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]

See FrozenMolecule.__init__

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)	See FrozenMolecule.__init__
`add_atom`(atomic_number, formal_charge, ...)	Add an atom to the molecule.
`add_bond`(atom1, atom2, bond_order, is_aromatic)	Add a bond between two specified atom indices
`add_conformer`(coordinates)	Add a conformation of the molecule
`add_default_hierarchy_schemes`([...])	Adds `chain` and `residue` hierarchy schemes.
`add_hierarchy_scheme`(uniqueness_criteria, ...)	Use the molecule's metadata to facilitate iteration over its atoms.
`apply_elf_conformer_selection`([percentage, ...])	Select a set of diverse conformers from the molecule's conformers with ELF.
`are_isomorphic`(mol1, mol2[, ...])	Determine if `mol1` is isomorphic to `mol2`.
`assign_fractional_bond_orders`([...])	Update and store list of bond orders this molecule.
`assign_partial_charges`(partial_charge_method)	Calculate partial atomic charges and store them in the molecule.
`atom`(index)	Get the atom with the specified index.
`atom_index`(atom)	Returns the index of the given atom in this molecule
`bond`(index)	Get the bond with the specified index.
`canonical_order_atoms`([toolkit_registry])	Produce a copy of the molecule with the atoms reordered canonically.
`chemical_environment_matches`(query[, ...])	Find matches in the molecule for a SMARTS string
`delete_hierarchy_scheme`(iter_name)	Remove an existing `HierarchyScheme` specified by its iterator name.
`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 a `Molecule` from a SMILES string, ordering atoms from mappings
`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_polymer_pdb`(file_path[, ...])	Loads a polymer from a PDB file.
`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 from the element symbol and count.
`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 nx.Graph().
`nth_degree_neighbors`(n_degrees)	Return canonicalized pairs of atoms whose shortest separation is exactly n bonds.
`ordered_connection_table_hash`()	Compute an ordered hash of the atoms and bonds in the molecule
`perceive_residues`([substructure_file_path, ...])	Perceive a polymer's residues and permit iterating over them.
`remap`(mapping_dict[, current_to_new, partial])	Reorder the atoms in the molecule according to 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`([toolkit_registry, 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, toolkit_registry])	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.
`update_hierarchy_schemes`([iter_names])	Infer a hierarchy from atom metadata according to the existing hierarchy schemes.
`visualize`()	Render a visualization of the molecule in Jupyter

Attributes

`amber_impropers`	Iterate over all impropers with trivalent centers, reporting the central atom first.
`angles`	Get an iterator over all i-j-k angles.
`atoms`	Iterate over all Atom objects in the molecule.
`bonds`	Iterate over all Bond objects in the molecule.
`conformers`	Returns the list of conformers for this molecule.
`has_unique_atom_names`	`True` if the molecule has unique atom names, `False` otherwise.
`hierarchy_schemes`	The hierarchy schemes available on the molecule.
`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 in the molecule.
`n_conformers`	The number of conformers for this molecule.
`n_impropers`	Number of possible improper torsions in the molecule.
`n_propers`	Number of proper torsions in the molecule.
`name`	The name (or title) of the molecule
`partial_charges`	Returns the partial charges (if present) on the molecule.
`propers`	Iterate over all proper torsions in the molecule
`properties`	The properties dictionary of the molecule
`smirnoff_impropers`	Iterate over all impropers with trivalent centers, reporting the central atom second.
`torsions`	Get an iterator over all i-j-k-l torsions.
`total_charge`	Return the total charge on the molecule

add_atom(atomic_number: int, formal_charge: int, is_aromatic: bool, stereochemistry: Optional[str] = None, name: Optional[str] = None, metadata: Optional[Dict[str, Union[int, str]]] = None) → int[source]

Add an atom to the molecule.

Parameters:

atomic_number (int) – Atomic number of the atom
formal_charge (int) – Formal charge of the atom
is_aromatic (bool) – If True, atom is aromatic; if False, not aromatic
stereochemistry (str, optional, default None) – Either 'R' or 'S' for specified stereochemistry, or None if stereochemistry is irrelevant
name (str, optional) – An optional name for the atom
metadata (dict[str: (int, str)], default None) – An optional dictionary where keys are strings and values are strings or ints. This is intended to record atom-level information used to inform hierarchy definition and iteration, such as grouping atom by residue and chain.

