openff.toolkit.topology.FrozenMolecule
- class openff.toolkit.topology.FrozenMolecule(other=None, file_format=None, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, allow_undefined_stereo=False)[source]
Immutable chemical representation of a molecule, such as a small molecule or biopolymer.
Examples
Create a molecule from a sdf file
>>> from openff.toolkit.utils import get_data_file_path >>> sdf_filepath = get_data_file_path('molecules/ethanol.sdf') >>> molecule = FrozenMolecule.from_file(sdf_filepath)
Convert to OpenEye OEMol object
>>> oemol = molecule.to_openeye()
Create a molecule from an OpenEye molecule
>>> molecule = FrozenMolecule.from_openeye(oemol)
Convert to RDKit Mol object
>>> rdmol = molecule.to_rdkit()
Create a molecule from an RDKit molecule
>>> molecule = FrozenMolecule.from_rdkit(rdmol)
Create a molecule from IUPAC name (requires the OpenEye toolkit)
>>> molecule = FrozenMolecule.from_iupac('imatinib')
Create a molecule from SMILES
>>> molecule = FrozenMolecule.from_smiles('Cc1ccccc1')
Warning
This API is experimental and subject to change.
- __init__(other=None, file_format=None, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, allow_undefined_stereo=False)[source]
Create a new FrozenMolecule object
- Parameters
- otheroptional, default=None
If specified, attempt to construct a copy of the Molecule from the specified object. This can be any one of the following:
- file_formatstr, optional, default=None
If providing a file-like object, you must specify the format of the data. If providing a file, the file format will attempt to be guessed from the suffix.
- toolkit_registrya
ToolkitRegistry
or ToolkitWrapper
object, optional, default=GLOBAL_TOOLKIT_REGISTRYToolkitRegistry
orToolkitWrapper
to use for I/O operations- allow_undefined_stereobool, default=False
If loaded from a file and
False
, raises an exception if undefined stereochemistry is detected during the molecule’s construction.
Examples
Create an empty molecule:
>>> empty_molecule = FrozenMolecule()
Create a molecule from a file that can be used to construct a molecule, using either a filename or file-like object:
>>> from openff.toolkit.utils import get_data_file_path >>> sdf_filepath = get_data_file_path('molecules/ethanol.sdf') >>> molecule = FrozenMolecule(sdf_filepath) >>> molecule = FrozenMolecule(open(sdf_filepath, 'r'), file_format='sdf')
>>> import gzip >>> mol2_gz_filepath = get_data_file_path('molecules/toluene.mol2.gz') >>> molecule = FrozenMolecule(gzip.GzipFile(mol2_gz_filepath, 'r'), file_format='mol2')
Create a molecule from another molecule:
>>> molecule_copy = FrozenMolecule(molecule)
Convert to OpenEye OEMol object
>>> oemol = molecule.to_openeye()
Create a molecule from an OpenEye molecule:
>>> molecule = FrozenMolecule(oemol)
Convert to RDKit Mol object
>>> rdmol = molecule.to_rdkit()
Create a molecule from an RDKit molecule:
>>> molecule = FrozenMolecule(rdmol)
Create a molecule from a serialized molecule object:
>>> serialized_molecule = molecule.__getstate__() >>> molecule_copy = Molecule(serialized_molecule)
Methods
__init__
([other, file_format, ...])Create a new FrozenMolecule object
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.
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.
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 the positions of the virtual sites in this molecule given a set of external coordinates.
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 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
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.
Return a MessagePack representation.
Generate a NetworkX undirected graph from the Molecule.
to_openeye
([aromaticity_model])Create an OpenEye molecule
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.
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.
Attributes
Iterate over improper torsions in the molecule, but only those with trivalent centers, reporting the central atom first in each improper.
Get an iterator over all i-j-k angles.
Iterate over all Atom objects.
Iterate over all Bond objects.
Returns the list of conformers for this molecule.
True if the molecule has unique atom names, False otherwise.
Get the Hill formula of the molecule
Iterate over all improper torsions in the molecule.
int: number of angles in the Molecule.
The number of Atom objects.
The number of Bond objects.
Returns the number of conformers for this molecule.
int: number of possible improper torsions in the Molecule.
The number of Particle objects, which corresponds to how many positions must be used.
int: number of proper torsions in the Molecule.
Return the number of rings found in the Molecule
The number of VirtualParticle objects.
The number of VirtualSite objects.
