openff.toolkit.topology.Molecule

class openff.toolkit.topology.Molecule(*args, **kwargs)[source]

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

Todo

What other API calls would be useful for supporting biopolymers as small molecules? Perhaps iterating over chains and residues?

Examples

Create a molecule from an sdf file

>>> from openff.toolkit.utils import get_data_file_path
>>> sdf_filepath = get_data_file_path('molecules/ethanol.sdf')
>>> molecule = Molecule(sdf_filepath)

Convert to OpenEye OEMol object

>>> oemol = molecule.to_openeye()

Create a molecule from an OpenEye molecule

>>> molecule = Molecule.from_openeye(oemol)

Convert to RDKit Mol object

>>> rdmol = molecule.to_rdkit()

Create a molecule from an RDKit molecule

>>> molecule = Molecule.from_rdkit(rdmol)

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

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

Create a molecule from SMILES

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

Warning

This API is experimental and subject to change.

__init__(*args, **kwargs)[source]

Create a new Molecule 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

Examples

Create an empty molecule:

>>> empty_molecule = Molecule()

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

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

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

Create a molecule from another molecule:

>>> molecule_copy = Molecule(molecule)

Convert to OpenEye OEMol object

>>> oemol = molecule.to_openeye()

Create a molecule from an OpenEye molecule:

>>> molecule = Molecule(oemol)

Convert to RDKit Mol object

>>> rdmol = molecule.to_rdkit()

Create a molecule from an RDKit molecule:

>>> molecule = Molecule(rdmol)

Create a molecule from a serialized molecule object:

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

Todo

If a filename or file-like object is specified but the file contains more than one molecule, what is the proper behavior? Read just the first molecule, or raise an exception if more than one molecule is found?
Should we also support SMILES strings or IUPAC names for other?

Methods

`__init__`(args, *kwargs)	Create a new Molecule object
`add_atom`(atomic_number, formal_charge, ...)	Add an atom
`add_bond`(atom1, atom2, bond_order, is_aromatic)	Add a bond between two specified atom indices
`add_bond_charge_virtual_site`(atoms, distance)	Add a virtual site representing the charge on a bond.
`add_conformer`(coordinates)	Add a conformation of the molecule
`add_divalent_lone_pair_virtual_site`(atoms, ...)	Create a divalent lone pair-type virtual site, in which the location of the charge is specified by the position of three atoms.
`add_monovalent_lone_pair_virtual_site`(atoms, ...)	Create a bond charge-type virtual site, in which the location of the charge is specified by the position of three atoms.
`add_trivalent_lone_pair_virtual_site`(atoms, ...)	Create a trivalent lone pair-type virtual site, in which the location of the charge is specified by the position of four atoms.
`apply_elf_conformer_selection`([percentage, ...])	Applies the ELF method to select a set of diverse conformers which have minimal electrostatically strongly interacting functional groups from a molecules conformers.
`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.
`compute_virtual_site_positions_from_atom_positions`(...)	Compute the positions of the virtual sites in this molecule given a set of external coordinates.
`compute_virtual_site_positions_from_conformer`(...)	Compute the position of all virtual sites given an existing conformer specified by its index.
`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 `Molecule` from a mapped SMILES made with cmiles.
`from_messagepack`(serialized)	Instantiate an object from a MessagePack serialized representation.
`from_openeye`(oemol[, allow_undefined_stereo])	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 molecule record or dataset entry based on attached cmiles information.
`from_rdkit`(rdmol[, allow_undefined_stereo, ...])	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 OpenFF 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 openff.toolkit.topology.Molecule, or TopologyMolecule or nx.Graph().
`nth_degree_neighbors`(n_degrees)	Return canonicalized pairs of atoms whose shortest separation is exactly n bonds.
`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`()	Generate the Hill formula of this 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])	Create a QCElemental Molecule.
`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 OpenFF Topology representation containing one copy of this molecule
`to_xml`([indent])	Return an XML representation.
`to_yaml`()	Return a YAML serialized representation.
`visualize`([backend, width, height, ...])	Render a visualization of the molecule in Jupyter