Returns:

index (int) – 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, 1, False)
>>> bond_idx = molecule.add_bond(C, H2, 1, False)
>>> bond_idx = molecule.add_bond(C, H3, 1, False)
>>> bond_idx = molecule.add_bond(C, H4, 1, False)
>>> molecule.to_smiles(explicit_hydrogens=False)
'C'

add_bond(atom1: Union[int, Atom], atom2: Union[int, Atom], bond_order: int, is_aromatic: bool, stereochemistry: Optional[str] = None, fractional_bond_order: Optional[float] = None)[source]

Add a bond between two specified atom indices

Parameters:

atom1 (int or openff.toolkit.topology.molecule.Atom) – Index of first atom
atom2 (int or openff.toolkit.topology.molecule.Atom) – Index of second atom
bond_order (int) – Integral bond order of Kekulized form
is_aromatic (bool) – True if this bond is aromatic, False otherwise
stereochemistry (str, optional, default None) – Either 'E' or 'Z' for specified stereochemistry, or None if stereochemistry is irrelevant
fractional_bond_order (float, optional, default None) – The fractional (eg. Wiberg) bond order

Returns:

index (int) – Index of the bond in this molecule

Examples

For an example of use, see add_atom().

add_conformer(coordinates)[source]

Add a conformation of the molecule

Parameters:: coordinates (unit-wrapped 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: Literal['rdkit']) → IPython.display.SVG[source]

visualize(backend: Literal['openeye']) → IPython.display.Image

visualize(backend: Literal['nglview']) → nglview.NGLWidget

Render a visualization of the molecule in Jupyter

Parameters:

backend (str, optional, default 'rdkit') –
The visualization engine to use. Choose from:
- "rdkit"
- "openeye"
- "nglview" (requires conformers)
width (int, default 500) – Width of the generated representation (only applicable to backend="openeye" or backend="rdkit")
height (int, default 300) – Width of the generated representation (only applicable to backend="openeye" or backend="rdkit")
show_all_hydrogens (bool, 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

perceive_residues(substructure_file_path=None, strict_chirality=True)[source]

Perceive a polymer’s residues and permit iterating over them.

Perceives residues by matching substructures in the current molecule with a substructure dictionary file, using SMARTS, and assigns residue names and numbers to atom metadata. It then constructs a residue hierarchy scheme to allow iterating over residues.

Parameters:

substructure_file_path (str, optional, default None) – Path to substructure library file in JSON format. Defaults to using built-in substructure file.
strict_chirality (bool, optional, default True) – Whether to use strict chirality symbols (stereomarks) for substructure matchings with SMARTS.

add_default_hierarchy_schemes(overwrite_existing=True)

Adds chain and residue hierarchy schemes.

The Open Force Field Toolkit has no native understanding of hierarchical atom organisation schemes common to other biomolecular software, such as “residues” or “chains” (see userguide_hierarchy). Hierarchy schemes allow iteration over groups of atoms according to their metadata. For more information, see HierarchyScheme.

If a Molecule with the default hierarchy schemes changes, Molecule.update_hierarchy_schemes() must be called before the residues or chains are iterated over again or else the iteration may be incorrect.

Parameters:: overwrite_existing (bool, default True) – Whether to overwrite existing instances of the residue and chain hierarchy schemes. If this is False and either of the hierarchy schemes are already defined on this molecule, an exception will be raised.
Raises:: HierarchySchemeWithIteratorNameAlreadyRegisteredException – When overwrite_existing=False and either the chains or residues hierarchy scheme is already configured.

add_hierarchy_scheme(uniqueness_criteria, iterator_name)

Use the molecule’s metadata to facilitate iteration over its atoms.

This method will add an attribute with the name given by the iterator_name argument that provides an iterator over groups of atoms. Atoms are grouped by the values in their atom.metadata dictionary; any atoms with the same values for the keys given in the uniqueness_criteria argument will be in the same group. These groups have the type HierarchyElement.

Hierarchy schemes are not updated dynamically; if a Molecule with hierarchy schemes changes, Molecule.update_hierarchy_schemes() must be called before the scheme is iterated over again or else the grouping may be incorrect.

Hierarchy schemes allow iteration over groups of atoms according to their metadata. For more information, see HierarchyScheme.

Parameters:

uniqueness_criteria (tuple of str) – The names of Atom metadata entries that define this scheme. An atom belongs to a HierarchyElement only if its metadata has the same values for these criteria as the other atoms in the HierarchyElement.
iterator_name (str) – Name of the iterator that will be exposed to access the hierarchy elements generated by this scheme. Must not match an existing attribute of the Molecule, i.e. atoms, angles, etc.

Returns:

new_hier_scheme (openff.toolkit.topology.HierarchyScheme) – The newly created HierarchyScheme

property amber_impropers: Set[Tuple[Atom, Atom, Atom, Atom]]

Iterate over all impropers with trivalent centers, reporting the central atom first.

The central atom is reported first in each torsion. This method reports an improper for each trivalent atom in the molecule, whether or not any given force field would assign it improper torsion parameters.

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:: impropers (set 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: Set[Tuple[Atom, Atom, Atom]]: Get an iterator over all i-j-k angles.

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

Select a set of diverse conformers from the molecule’s conformers with ELF.

Applies the Electrostatically Least-interacting Functional groups method to select a set of diverse conformers which have minimal electrostatically strongly interacting functional groups from the molecule’s 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.

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.