The name (or title) of the molecule
Returns the partial charges (if present) on the molecule.
Iterate over all Particle objects.
Iterate over all proper torsions in the molecule
The properties dictionary of the molecule
Return the number of rings in this molecule.
Iterate over improper torsions in the molecule, but only those with trivalent centers, reporting the central atom second in each improper.
Get an iterator over all i-j-k-l torsions.
Return the total charge on the molecule
Iterate over all VirtualSite objects.
- generate_unique_atom_names()[source]
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.
- strip_atom_stereochemistry(smarts, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)[source]
Delete stereochemistry information for certain atoms, if it is present. This method can be used to “normalize” molecules imported from different cheminformatics toolkits, which differ in which atom centers are considered stereogenic.
- Parameters
- smarts: str or ChemicalEnvironment
Tagged SMARTS with a single atom with index 1. Any matches for this atom will have any assigned stereocheistry information removed.
- toolkit_registrya
ToolkitRegistry
orToolkitWrapper
object, optional, default=GLOBAL_TOOLKIT_REGISTRY ToolkitRegistry
orToolkitWrapper
to use for I/O operations
- to_dict()[source]
Return a dictionary representation of the molecule.
- Returns
- molecule_dictOrderedDict
A dictionary representation of the molecule.
- classmethod from_dict(molecule_dict)[source]
Create a new Molecule from a dictionary representation
- Parameters
- molecule_dictOrderedDict
A dictionary representation of the molecule.
- Returns
- moleculeMolecule
A Molecule created from the dictionary representation
- to_smiles(isomeric=True, explicit_hydrogens=True, mapped=False, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)[source]
Return a canonical isomeric SMILES representation of the current molecule. A partially mapped smiles can also be generated for atoms of interest by supplying an atom_map to the properties dictionary.
Note
RDKit and OpenEye versions will not necessarily return the same representation.
- Parameters
- isomeric: bool optional, default= True
return an isomeric smiles
- explicit_hydrogens: bool optional, default=True
return a smiles string containing all hydrogens explicitly
- mapped: bool optional, default=False
return a explicit hydrogen mapped smiles, the atoms to be mapped can be controlled by supplying an atom map into the properties dictionary. If no mapping is passed all atoms will be mapped in order, else an atom map dictionary from the current atom index to the map id should be supplied with no duplicates. The map ids (values) should start from 0 or 1.
- toolkit_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, optional, default=None
ToolkitRegistry
orToolkitWrapper
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()
- classmethod from_inchi(inchi, allow_undefined_stereo=False, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit)[source]
Construct a Molecule from a InChI representation
- Parameters
- inchistr
The InChI representation of the molecule.
- allow_undefined_stereobool, default=False
Whether to accept InChI with undefined stereochemistry. If False, an exception will be raised if a InChI with undefined stereochemistry is passed into this function.
- toolkit_registryopenff.toolkit.utils.toolkits.ToolRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, optional, default=None
ToolkitRegistry
orToolkitWrapper
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-')
- to_inchi(fixed_hydrogens=False, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)[source]
Create an InChI string for the molecule using the requested toolkit backend. InChI is a standardised representation that does not capture tautomers unless specified using the fixed hydrogen layer.
For information on InChi see here https://iupac.org/who-we-are/divisions/division-details/inchi/
- Parameters
- fixed_hydrogens: bool, default=False
If a fixed hydrogen layer should be added to the InChI, if True this will produce a non standard specific InChI string of the molecule.
- toolkit_registryopenff.toolkit.utils.toolkits.ToolRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, optional, default=None
ToolkitRegistry
orToolkitWrapper
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)[source]
Create an InChIKey for the molecule using the requested toolkit backend. InChIKey is a standardised representation that does not capture tautomers unless specified using the fixed hydrogen layer.
For information on InChi see here https://iupac.org/who-we-are/divisions/division-details/inchi/
- Parameters
- fixed_hydrogens: bool, default=False
If a fixed hydrogen layer should be added to the InChI, if True this will produce a non standard specific InChI string of the molecule.
- toolkit_registryopenff.toolkit.utils.toolkits.ToolRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, optional, default=None
ToolkitRegistry
orToolkitWrapper
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
- classmethod from_smiles(smiles, hydrogens_are_explicit=False, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit, allow_undefined_stereo=False)[source]
Construct a Molecule from a SMILES representation
- Parameters
- smilesstr
The SMILES representation of the molecule.