Attributes

`amber_impropers`	Iterate over improper torsions in the molecule, but only those with trivalent centers, reporting the central atom first in each improper.
`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 improper torsions in the molecule.
`n_angles`	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`	number of possible improper torsions in the Molecule.
`n_particles`	The number of Particle objects, which corresponds to how many positions must be used.
`n_propers`	number of proper torsions 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
`smirnoff_impropers`	Iterate over improper torsions in the molecule, but only those with trivalent centers, reporting the central atom second in each improper.
`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.

add_atom(atomic_number, formal_charge, is_aromatic, stereochemistry=None, name=None)[source]

Add an atom

Parameters

atomic_numberint: Atomic number of the atom
formal_chargeint: Formal charge of the atom
is_aromaticbool: If True, atom is aromatic; if False, not aromatic
stereochemistrystr, optional, default=None: Either 'R' or 'S' for specified stereochemistry, or None if stereochemistry is irrelevant
namestr, optional: An optional name for the atom

Returns

indexint: The index of the atom in the molecule

Examples

Define a methane molecule

>>> molecule = Molecule()
>>> molecule.name = 'methane'
>>> C = molecule.add_atom(6, 0, False)
>>> H1 = molecule.add_atom(1, 0, False)
>>> H2 = molecule.add_atom(1, 0, False)
>>> H3 = molecule.add_atom(1, 0, False)
>>> H4 = molecule.add_atom(1, 0, False)
>>> bond_idx = molecule.add_bond(C, H1, False, 1)
>>> bond_idx = molecule.add_bond(C, H2, False, 1)
>>> bond_idx = molecule.add_bond(C, H3, False, 1)
>>> bond_idx = molecule.add_bond(C, H4, False, 1)

add_bond_charge_virtual_site(atoms, distance, name='', symmetric=True, replace=False)[source]

Add a virtual site representing the charge on a bond.

Create a bond charge-type virtual site, in which the location of the charge is specified by the position of two atoms. This supports placement of a virtual site \(S\) along a vector between two specified atoms, e.g. to allow for a sigma hole for halogens or similar contexts. With positive values of the distance, the virtual site lies outside the first indexed atom.

Parameters

atomslist of openff.toolkit.topology.molecule.Atom objects: The atoms defining the virtual site’s position
distanceopenmm.unit.Quantity of dimension [Length] wrapping a scalar
namestring or None, default=’’: The name of this virtual site. Default is ‘’.
symmetricbool, default=True: Whether to make virtual site symmetric by creating two particles instead of just one. As an example, for N_2 this should be set to True to model both lone pairs with the same parameters.

Returns

indexint: The index of the newly-added virtual site in the molecule

property amber_impropers

Iterate over improper torsions in the molecule, but only those with trivalent centers, reporting the central atom first in each improper.

Note that it’s possible that a trivalent center will not have an improper assigned. This will depend on the force field that is used.

Also note that this will return 6 possible atom orderings around each improper center. In current AMBER parameterization, one of these six orderings will be used for the actual assignment of the improper term and measurement of the angle. This method does not encode the logic to determine which of the six orderings AMBER would use.

Returns

impropersset of tuple: An iterator of tuples, each containing the indices of atoms making up a possible improper torsion. The central atom is listed first in each tuple.

See also

impropers, smirnoff_impropers

property angles

Get an iterator over all i-j-k angles.

apply_elf_conformer_selection(percentage: float = 2.0, limit: int = 10, toolkit_registry: Optional[Union[openff.toolkit.utils.toolkit_registry.ToolkitRegistry, openff.toolkit.utils.base_wrapper.ToolkitWrapper]] = GLOBAL_TOOLKIT_REGISTRY, **kwargs)

Applies the ELF method to select a set of diverse conformers which have minimal electrostatically strongly interacting functional groups from a molecules conformers.

Parameters

toolkit_registry: The underlying toolkit to use to select the ELF conformers.
percentage: The percentage of conformers with the lowest electrostatic interaction energies to greedily select from.
limit: The maximum number of conformers to select.