See also

openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper.apply_elf_conformer_selection, openff.toolkit.utils.toolkits.RDKitToolkitWrapper.apply_elf_conformer_selection

static are_isomorphic(mol1: Union[FrozenMolecule, _SimpleMolecule, Graph], mol2: Union[FrozenMolecule, _SimpleMolecule, Graph], return_atom_map: bool = False, aromatic_matching: bool = True, formal_charge_matching: bool = True, bond_order_matching: bool = True, atom_stereochemistry_matching: bool = True, bond_stereochemistry_matching: bool = True, strip_pyrimidal_n_atom_stereo: bool = True, toolkit_registry: Union[ToolkitRegistry, ToolkitWrapper] = GLOBAL_TOOLKIT_REGISTRY) → Tuple[bool, Optional[Dict[int, int]]]

Determine if mol1 is isomorphic to mol2.

are_isomorphic() compares two molecule’s graph representations and the chosen node/edge attributes. Connections and atomic numbers are always checked.

If nx.Graphs() are given they must at least have atomic_number attributes on nodes. Other attributes that are_isomorphic() can optionally check…

… in nodes are:
- is_aromatic
- formal_charge
- stereochemistry
… in edges are:
- is_aromatic
- bond_order
- stereochemistry

By default, all attributes are checked, but stereochemistry around pyrimidal nitrogen is ignored.

Warning

This API is experimental and subject to change.

Parameters:

mol1 (an openff.toolkit.topology.molecule.FrozenMolecule or nx.Graph()) – The first molecule to test for isomorphism.
mol2 (an openff.toolkit.topology.molecule.FrozenMolecule or nx.Graph()) – The second molecule to test for isomorphism.
return_atom_map (bool, default False, optional) – Return a dict containing the atomic mapping, otherwise None. Only processed if inputs are isomorphic, will always return None if inputs are not isomorphic.
aromatic_matching (bool, default True, optional) – If False, aromaticity of graph nodes and edges are ignored for the purpose of determining isomorphism.
formal_charge_matching (bool, default True, optional) – If False, formal charges of graph nodes are ignored for the purpose of determining isomorphism.
bond_order_matching (bool, default True, optional) – If False, bond orders of graph edges are ignored for the purpose of determining isomorphism.
atom_stereochemistry_matching (bool, default True, optional) – If False, atoms’ stereochemistry is ignored for the purpose of determining isomorphism.
bond_stereochemistry_matching (bool, default True, optional) – If False, bonds’ stereochemistry is ignored for the purpose of determining isomorphism.
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_registry (openff.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_isomorphic (bool)
atom_map (default 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_registry (openff.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_model (string, optional. Default=None) – The bond order model to use for fractional bond order calculation. If None, "am1-wiberg" is used.
use_conformers (iterable of openff.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.

Examples

>>> from openff.toolkit import Molecule
>>> molecule = Molecule.from_smiles('CCCCCC')
>>> molecule.assign_fractional_bond_orders()

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

assign_partial_charges(partial_charge_method: str, strict_n_conformers: bool = False, use_conformers: Optional[Iterable[Quantity]] = None, toolkit_registry: Union[ToolkitRegistry, ToolkitWrapper] = GLOBAL_TOOLKIT_REGISTRY, normalize_partial_charges: bool = True)

Calculate partial atomic charges and store them in the molecule.

assign_partial_charges computes charges using the specified toolkit and assigns the new values to the partial_charges attribute. Supported charge methods vary from toolkit to toolkit, but some supported methods are:

"am1bcc"
"am1bccelf10" (requires OpenEye Toolkits)
"am1-mulliken"
"mmff94"
"gasteiger"

By default, the conformers on the input molecule are not used in the charge calculation. Instead, any conformers needed for the charge calculation are generated by this method. If this behavior is undesired, specific conformers can be provided via the use_conformers argument.

ELF10 methods will neither fail nor warn when fewer than the expected number of conformers could be generated, as many small molecules are too rigid to provide a large number of conformers. Note that only the "am1bccelf10" partial charge method uses ELF conformer selection; the "am1bcc" method only uses a single conformer. This may confuse users as the ToolkitAM1BCC SMIRNOFF tag in a force field file defines that AM1BCC-ELF10 should be used if the OpenEye Toolkits are available.

For more supported charge methods and their details, see the corresponding methods in each toolkit wrapper:

OpenEyeToolkitWrapper.assign_partial_charges
RDKitToolkitWrapper.assign_partial_charges
AmberToolsToolkitWrapper.assign_partial_charges
BuiltInToolkitWrapper.assign_partial_charges

Parameters:

partial_charge_method (string) – The partial charge calculation method to use for partial charge calculation.
strict_n_conformers (bool, 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_conformers (Arrays with shape (n_atoms, 3) and dimensions of distance) – Coordinates to use for partial charge calculation. If None, an appropriate number of conformers will be generated.
toolkit_registry – ToolkitRegistry or ToolkitWrapper to use for the calculation.
normalize_partial_charges (bool, 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.

