source]¶

Create one or more molecules from a file

Parameters

file_pathstr or file-like object: The path to the file or file-like object to stream one or more molecules from.
file_formatstr, optional, default=None: Format specifier, usually file suffix (eg. ‘MOL2’, ‘SMI’) Note that not all toolkits support all formats. Check ToolkitWrapper.toolkit_file_read_formats for your loaded toolkits for details.
toolkit_registryopenforcefield.utils.toolkits.ToolkitRegistry or openforcefield.utils.toolkits.ToolkitWrapper,
optional, default=GLOBAL_TOOLKIT_REGISTRY: ToolkitRegistry or ToolkitWrapper to use for file loading. If a Toolkit is passed, only the highest-precedence toolkit is used
allow_undefined_stereobool, default=False: If false, raises an exception if oemol contains undefined stereochemistry.

Returns

moleculesMolecule or list of Molecules: If there is a single molecule in the file, a Molecule is returned; otherwise, a list of Molecule objects is returned.

Examples

>>> from openforcefield.tests.utils import get_monomer_mol2_file_path
>>> mol2_file_path = get_monomer_mol2_file_path('cyclohexane')
>>> molecule = Molecule.from_file(mol2_file_path)

to_file(file_path, file_format, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit)[source]¶

Write the current molecule to a file or file-like object

Parameters

file_pathstr or file-like object: A file-like object or the path to the file to be written.
file_formatstr: Format specifier, one of [‘MOL2’, ‘MOL2H’, ‘SDF’, ‘PDB’, ‘SMI’, ‘CAN’, ‘TDT’] Note that not all toolkits support all formats
toolkit_registryopenforcefield.utils.toolkits.ToolkitRegistry or openforcefield.utils.toolkits.ToolkitWrapper,
optional, default=GLOBAL_TOOLKIT_REGISTRY: ToolkitRegistry or ToolkitWrapper to use for file writing. If a Toolkit is passed, only the highest-precedence toolkit is used

Raises

ValueError: If the requested file_format is not supported by one of the installed cheminformatics toolkits

Examples

>>> molecule = Molecule.from_iupac('imatinib')
>>> molecule.to_file('imatinib.mol2', file_format='mol2')  
>>> molecule.to_file('imatinib.sdf', file_format='sdf')  
>>> molecule.to_file('imatinib.pdb', file_format='pdb')  

enumerate_tautomers(max_states=20, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit)[source]¶

Enumerate the possible tautomers of the current molecule

Parameters

max_states: int optional, default=20: The maximum amount of molecules that should be returned
toolkit_registry: openforcefield.utils.toolkits.ToolkitRegistry or openforcefield.utils.toolkits.ToolkitWrapper,
optional, default=GLOBAL_TOOLKIT_REGISTRY: ToolkitRegistry or ToolkitWrapper to use to enumerate the tautomers.

Returns

molecules: List[openforcefield.topology.Molecule]: A list of openforcefield.topology.Molecule instances not including the input molecule.

enumerate_stereoisomers(undefined_only=False, max_isomers=20, rationalise=True, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit)[source]¶

Enumerate the stereocenters and bonds of the current molecule.

Parameters

undefined_only: bool optional, default=False: If we should enumerate all stereocenters and bonds or only those with undefined stereochemistry
max_isomers: int optional, default=20: The maximum amount of molecules that should be returned
rationalise: bool optional, default=True: If we should try to build and rationalise the molecule to ensure it can exist
toolkit_registry: openforcefield.utils.toolkits.ToolkitRegistry or openforcefield.utils.toolkits.ToolkitWrapper,
optional, default=GLOBAL_TOOLKIT_REGISTRY: ToolkitRegistry or ToolkitWrapper to use to enumerate the stereoisomers.

Returns

molecules: List[openforcefield.topology.Molecule]: A list of openforcefield.topology.Molecule instances not including the input molecule.

enumerate_protomers(max_states=10)[source]¶

Enumerate the formal charges of a molecule to generate different protomoers.

Parameters

max_states: int optional, default=10,: The maximum number of protomer states to be returned.

Returns

molecules: List[openforcefield.topology.Molecule],: A list of the protomers of the input molecules not including the input.

static from_rdkit(*args, **kwargs)[source]¶

Create a Molecule from an RDKit molecule.

Requires the RDKit to be installed.

Parameters

rdmolrkit.RDMol: An RDKit molecule
allow_undefined_stereobool, default=False: If false, raises an exception if oemol contains undefined stereochemistry.

Returns

moleculeopenforcefield.Molecule: An openforcefield molecule

Examples

Create a molecule from an RDKit molecule

>>> from rdkit import Chem
>>> from openforcefield.tests.utils import get_data_file_path
>>> rdmol = Chem.MolFromMolFile(get_data_file_path('systems/monomers/ethanol.sdf'))
>>> molecule = Molecule.from_rdkit(rdmol)

to_rdkit(aromaticity_model='OEAroModel_MDL')[source]¶

Create an RDKit molecule

Requires the RDKit to be installed.