See also

OpenEyeToolkitWrapper.apply_elf_conformer_selection
RDKitToolkitWrapper.apply_elf_conformer_selection

Notes

The input molecule should have a large set of conformers already generated to select the ELF conformers from.
The selected conformers will be retained in the conformers list while unselected conformers will be discarded.

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=GLOBAL_TOOLKIT_REGISTRY)

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 openff.toolkit.topology.molecule.FrozenMolecule or TopologyMolecule or nx.Graph()
mol2an openff.toolkit.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_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.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.

assign_fractional_bond_orders(bond_order_model=None, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, use_conformers=None)

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_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.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 openmm.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()

assign_partial_charges(partial_charge_method, strict_n_conformers=False, use_conformers=None, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, normalize_partial_charges=True)

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 openmm.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_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for the calculation.
normalize_partial_chargesbool, default=True: Whether to offset partial charges so that they sum to the total formal charge of the molecule. This is used to prevent accumulation of rounding errors when the partial charge assignment method returns values at limited precision.

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')

property atoms

Iterate over all Atom objects.

property bonds

Iterate over all Bond objects.

canonical_order_atoms(toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)

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_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, optional: ToolkitRegistry or ToolkitWrapper to use for SMILES-to-molecule conversion

Returns

moleculeopenff.toolkit.topology.Molecule: An new OpenFF style molecule with atoms in the canonical order.

chemical_environment_matches(query, unique=False, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)

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_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.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]')

Todo

Do we want to generalize query to allow other kinds of queries, such as mdtraj DSL, pymol selections, atom index slices, etc? We could call it topology.matches(query) instead of chemical_environment_matches

compute_partial_charges_am1bcc(use_conformers=None, strict_n_conformers=False, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)

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 openmm.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_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.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()

compute_virtual_site_positions_from_atom_positions(atom_positions)

Compute the positions of the virtual sites in this molecule given a set of external coordinates. The coordinates do not need come from an internal conformer, but are assumed to have the same shape and be in the same order.

Parameters

atom_positionsopenmm.unit.Quantity of dimension [Length] wrapping a
numpy.ndarray: The positions of all atoms in the molecule. The array is the size (N, 3) where N is the number of atoms in the molecule.

Returns

openmm.unit.Quantity of dimension [Length] in unit Angstroms wrapping a
numpy.ndarray: The positions of the virtual particles belonging to this virtual site. The array is the size (M, 3) where M is the number of virtual particles belonging to this virtual site.

compute_virtual_site_positions_from_conformer(conformer_idx)

Compute the position of all virtual sites given an existing conformer specified by its index.

Parameters

conformer_idxint: The index of the conformer.

Returns

openmm.unit.Quantity of dimension [Length] in unit Angstroms wrapping a
numpy.ndarray: The positions of the virtual particles belonging to this virtual site. The array is the size (M, 3) where M is the number of virtual particles belonging to this virtual site.

property conformers

Returns the list of conformers for this molecule. This returns a list of openmm.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.

enumerate_protomers(max_states=10)

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

enumerate_stereoisomers(undefined_only=False, max_isomers=20, rationalise=True, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)

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: openff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, default=GLOBAL_TOOLKIT_REGISTRY: ToolkitRegistry or ToolkitWrapper to use to enumerate the stereoisomers.

Returns

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

enumerate_tautomers(max_states=20, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)

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: openff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, default=GLOBAL_TOOLKIT_REGISTRY: ToolkitRegistry or ToolkitWrapper to use to enumerate the tautomers.

Returns

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

find_rotatable_bonds(ignore_functional_groups=None, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)

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: openff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for SMARTS matching

Returns

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

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_dict(molecule_dict)

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

classmethod from_file(file_path, file_format=None, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit, allow_undefined_stereo=False)

Create one or more molecules from a file

Todo

Extend this to also include some form of .offmol Open Force Field Molecule format?
Generalize this to also include file-like objects?