Examples

Generate AM1 Mulliken partial charges. Conformers for the AM1 calculation are generated automatically:

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

To use pre-generated conformations, use the use_conformers argument:

>>> molecule = Molecule.from_smiles('CCCCCC')
>>> molecule.generate_conformers(n_conformers=1)
>>> molecule.assign_partial_charges(
...     'am1-mulliken',
...     use_conformers=molecule.conformers
... )

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

See also

openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper.assign_partial_charges, openff.toolkit.utils.toolkits.RDKitToolkitWrapper.assign_partial_charges, openff.toolkit.utils.toolkits.AmberToolsToolkitWrapper.assign_partial_charges, openff.toolkit.utils.toolkits.BuiltInToolkitWrapper.assign_partial_charges

atom(index: int) → Atom

Get the atom with the specified index.

Parameters:: index (int) –
Returns:: atom (openff.toolkit.topology.Atom)

atom_index(atom: Atom) → int

Returns the index of the given atom in this molecule

Parameters:: atom (openff.toolkit.topology.Atom) –
Returns:: index (int) – The index of the given atom in this molecule

property atoms: Iterate over all Atom objects in the molecule.

bond(index: int) → Bond

Get the bond with the specified index.

Parameters:: index (int) –
Returns:: bond (openff.toolkit.topology.Bond)

property bonds: List[Bond]: Iterate over all Bond objects in the molecule.

canonical_order_atoms(toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)

Produce a copy of the molecule with the atoms reordered canonically.

Each toolkit defines its own canonical ordering of atoms. The canonical order may change from toolkit version to toolkit version or between toolkits.

Warning

This API is experimental and subject to change.

Parameters:: toolkit_registry (openff.toolkit.utils.toolkits.ToolkitRegistry or) – openff.toolkit.utils.toolkits.ToolkitWrapper, optional ToolkitRegistry or ToolkitWrapper to use for SMILES-to-molecule conversion
Returns:: molecule (openff.toolkit.topology.Molecule) – An new OpenFF style molecule with atoms in the canonical order.

chemical_environment_matches(query: str, unique: bool = False, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)

Find matches in the molecule for a SMARTS string

Parameters:

query (str) – SMARTS string (with one or more tagged atoms).
unique (bool, default False) –
toolkit_registry (openff.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:

matches (list 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

property conformers

Returns the list of conformers for this molecule.

Conformers are presented as a list of 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.

delete_hierarchy_scheme(iter_name)

Remove an existing HierarchyScheme specified by its iterator name.

Hierarchy schemes allow iteration over groups of atoms according to their metadata. For more information, see HierarchyScheme.

Parameters:: iter_name (str) –

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) – lopenff.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.ToolkitWrapperl, 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:: serialized (bytes) – A BSON serialized representation of the object
Returns:: instance (cls) – An instantiated object

classmethod from_dict(molecule_dict: dict)

Create a new Molecule from a dictionary representation

Parameters:: molecule_dict (dict) – A dictionary representation of the molecule.
Returns:: molecule (Molecule) – A Molecule created from the dictionary representation

classmethod from_file(file_path: Union[str, Path, TextIO], file_format=None, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, 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_path (str, pathlib.Path, or file-like object) – The path to the file or file-like object to stream one or more molecules from.
file_format (str, 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_registry (openff.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_stereo (bool, default False) – If false, raises an exception if oemol contains undefined stereochemistry.

Returns:

molecules (Molecule 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 import Molecule
>>> from openff.toolkit.utils.utils import get_data_file_path
>>> sdf_file_path = get_data_file_path("molecules/toluene.sdf")
>>> molecule = Molecule.from_file(sdf_file_path)

classmethod from_inchi(inchi: str, allow_undefined_stereo: bool = False, toolkit_registry: Union[ToolkitRegistry, ToolkitWrapper] = GLOBAL_TOOLKIT_REGISTRY, name: str = '')

Construct a Molecule from a InChI representation

Parameters:

inchi (str) – The InChI representation of the molecule.
allow_undefined_stereo (bool, 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_registry (openff.toolkit.utils.toolkits.ToolRegistry) – or openff.toolkit.utils.toolkits.ToolkitWrapper, optional, default=None ToolkitRegistry or ToolkitWrapper to use for InChI-to-molecule conversion
name (str, default "") – An optional name for the output molecule

Returns:

molecule (openff.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=GLOBAL_TOOLKIT_REGISTRY, allow_undefined_stereo=False, **kwargs)

Generate a molecule from IUPAC or common name

Note

This method requires the OpenEye toolkit to be installed.

Parameters:

iupac_name (str) – IUPAC name of molecule to be generated
toolkit_registry (openff.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_stereo (bool, default False) – If false, raises an exception if molecule contains undefined stereochemistry.

Returns:

molecule (Molecule) – The resulting molecule with position

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')  # noqa

Create a molecule from a common name

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

classmethod from_json(serialized: str)

Instantiate an object from a JSON serialized representation.