Parameters

aromaticity_modelstr, optional, default=DEFAULT_AROMATICITY_MODEL: The aromaticity model to use

Returns

rdmolrkit.RDMol: An RDKit molecule

Examples

Convert a molecule to RDKit

>>> from openforcefield.utils import get_data_file_path
>>> sdf_filepath = get_data_file_path('molecules/ethanol.sdf')
>>> molecule = Molecule(sdf_filepath)
>>> rdmol = molecule.to_rdkit()

static from_openeye(*args, **kwargs)[source]¶

Create a Molecule from an OpenEye molecule.

Requires the OpenEye toolkit to be installed.

Parameters

oemolopeneye.oechem.OEMol: An OpenEye molecule
allow_undefined_stereobool, default=False: If false, raises an exception if oemol contains undefined stereochemistry.

Returns

moleculeopenforcefield.topology.Molecule: An openforcefield molecule

Examples

Create a Molecule from an OpenEye OEMol

>>> from openeye import oechem
>>> from openforcefield.tests.utils import get_data_file_path
>>> ifs = oechem.oemolistream(get_data_file_path('systems/monomers/ethanol.mol2'))
>>> oemols = list(ifs.GetOEGraphMols())
>>> molecule = Molecule.from_openeye(oemols[0])

to_qcschema(multiplicity=1, conformer=0, extras=None)[source]¶

Generate the qschema input format used to submit jobs to archive or run qcengine calculations locally, spec can be found here <https://molssi-qc-schema.readthedocs.io/en/latest/index.html>

Warning

This API is experimental and subject to change.

Parameters

multiplicityint, default=1,: The multiplicity of the molecule required for qcschema
conformerint, default=0,: The index of the conformer that should be used for qcschema
extrasdict, default=None: The extras dictionary that should be included into the qcelemental.models.Molecule. This can be used to include extra information such as the smiles representation.

Returns

qcelemental.models.Molecule :: A validated qcschema

Raises

ImportErrorif qcelemental is not installed; the qcschema can not be validated.
InvalidConformerErrorif there is no conformer found at the given index.

classmethod from_mapped_smiles(mapped_smiles, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit, allow_undefined_stereo=False)[source]¶

Create an openforcefield.topology.molecule.Molecule from a mapped SMILES made with cmiles. The molecule will be in the order of the indexing in the mapped smiles string.

Warning

This API is experimental and subject to change.

Parameters

mapped_smiles: str,: A CMILES-style mapped smiles string with explicit hydrogens.
toolkit_registryopenforcefield.utils.toolkits.ToolkitRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for SMILES-to-molecule conversion
allow_undefined_stereobool, default=False: If false, raises an exception if oemol contains undefined stereochemistry.

Returns

offmolopenforcefield.topology.molecule.Molecule: An openforcefiled molecule instance.

Raises

SmilesParsingErrorif the given SMILES had no indexing picked up by the toolkits.

classmethod from_qcschema(qca_record, client=None, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit, allow_undefined_stereo=False)[source]¶

Create a Molecule from a QCArchive entry based on the cmiles information.

If we also have a client instance/address we can go and attach the starting geometry.

Parameters

qca_recorddict,: A QCArchive dict with json encoding or record instance
clientoptional, default=None,: A qcportal.FractalClient instance so we can pull the initial molecule geometry.
toolkit_registryopenforcefield.utils.toolkits.ToolkitRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for SMILES-to-molecule conversion
allow_undefined_stereobool, default=False: If false, raises an exception if oemol contains undefined stereochemistry.

Returns

moleculeopenforcefield.topology.Molecule: An openforcefield molecule instance.

Raises

AttributeErrorif the record dict can not be made from a record instance.: if a client is passed, because the client could not retrive the initial molecule.
KeyErrorif the dict does not contain the canonical_isomeric_explicit_hydrogen_mapped_smiles.
InvalidConformerErrorsilent error, if the conformer could not be attached.

classmethod from_pdb_and_smiles(file_path, smiles, allow_undefined_stereo=False)[source]¶

Create a Molecule from a pdb file and a SMILES string using RDKit.

Requires RDKit to be installed.

Warning

This API is experimental and subject to change.

The molecule is created and sanitised based on the SMILES string, we then find a mapping between this molecule and one from the PDB based only on atomic number and connections. The SMILES molecule is then reindex to match the PDB, the conformer is attached and the molecule returned.

Parameters

file_path: str: PDB file path
smilesstr: a valid smiles string for the pdb, used for seterochemistry and bond order
allow_undefined_stereobool, default=False: If false, raises an exception if oemol contains undefined stereochemistry.

Returns

moleculeopenforcefield.Molecule: An OFFMol instance with ordering the same as used in the PDB file.