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_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.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 openff.toolkit.tests.utils import get_monomer_mol2_file_path
>>> mol2_file_path = get_monomer_mol2_file_path('cyclohexane')
>>> molecule = Molecule.from_file(mol2_file_path)

classmethod from_inchi(inchi, allow_undefined_stereo=False, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit)

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_registryopenff.toolkit.utils.toolkits.ToolRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for InChI-to-molecule conversion

Returns

moleculeopenff.toolkit.topology.Molecule

Examples

Make cis-1,2-Dichloroethene:

>>> molecule = Molecule.from_inchi('InChI=1S/C2H2Cl2/c3-1-2-4/h1-2H/b2-1-')

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

Generate a molecule from IUPAC or common name

Parameters

iupac_namestr: IUPAC name of molecule to be generated
toolkit_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.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')

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_mapped_smiles(mapped_smiles, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit, allow_undefined_stereo=False)

Create an 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_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, optional: 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

offmolopenff.toolkit.topology.molecule.Molecule: An OpenFF molecule instance.

Raises

SmilesParsingError: If the given SMILES had no indexing picked up by the toolkits.

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_openeye(oemol, allow_undefined_stereo=False)

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

moleculeopenff.toolkit.topology.Molecule: An OpenFF molecule

Examples

Create a Molecule from an OpenEye OEMol

>>> from openeye import oechem
>>> from openff.toolkit.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])

classmethod from_pdb_and_smiles(file_path, smiles, allow_undefined_stereo=False)

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 reindexed to match the PDB, the conformer is attached, and the molecule returned.

Note that any stereochemistry in the molecule is set by the SMILES, and not the coordinates of the PDB.

Parameters

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

Returns

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

Raises

InvalidConformerError: If the SMILES and PDB molecules are not isomorphic.

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_qcschema(qca_record, client=None, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit, allow_undefined_stereo=False)

Create a Molecule from a QCArchive molecule record or dataset entry based on attached cmiles information.

For a molecule record, a conformer will be set from its geometry.

For a dataset entry, if a corresponding client instance is provided, the starting geometry for that entry will be used as a conformer.

A QCElemental Molecule produced from Molecule.to_qcschema can be round-tripped through this method to produce a new, valid Molecule.

Parameters

qca_recorddict: A QCArchive molecule record or dataset entry.
clientoptional, default=None,: A qcportal.FractalClient instance to use for fetching an initial geometry. Only used if qca_record is a dataset entry.
toolkit_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, optional: ToolkitRegistry or ToolkitWrapper to use for SMILES-to-molecule conversion
allow_undefined_stereobool, default=False: If false, raises an exception if qca_record contains undefined stereochemistry.

Returns

moleculeopenff.toolkit.topology.Molecule: An OpenFF molecule instance.

Raises

AttributeError

If the record dict can not be made from qca_record.
If a client is passed and it could not retrieve the initial molecule.

KeyError

If the dict does not contain the canonical_isomeric_explicit_hydrogen_mapped_smiles.

InvalidConformerError

Silent error, if the conformer could not be attached.

Examples

Get Molecule from a QCArchive molecule record:

>>> from qcportal import FractalClient
>>> client = FractalClient()
>>> offmol = Molecule.from_qcschema(client.query_molecules(molecular_formula="C16H20N3O5")[0])

Get Molecule from a QCArchive optimization entry:

>>> from qcportal import FractalClient
>>> client = FractalClient()
>>> optds = client.get_collection("OptimizationDataset",
                                  "SMIRNOFF Coverage Set 1")
>>> offmol = Molecule.from_qcschema(optds.get_entry('coc(o)oc-0'))

Same as above, but with conformer(s) from initial molecule(s) by providing client to database:

>>> offmol = Molecule.from_qcschema(optds.get_entry('coc(o)oc-0'), client=client)

classmethod from_rdkit(rdmol, allow_undefined_stereo=False, hydrogens_are_explicit=False)

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 rdmol contains undefined stereochemistry.
hydrogens_are_explicitbool, default=False: If False, RDKit will perform hydrogen addition using Chem.AddHs

Returns

moleculeopenff.toolkit.topology.Molecule: An OpenFF molecule

Examples

Create a molecule from an RDKit molecule

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

classmethod from_smiles(smiles, hydrogens_are_explicit=False, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit, allow_undefined_stereo=False)