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

Parameters:: serialized (str) – A JSON serialized representation of the object
Returns:: instance (cls) – An instantiated object

classmethod from_mapped_smiles(mapped_smiles: str, toolkit_registry: Union[ToolkitRegistry, ToolkitWrapper] = GLOBAL_TOOLKIT_REGISTRY, allow_undefined_stereo: bool = False)

Create a Molecule from a SMILES string, ordering atoms from mappings

SMILES strings support mapping integer indices to each atom by ending a bracketed atom declaration with a colon followed by a 1-indexed integer:

This method creates a Molecule from such a SMILES string whose atoms are ordered according to the mapping. Each atom must be mapped exactly once; any duplicate, missing, or out-of-range mappings will cause the method to fail.

Warning

This API is experimental and subject to change.

Parameters:

mapped_smiles (str) – A mapped SMILES string with explicit hydrogens.
toolkit_registry – Cheminformatics toolkit to use for SMILES-to-molecule conversion
allow_undefined_stereo – If false, raise an exception if the SMILES contains undefined stereochemistry.

Returns:

offmol – An OpenFF molecule instance.

Raises:

SmilesParsingError – If the given SMILES had no indexing picked up by the toolkits, or if the indexing is missing indices.
RemapIndexError – If the mapping has duplicate or out-of-range indices.

Examples

Create a mapped chlorofluoroiodomethane molecule and check the atoms are placed accordingly:

>>> molecule = Molecule.from_mapped_smiles(
...     "[Cl:2][C@:1]([F:3])([I:4])[H:5]"
... )
>>> assert molecule.atom(0).symbol == "C"
>>> assert molecule.atom(1).symbol == "Cl"
>>> assert molecule.atom(2).symbol == "F"
>>> assert molecule.atom(3).symbol == "I"
>>> assert molecule.atom(4).symbol == "H"

See also

from_smiles, remap

classmethod from_messagepack(serialized)

Instantiate an object from a MessagePack serialized representation.

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

Parameters:: serialized (bytes) – A MessagePack-encoded bytes serialized representation
Returns:: instance (cls) – 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:

oemol (openeye.oechem.OEMol) – An OpenEye molecule
allow_undefined_stereo (bool, default False) – If False, raises an exception if oemol contains undefined stereochemistry.

Returns:

molecule (openff.toolkit.topology.Molecule) – An OpenFF molecule

Examples

Create a Molecule from an OpenEye OEMol

>>> from openff.toolkit import Molecule
>>> from openeye import oechem
>>> oemol = oechem.OEMol()
>>> oechem.OESmilesToMol(oemol, '[H]C([H])([H])C([H])([H])O[H]')
True
>>> molecule = Molecule.from_openeye(oemol)

classmethod from_pdb_and_smiles(file_path, smiles, allow_undefined_stereo=False, name='')

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
smiles (str) – a valid smiles string for the pdb, used for stereochemistry, formal charges, and bond order
allow_undefined_stereo (bool, default False) – If false, raises an exception if SMILES contains undefined stereochemistry.
name (str, default "") – An optional name for the output molecule

Returns:

molecule (openff.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:: serialized (str) – A pickled representation of the object
Returns:: instance (cls) – An instantiated object

classmethod from_polymer_pdb(file_path: Union[str, Path, TextIO], toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, name: str = '')

Loads a polymer from a PDB file.

Also see Topology.from_multicomponent_pdb(), which can do everything this method can and more.

Currently only supports proteins with canonical amino acids that are either uncapped or capped by ACE/NME groups, but may later be extended to handle other common polymers, or accept user-defined polymer templates. Only one polymer chain may be present in the PDB file, and it must be the only molecule present.

Connectivity and bond orders are assigned by matching SMARTS codes for the supported residues against atom names. The PDB file must include all atoms with the correct standard atom names described in the PDB Chemical Component Dictionary. Residue names are used to assist trouble-shooting failed assignments, but are not used in the actual assignment process.

Metadata such as residues, chains, and atom names are recorded in the Atom.metadata attribute, which is a dictionary mapping from strings like “residue_name” to the appropriate value. from_polymer_pdb returns a molecule that can be iterated over with the .residues and .chains attributes, as well as the usual .atoms.

Parameters:

file_path (str or file object) – PDB information to be passed to OpenMM PDBFile object for loading
None (toolkit_registry = ToolkitWrapper or ToolkitRegistry. Default =) – Either a ToolkitRegistry, ToolkitWrapper
name (str, default "") – An optional name for the output molecule

Returns:

molecule (openff.toolkit.topology.Molecule)

Raises:

UnassignedChemistryInPDBError – If an atom or bond could not be assigned; the exception will provide a detailed diagnostic of what went wrong.
MultipleMoleculesInPDBError – If all atoms and bonds could be assigned, but the PDB includes multiple chains or molecules.

classmethod from_qcschema(qca_record, client=None, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, 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_record (dict) – A QCArchive molecule record or dataset entry.
client (optional, default None,) – A qcportal.FractalClient instance to use for fetching an initial geometry. Only used if qca_record is a dataset entry.
toolkit_registry (openff.toolkit.utils.toolkits.ToolkitRegistry or) – openff.toolkit.utils.toolkits.ToolkitWrapper, optional ToolkitRegistry or ToolkitWrapper to use for SMILES-to-molecule conversion
allow_undefined_stereo (bool, default False) – If false, raises an exception if qca_record contains undefined stereochemistry.