Raises

InvalidConformerErrorif the SMILES and PDB molecules are not isomorphic.

canonical_order_atoms(toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit)[source]¶

Canonical order the atoms in a copy of the molecule using a toolkit, returns a new copy.

Warning

This API is experimental and subject to change.

Parameters

toolkit_registryopenforcefield.utils.toolkits.ToolkitRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for SMILES-to-molecule conversion

Returns

moleculeopenforcefield.topology.Molecule: An new openforcefield-style molecule with atoms in the canonical order.

remap(mapping_dict, current_to_new=True)[source]¶

Remap all of the indexes in the molecule to match the given mapping dict

Warning

This API is experimental and subject to change.

Parameters

mapping_dictdict,: A dictionary of the mapping between in the indexes, this should start from 0.
current_to_newbool, default=True: The dict is {current_index: new_index} if True else {new_index: current_index}

Returns

new_moleculeopenforcefield.topology.molecule.Molecule: An openforcefield.Molecule instance with all attributes transferred, in the PDB order.

to_openeye(aromaticity_model='OEAroModel_MDL')[source]¶

Create an OpenEye molecule

Requires the OpenEye toolkit to be installed.

Parameters

aromaticity_modelstr, optional, default=DEFAULT_AROMATICITY_MODEL: The aromaticity model to use

Returns

oemolopeneye.oechem.OEMol: An OpenEye molecule

Examples

Create an OpenEye molecule from a Molecule

>>> molecule = Molecule.from_smiles('CC')
>>> oemol = molecule.to_openeye()

get_bond_between(i, j)[source]¶

Returns the bond between two atoms

Parameters

i, jint or Atom: Atoms or atom indices to check

Returns

bondBond: The bond between i and j.

property rings¶

Return the number of rings in this molecule.

Requires the RDKit to be installed.

Note

classmethod from_bson(serialized)¶

Instantiate an object from a BSON serialized representation.

Specification: http://bsonspec.org/

Parameters

serializedbytes: A BSON serialized representation of the object

Returns

instancecls: An instantiated object

classmethod from_json(serialized)¶

Instantiate an object from a JSON serialized representation.

Specification: https://www.json.org/

Parameters

serializedstr: A JSON serialized representation of the object

Returns

instancecls: An instantiated object

classmethod from_messagepack(serialized)¶

Instantiate an object from a MessagePack serialized representation.

Specification: https://msgpack.org/index.html

Parameters

serializedbytes: A MessagePack-encoded bytes serialized representation

Returns

instancecls: Instantiated object.

classmethod from_pickle(serialized)¶

Instantiate an object from a pickle serialized representation.

Warning

This is not recommended for safe, stable storage since the pickle specification may change between Python versions.

Parameters

serializedstr: A pickled representation of the object

Returns

instancecls: An instantiated object

classmethod from_toml(serialized)¶

Instantiate an object from a TOML serialized representation.

Specification: https://github.com/toml-lang/toml

Parameters

serlializedstr: A TOML serialized representation of the object

Returns

instancecls: An instantiated object

classmethod from_xml(serialized)¶

Instantiate an object from an XML serialized representation.

Specification: https://www.w3.org/XML/

Parameters

serializedbytes: An XML serialized representation

Returns

instancecls: Instantiated object.

classmethod from_yaml(serialized)¶

Instantiate from a YAML serialized representation.

Specification: http://yaml.org/

Parameters

serializedstr: A YAML serialized representation of the object

Returns

instancecls: Instantiated object

to_bson()¶

Return a BSON serialized representation.

Specification: http://bsonspec.org/

Returns

serializedbytes: A BSON serialized representation of the objecft

to_json(indent=None)¶

Return a JSON serialized representation.

Specification: https://www.json.org/

Parameters

indentint, optional, default=None: If not None, will pretty-print with specified number of spaces for indentation

Returns

serializedstr: A JSON serialized representation of the object

to_messagepack()¶

Return a MessagePack representation.

Specification: https://msgpack.org/index.html

Returns

serializedbytes: A MessagePack-encoded bytes serialized representation of the object

to_pickle()¶

Return a pickle serialized representation.

Warning

This is not recommended for safe, stable storage since the pickle specification may change between Python versions.

Returns

serializedstr: A pickled representation of the object

to_toml()¶

Return a TOML serialized representation.

Specification: https://github.com/toml-lang/toml

Returns

serializedstr: A TOML serialized representation of the object

to_xml(indent=2)¶

Return an XML representation.

Specification: https://www.w3.org/XML/

Parameters

indentint, optional, default=2: If not None, will pretty-print with specified number of spaces for indentation

Returns

serializedbytes: A MessagePack-encoded bytes serialized representation.

to_yaml()¶

Return a YAML serialized representation.

Specification: http://yaml.org/

Returns

serializedstr: A YAML serialized representation of the object