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_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.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

moleculeopenff.toolkit.topology.Molecule

Examples

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

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_topology(topology)

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

Parameters

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

Returns

moleculeopenff.toolkit.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)  

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

generate_conformers(toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, n_conformers=10, rms_cutoff=None, clear_existing=True, make_carboxylic_acids_cis=True)

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_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.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_cutoffopenmm.unit.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
make_carboxylic_acids_cis: bool, default=True: Guarantee all conformers have exclusively cis carboxylic acid groups (COOH) by rotating the proton in any trans carboxylic acids 180 degrees around the C-O bond. Works around a bug in conformer generation by the OpenEye toolkit where trans COOH is much more common than it should be.

Raises

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

Examples

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

generate_unique_atom_names()

Generate unique atom names using element name and number of times that element has occurred e.g. ‘C1x’, ‘H1x’, ‘O1x’, ‘C2x’, …

The character ‘x’ is appended to these generated names to reduce the odds that they clash with an atom name or type imported from another source.

get_bond_between(i, j)

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 has_unique_atom_names

True if the molecule has unique atom names, False otherwise.

property hill_formula

Get the Hill formula of the molecule

property impropers

Iterate over all improper torsions in the molecule.

Todo

Do we need to return a Torsion object that collects information about fractional bond orders?

Returns

impropersset of tuple: An iterator of tuples, each containing the indices of atoms making up a possible improper torsion.

See also

smirnoff_impropers, amber_impropers

is_isomorphic_with(other, **kwargs)

Check if the molecule is isomorphic with the other molecule which can be an openff.toolkit.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: openff.toolkit.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_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for removing stereochemistry from pyrimidal nitrogens.

Returns

isomorphicbool

property n_angles

number of angles in the Molecule.

Type: int

property n_atoms

The number of Atom objects.

property n_bonds

The number of Bond objects.

property n_conformers

Returns the number of conformers for this molecule.

property n_impropers

number of possible improper torsions in the Molecule.

Type: int

property n_particles

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

property n_propers

number of proper torsions in the Molecule.

Type: int

property n_virtual_particles

The number of VirtualParticle objects.

property n_virtual_sites

The number of VirtualSite objects.

property name

The name (or title) of the molecule

nth_degree_neighbors(n_degrees)

Return canonicalized pairs of atoms whose shortest separation is exactly n bonds. Only pairs with increasing atom indices are returned.

Parameters

n: int: The number of bonds separating atoms in each pair

Returns

neighbors: iterator of tuple of Atom: Tuples (len 2) of atom that are separated by n bonds.

Notes

The criteria used here relies on minimum distances; when there are multiple valid paths between atoms, such as atoms in rings, the shortest path is considered. For example, two atoms in “meta” positions with respect to each other in a benzene are separated by two paths, one length 2 bonds and the other length 4 bonds. This function would consider them to be 2 apart and would not include them if n=4 was passed.

property partial_charges

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

Returns

partial_chargesa openmm.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 particles

Iterate over all Particle objects.

property propers

Iterate over all proper torsions in the molecule

Todo

Do we need to return a Torsion object that collects information about fractional bond orders?

property properties

The properties dictionary of the molecule

remap(mapping_dict, current_to_new=True)

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 indexes, this should start from 0.
current_to_newbool, default=True: If this is True, then mapping_dict is of the form {current_index: new_index}; otherwise, it is of the form {new_index: current_index}

Returns

new_moleculeopenff.toolkit.topology.molecule.Molecule: An openff.toolkit.Molecule instance with all attributes transferred, in the PDB order.

property smirnoff_impropers

Iterate over improper torsions in the molecule, but only those with trivalent centers, reporting the central atom second in each improper.

Note that it’s possible that a trivalent center will not have an improper assigned. This will depend on the force field that is used.

Also note that this will return 6 possible atom orderings around each improper center. In current SMIRNOFF parameterization, three of these six orderings will be used for the actual assignment of the improper term and measurement of the angles. These three orderings capture the three unique angles that could be calculated around the improper center, therefore the sum of these three terms will always return a consistent energy.