Returns:

molecule (openff.toolkit.topology.Molecule) – An OpenFF molecule instance.

Examples

Get Molecule from a QCArchive molecule record:

>>> from qcportal import FractalClient
>>> client = FractalClient()
>>> offmol = Molecule.from_qcschema(
...     client.query_molecules(molecular_formula="C7H12N2O4")[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
... )

Raises:

AttributeError – If the record dict can not be made from qca_record, or if the provided client could not retrieve the initial molecule.
KeyError – If the record does not contain the canonical_isomeric_explicit_hydrogen_mapped_smiles.
InvalidConformerError – Silent error, if the conformer could not be attached.

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:

rdmol (rkit.RDMol) – An RDKit molecule
allow_undefined_stereo (bool, default False) – If False, raises an exception if rdmol contains undefined stereochemistry.
hydrogens_are_explicit (bool, default False) – If False, RDKit will perform hydrogen addition using Chem.AddHs

Returns:

molecule (openff.toolkit.topology.Molecule) – An OpenFF molecule

Examples

Create a molecule from an RDKit molecule

>>> from openff.toolkit import Molecule
>>> from rdkit import Chem
>>> rdmol = Chem.MolFromSmiles("CCO")
>>> molecule = Molecule.from_rdkit(rdmol)

classmethod from_smiles(smiles: str, hydrogens_are_explicit: bool = False, toolkit_registry: Union[ToolkitRegistry, ToolkitWrapper] = GLOBAL_TOOLKIT_REGISTRY, allow_undefined_stereo: bool = False, name: str = '') → Molecule

Construct a Molecule from a SMILES representation

The order of atoms in the Molecule is unspecified and may change from version to version or with different toolkits. SMILES atom indices (also known as atom maps) are not used to order atoms; instead, they are stored in the produced molecule’s properties attribute, accessible via molecule.properties["atom_map"]. The atom map is stored as a dictionary mapping molecule atom indices to SMILES atom maps. To order atoms according to SMILES atom indices, see Molecule.from_mapped_smiles(), which helpfully raises an exception if any atom map is missing, duplicated, or out-of-range, or else Molecule.remap() for arbitrary remaps.

Parameters:

smiles – The SMILES representation of the molecule.
hydrogens_are_explicit – If True, forbid the cheminformatics toolkit from inferring hydrogen atoms not explicitly specified in the SMILES.
toolkit_registry – The cheminformatics toolkit to use to interpret the SMILES.
allow_undefined_stereo – 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.
name (str, default "") – An optional name for the output molecule

Raises:

RadicalsNotSupportedError – If any atoms in the input molecule contain radical electrons.

Examples

Create a Molecule representing toluene from SMILES:

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

Create a Molecule representing phenol from SMILES with the oxygen at atom index 0 (SMILES indices begin at 1):

>>> molecule = Molecule.from_smiles('c1ccccc1[OH:1]')
>>> molecule = molecule.remap(
...     {k: v - 1 for k, v in molecule.properties["atom_map"].items()},
...     partial=True,
... )
>>> assert molecule.atom(0).symbol == "O"

See also

from_mapped_smiles, remap

classmethod from_toml(serialized)

Instantiate an object from a TOML serialized representation.

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

Parameters:: serlialized (str) – A TOML serialized representation of the object
Returns:: instance (cls) – An instantiated object

classmethod from_topology(topology)

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

Parameters:: topology (openff.toolkit.topology.Topology) – The Topology object containing a single Molecule object. Note that OpenMM and MDTraj Topology objects are not supported.
Returns:: molecule (openff.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

>>> from openff.toolkit import Molecule, Topology
>>> topology = Topology.from_molecules(Molecule.from_smiles('[CH4]'))
>>> molecule = Molecule.from_topology(topology)

classmethod from_xml(serialized)

Instantiate an object from an XML serialized representation.

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

Parameters:: serialized (bytes) – An XML serialized representation
Returns:: instance (cls) – Instantiated object.

classmethod from_yaml(serialized)

Instantiate from a YAML serialized representation.

Specification: http://yaml.org/

Parameters:: serialized (str) – A YAML serialized representation of the object
Returns:: instance (cls) – Instantiated object

generate_conformers(toolkit_registry: Union[ToolkitRegistry, ToolkitWrapper] = GLOBAL_TOOLKIT_REGISTRY, n_conformers: int = 10, rms_cutoff: Optional[Quantity] = None, clear_existing: bool = True, make_carboxylic_acids_cis: bool = 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_registry (openff.toolkit.utils.toolkits.ToolkitRegistry or) – openff.toolkit.utils.toolkits.ToolkitWrapper, optional, default=None ToolkitRegistry or ToolkitWrapper to use for SMILES-to-molecule conversion
n_conformers (int, default 1) – The maximum number of conformers to produce
rms_cutoff (openff.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_existing (bool, 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.