The exact three orderings that will be applied during parameterization can not be determined in this method, since it requires sorting the particle indices, and those indices may change when this molecule is added to a Topology.

For more details on the use of three-fold (‘trefoil’) impropers, see https://openforcefield.github.io/standards/standards/smirnoff/#impropertorsions

Returns

impropersset of tuple: An iterator of tuples, each containing the indices of atoms making up a possible improper torsion. The central atom is listed second in each tuple.

See also

impropers, amber_impropers

strip_atom_stereochemistry(smarts, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)

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_bson()

Return a BSON serialized representation.

Specification: http://bsonspec.org/

Returns

serializedbytes: A BSON serialized representation of the objecft

to_dict()

Return a dictionary representation of the molecule.

Todo

Document the representation standard.
How do we do version control with this standard?

Returns

molecule_dictOrderedDict: A dictionary representation of the molecule.

to_file(file_path, file_format, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)

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_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.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')  

to_hill_formula() → str

Generate the Hill formula of this molecule.

Returns

formulathe Hill formula of the molecule

Raises

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

to_inchi(fixed_hydrogens=False, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)

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_registryopenff.toolkit.utils.toolkits.ToolRegistry or openff.toolkit.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=GLOBAL_TOOLKIT_REGISTRY)

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_registryopenff.toolkit.utils.toolkits.ToolRegistry or openff.toolkit.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

to_iupac(toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)

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

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_networkx()

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.

Todo

Do we need a from_networkx() method? If so, what would the Graph be required to provide?
Should edges be labeled with discrete bond types in some aromaticity model?
Should edges be labeled with fractional bond order if a method is specified?
Should we add other per-atom and per-bond properties (e.g. partial charges) if present?
Can this encode bond/atom chirality?

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()

to_openeye(aromaticity_model=DEFAULT_AROMATICITY_MODEL)

Create an OpenEye molecule

Requires the OpenEye toolkit to be installed.

Todo

Use stored conformer positions instead of an argument.
Should the aromaticity model be specified in some other way?

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()

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_qcschema(multiplicity=1, conformer=0, extras=None)

Create a QCElemental Molecule.

Warning

This API is experimental and subject to change.

Parameters

multiplicityint, default=1,: The multiplicity of the molecule; sets molecular_multiplicity field for QCElemental Molecule.
conformerint, default=0,: The index of the conformer to use for the QCElemental Molecule geometry.
extrasdict, default=None: A dictionary that should be included in the extras field on the QCElemental Molecule. This can be used to include extra information, such as a smiles representation.

Returns

qcelemental.models.Molecule: A validated QCElemental Molecule.

Raises

MissingDependencyError: If qcelemental is not installed, the qcschema can not be validated.
InvalidConformerError: No conformer found at the given index.

Examples

Create a QCElemental Molecule:

>>> import qcelemental as qcel
>>> mol = Molecule.from_smiles('CC')
>>> mol.generate_conformers(n_conformers=1)
>>> qcemol = mol.to_qcschema()

to_rdkit(aromaticity_model=DEFAULT_AROMATICITY_MODEL)

Create an RDKit molecule

Requires the RDKit to be installed.

Parameters

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

Returns

rdmolrdkit.RDMol: An RDKit molecule

Examples

Convert a molecule to RDKit

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

to_smiles(isomeric=True, explicit_hydrogens=True, mapped=False, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)

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_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, optional, default=None: ToolkitRegistry or ToolkitWrapper to use for SMILES conversion

Returns

smilesstr: Canonical isomeric explicit-hydrogen SMILES

Examples

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

to_toml()

Return a TOML serialized representation.

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

Returns

serializedstr: A TOML serialized representation of the object

to_topology()

Return an OpenFF Topology representation containing one copy of this molecule

Returns

topologyopenff.toolkit.topology.Topology: A Topology representation of this molecule

Examples

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

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

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 total_charge

Return the total charge on the molecule

property virtual_sites

Iterate over all VirtualSite objects.

add_monovalent_lone_pair_virtual_site(atoms, distance, out_of_plane_angle, in_plane_angle, name='', symmetric=False, replace=False)[source]

Create a bond charge-type virtual site, in which the location of the charge is specified by the position of three atoms.