Examples

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

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

generate_unique_atom_names()

Generate unique atom names from the element symbol and count.

Names are generated from the elemental symbol and the number of times that element is found in the molecule. 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. For example, generated atom names might begin ‘C1x’, ‘H1x’, ‘O1x’, ‘C2x’, etc.

get_bond_between(i: Union[int, Atom], j: Union[int, Atom]) → Bond

Returns the bond between two atoms

Parameters:

i (int or Atom) – Atoms or atom indices to check
j (int or Atom) – Atoms or atom indices to check

Returns:

bond (Bond) – The bond between i and j.

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

property hierarchy_schemes: Dict[str, HierarchyScheme]

The hierarchy schemes available on the molecule.

Hierarchy schemes allow iteration over groups of atoms according to their metadata. For more information, see HierarchyScheme.

Returns:: A dict of the form {str (HierarchyScheme``}``) – The HierarchySchemes associated with the molecule.

See also

Molecule.add_hierarchy_scheme, Molecule.delete_hierarchy_scheme, Molecule.update_hierarchy_schemes, Topology.hierarchy_iterator, HierarchyScheme

property hill_formula: str: Get the Hill formula of the molecule

property impropers: Set[Tuple[Atom, Atom, Atom, Atom]]

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:: impropers (set of tuple) – An iterator of tuples, each containing the atoms making up a possible improper torsion.

See also

smirnoff_impropers, amber_impropers

is_isomorphic_with(other: Union[FrozenMolecule, _SimpleMolecule, Graph], **kwargs) → bool

Check if the molecule is isomorphic with the other molecule which can be an openff.toolkit.topology.Molecule 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 nx.Graph()) –
aromatic_matching (bool, default True, optional) –
atoms. (compare the formal charges attributes of the) –
formal_charge_matching (bool, default True, optional) –
atoms. –
bond_order_matching (bool, deafult=True, optional) –
bonds. (compare the bond order on attributes of the) –
atom_stereochemistry_matching (bool, default True, optional) – If False, atoms’ stereochemistry is ignored for the purpose of determining equality.
bond_stereochemistry_matching (bool, 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_registry (openff.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:

isomorphic (bool)

property n_angles: int: Number of angles in the molecule.

property n_atoms: int: The number of Atom objects.

property n_bonds: int: The number of Bond objects in the molecule.

property n_conformers: int: The number of conformers for this molecule.

property n_impropers: int: Number of possible improper torsions in the molecule.

property n_propers: int: Number of proper torsions in the molecule.

property name: str: 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.

ordered_connection_table_hash(): Compute an ordered hash of the atoms and bonds in the molecule

property partial_charges

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

Returns:: partial_charges (a openff.unit.Quantity - wrapped numpy array [1 x n_atoms] or None) – The partial charges on the molecule’s atoms. Returns None if no charges have been specified.

property propers: Set[Tuple[Atom, Atom, Atom, Atom]]

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: Dict[str, Any]: The properties dictionary of the molecule

remap(mapping_dict: Dict[int, int], current_to_new: bool = True, partial: bool = False)

Reorder the atoms in the molecule according to the given mapping dict.

The mapping dict must be a dictionary mapping atom indices to atom indices. Each atom index must be an integer in the half-open interval [0, n_atoms); ie, it must be a valid index into the self.atoms list. All atom indices in the molecule must be mapped from and to exactly once unless partial=True is given, in which case they must be mapped no more than once. Missing (unless partial=True), out-of-range (including non-integer), or duplicate indices are not allowed in the mapping_dict and will lead to an exception.

By default, the mapping dict’s keys are the source indices and its values are destination indices, but this can be changed with the current_to_new argument.

The keys of the self.properties["atom_map"] property are updated for the new ordering. Other values of the properties dictionary are transferred unchanged.

Warning

This API is experimental and subject to change.

Parameters:

mapping_dict – A dictionary of the mapping between indices. The mapping should be indexed starting from 0 for both the source and destination; note that SMILES atom mapping is typically 1-based.
current_to_new – 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}.
partial – If False (the default), an exception will be raised if any atom is lacking a destination in the atom map. Note that if this is True, atoms without entries in the mapping dict may be moved in addition to those in the dictionary. Note that partial maps must still be in-range and not include duplicates.

Returns:

new_molecule (openff.toolkit.topology.molecule.Molecule) – A copy of the molecule in the new order.

Raises:

RemapIndexError – When an out-of-range, duplicate, or missing index is found in the mapping_dict.

See also

from_mapped_smiles

property smirnoff_impropers: Set[Tuple[Atom, Atom, Atom, Atom]]

Iterate over all impropers with trivalent centers, reporting the central atom second.

The central atom is reported second in each torsion. This method reports an improper for each trivalent atom in the molecule, whether or not any given force field would assign it improper torsion parameters.

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 atom 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:: impropers (set 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: str, toolkit_registry: Union[ToolkitRegistry, ToolkitWrapper] = 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) – Tagged SMARTS with a single atom with index 1. Any matches for this atom will have any assigned stereocheistry information removed.
toolkit_registry (a :class:`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:: serialized (bytes) – A BSON serialized representation of the objecft

to_dict() → dict

Return a dictionary representation of the molecule.

Todo

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

Returns:: molecule_dict (dict) – 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_path (str or file-like object) – A file-like object or the path to the file to be written.
file_format (str) – Format specifier, one of [‘MOL2’, ‘MOL2H’, ‘SDF’, ‘PDB’, ‘SMI’, ‘CAN’, ‘TDT’] Note that not all toolkits support all formats
toolkit_registry (openff.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:: formula (the Hill formula of the molecule)

:raises NotImplementedError : if the molecule is not of one of the specified types.:

to_inchi(fixed_hydrogens: bool = False, toolkit_registry: Union[ToolkitRegistry, ToolkitWrapper] = GLOBAL_TOOLKIT_REGISTRY) → str

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_registry (openff.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: bool = False, toolkit_registry: Union[ToolkitRegistry, ToolkitWrapper] = 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_registry (openff.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_name (str) – 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) → str

Return a JSON serialized representation.

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

Parameters:: indent (int, optional, default None) – If not None, will pretty-print with specified number of spaces for indentation
Returns:: serialized (str) – A JSON serialized representation of the object

to_messagepack()

Return a MessagePack representation.

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

Returns:: serialized (bytes) – A MessagePack-encoded bytes serialized representation of the object

to_networkx()

Generate a NetworkX undirected graph from the molecule.

Nodes are Atoms labeled with atom indices and atomic elements (via the element node atrribute). Edges denote chemical bonds between Atoms.

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:: graph (networkx.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(toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, 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_model (str, optional, default "OEAroModel_MDL") – The aromaticity model to use. Only OEAroModel_MDL is supported.
Returns:: oemol (openeye.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:: serialized (str) – 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:

multiplicity (int, default 1,) – The multiplicity of the molecule; sets molecular_multiplicity field for QCElemental Molecule.
conformer (int, default 0,) – The index of the conformer to use for the QCElemental Molecule geometry.
extras (dict, 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.

Examples

Create a QCElemental Molecule:

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

Raises:

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

to_rdkit(aromaticity_model=DEFAULT_AROMATICITY_MODEL, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)

Create an RDKit molecule

Requires the RDKit to be installed.

Parameters:: aromaticity_model (str, optional, default "OEAroModel_MDL") – The aromaticity model to use. Only OEAroModel_MDL is supported.
Returns:: rdmol (rdkit.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: bool = True, explicit_hydrogens: bool = True, mapped: bool = False, toolkit_registry: Union[ToolkitRegistry, ToolkitWrapper] = 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_registry (openff.toolkit.utils.toolkits.ToolkitRegistry or) – openff.toolkit.utils.toolkits.ToolkitWrapper, optional, default=None ToolkitRegistry or ToolkitWrapper to use for SMILES conversion

Returns:

smiles (str) – 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:: serialized (str) – A TOML serialized representation of the object

to_topology()

Return an OpenFF Topology representation containing one copy of this molecule

Returns:: topology (openff.toolkit.topology.Topology) – A Topology representation of this molecule

Examples

>>> from openff.toolkit import Molecule
>>> molecule = Molecule.from_iupac('imatinib')
>>> topology = molecule.to_topology()

to_xml(indent=2)

Return an XML representation.

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

Parameters:: indent (int, optional, default 2) – If not None, will pretty-print with specified number of spaces for indentation
Returns:: serialized (bytes) – A MessagePack-encoded bytes serialized representation.

to_yaml()

Return a YAML serialized representation.

Specification: http://yaml.org/

Returns:: serialized (str) – A YAML serialized representation of the object

property torsions: Set[Tuple[Atom, Atom, Atom, Atom]]

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

Returns:: torsions (iterable of 4-Atom tuples)

property total_charge: Return the total charge on the molecule

update_hierarchy_schemes(iter_names=None)

Infer a hierarchy from atom metadata according to the existing hierarchy schemes.

Hierarchy schemes allow iteration over groups of atoms according to their metadata. For more information, see HierarchyScheme.

Parameters:: iter_names (Iterable of str, Optional) – Only perceive hierarchy for HierarchySchemes that expose these iterator names. If not provided, all known hierarchies will be perceived, overwriting previous results if applicable.

See also

Molecule.add_hierarchy_scheme, Molecule.delete_hierarchy_schemes, Molecule.hierarchy_schemes, HierarchyScheme