Parameters

atomslist of three openff.toolkit.topology.molecule.Atom objects: The three atoms defining the virtual site’s position
distanceopenmm.unit.Quantity of dimension [Length] wrapping a scalar
out_of_plane_angleopenmm.unit.Quantity of dimension [Angle] wrapping
a scalar
in_plane_angleopenmm.unit.Quantity of dimension [Angle] wrapping a
scalar
namestring or None, default=’’: The name of this virtual site. Default is ‘’.
symmetricbool, default=False: Whether to make virtual site symmetric by creating two particles instead of just one. Note that because this site is defined is placed on the noncentral atom, setting this to True will place one particle on atom1, and the other on atom3.

Returns

indexint: The index of the newly-added virtual site in the molecule

add_divalent_lone_pair_virtual_site(atoms, distance, out_of_plane_angle, name='', symmetric=True, replace=False)[source]

Create a divalent lone pair-type virtual site, in which the location of the charge is specified by the position of three atoms.

Parameters

atomslist of three openff.toolkit.topology.molecule.Atom objects: The three atoms defining the virtual site’s position
distanceopenmm.unit.Quantity of dimension [Length] wrapping a scalar
out_of_plane_angleopenmm.unit.Quantity of dimension [Angle] wrapping
a scalar
namestring or None, default=’’: The name of this virtual site. Default is ‘’.
symmetricbool, default=True: Whether to make virtual site symmetric by creating two particles instead of just one. As an example, for TIP5 should be set to True to model both lone pairs with the same parameters.

Returns

indexint: The index of the newly-added virtual site in the molecule

add_trivalent_lone_pair_virtual_site(atoms, distance, name='', replace=False)[source]

Create a trivalent lone pair-type virtual site, in which the location of the charge is specified by the position of four atoms.

Parameters

atomslist of four openff.toolkit.topology.molecule.Atom objects: The four atoms defining the virtual site’s position
distanceopenmm.unit.Quantity of dimension [Length] wrapping a scalar
namestring or None, default=’’: The name of this virtual site. Default is ‘’.

Returns

indexint: The index of the newly-added virtual site in the molecule

add_bond(atom1, atom2, bond_order, is_aromatic, stereochemistry=None, fractional_bond_order=None)[source]

Add a bond between two specified atom indices

Parameters

atom1int or openff.toolkit.topology.molecule.Atom: Index of first atom
atom2int or openff.toolkit.topology.molecule.Atom: Index of second atom
bond_orderint: Integral bond order of Kekulized form
is_aromaticbool: True if this bond is aromatic, False otherwise
stereochemistrystr, optional, default=None: Either 'E' or 'Z' for specified stereochemistry, or None if stereochemistry is irrelevant
fractional_bond_orderfloat, optional, default=None: The fractional (eg. Wiberg) bond order

Returns

index: int: Index of the bond in this molecule

add_conformer(coordinates)[source]

Add a conformation of the molecule

Parameters

coordinates: openmm.unit.Quantity(np.array) with shape (n_atoms, 3) and dimension of distance: Coordinates of the new conformer, with the first dimension of the array corresponding to the atom index in the Molecule’s indexing system.

Returns

index: int: The index of this conformer

visualize(backend='rdkit', width=None, height=None, show_all_hydrogens=True)[source]

Render a visualization of the molecule in Jupyter

Parameters

backendstr, optional, default=’rdkit’

Which visualization engine to use. Choose from:

rdkit
openeye
nglview (conformers needed)

widthint, optional, default=500

Width of the generated representation (only applicable to backend=openeye or backend=rdkit)

heightint, optional, default=300

Width of the generated representation (only applicable to backend=openeye or backend=rdkit)

show_all_hydrogensbool, optional, default=True

Whether to explicitly depict all hydrogen atoms. (only applicable to backend=openeye or backend=rdkit)

Returns

object

Depending on the backend chosen:

rdkit → IPython.display.SVG
openeye → IPython.display.Image
nglview → nglview.NGLWidget