- hydrogens_are_explicitbool, default = False
If False, the cheminformatics toolkit will perform hydrogen addition
- toolkit_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, optional, default=None
ToolkitRegistry
orToolkitWrapper
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')
- 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)[source]
Determines whether the two molecules are isomorphic by comparing their graph representations and the chosen node/edge attributes. Minimally connections and atomic_number are checked.
If nx.Graphs() are given they must at least have atomic_number attributes on nodes. other optional attributes for nodes are: is_aromatic, formal_charge and stereochemistry. optional attributes for edges are: is_aromatic, bond_order and stereochemistry.
Warning
This API is experimental and subject to change.
- Parameters
- mol1an 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
orToolkitWrapper
to use for removing stereochemistry from pyrimidal nitrogens.
- Returns
- molecules_are_isomorphicbool
- atom_mapdefault=None, Optional,
[Dict[int,int]] ordered by mol1 indexing {mol1_index: mol2_index} If molecules are not isomorphic given input arguments, will return None instead of dict.
- is_isomorphic_with(other, **kwargs)[source]
Check if the molecule is isomorphic with the other molecule which can be an 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
orToolkitWrapper
to use for removing stereochemistry from pyrimidal nitrogens.
- Returns
- isomorphicbool
- generate_conformers(toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, n_conformers=10, rms_cutoff=None, clear_existing=True)[source]
Generate conformers for this molecule using an underlying toolkit.
If
n_conformers=0
, no toolkit wrapper will be called. Ifn_conformers=0
andclear_existing=True
,molecule.conformers
will be set toNone
.- Parameters
- toolkit_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, optional, default=None
ToolkitRegistry
orToolkitWrapper
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 eachToolkitWrapper
(generally 1 Angstrom).- clear_existingbool, default=True
Whether to overwrite existing conformers for the molecule
- Raises
- InvalidToolkitRegistryError
If an invalid object is passed as the toolkit_registry parameter
Examples
>>> molecule = Molecule.from_smiles('CCCCCC') >>> molecule.generate_conformers()
- compute_virtual_site_positions_from_conformer(conformer_idx)[source]
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.
- compute_virtual_site_positions_from_atom_positions(atom_positions)[source]
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_positions
openmm.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.
- atom_positions
- 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.
- 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)[source]
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.
- compute_partial_charges_am1bcc(use_conformers=None, strict_n_conformers=False, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)[source]
Calculate partial atomic charges for this molecule using AM1-BCC run by an underlying toolkit and assign them to this molecule’s
partial_charges
attribute.- Parameters
- strict_n_conformersbool, default=False
Whether to raise an exception if an invalid number of conformers is provided for the given charge method. If this is False and an invalid number of conformers is found, a warning will be raised.
- use_conformersiterable of 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
orToolkitWrapper
to use for the calculation
- Raises
- InvalidToolkitRegistryError
If an invalid object is passed as the toolkit_registry parameter
Examples
>>> molecule = Molecule.from_smiles('CCCCCC') >>> molecule.generate_conformers() >>> molecule.compute_partial_charges_am1bcc()
- assign_partial_charges(partial_charge_method, strict_n_conformers=False, use_conformers=None, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, normalize_partial_charges=True)[source]
Calculate partial atomic charges for this molecule using an underlying toolkit, and assign the new values to the partial_charges attribute.
- Parameters
- partial_charge_methodstring
The partial charge calculation method to use for partial charge calculation.
- strict_n_conformersbool, default=False
Whether to raise an exception if an invalid number of conformers is provided for the given charge method. If this is False and an invalid number of conformers is found, a warning will be raised.
- use_conformersiterable of 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
orToolkitWrapper
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')
- assign_fractional_bond_orders(bond_order_model=None, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY, use_conformers=None)[source]
Update and store list of bond orders this molecule. Bond orders are stored on each bond, in the
bond.fractional_bond_order
attribute.Warning
This API is experimental and subject to change.
- Parameters
- toolkit_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, optional, default=None
ToolkitRegistry
orToolkitWrapper
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()
- to_networkx()[source]
Generate a NetworkX undirected graph from the Molecule.
Nodes are Atoms labeled with particle indices and atomic elements (via the
element
node atrribute). Edges denote chemical bonds between Atoms. Virtual sites are not included, since they lack a concept of chemical connectivity.- Returns
- graphnetworkx.Graph
The resulting graph, with nodes (atoms) labeled with atom indices, elements, stereochemistry and aromaticity flags and bonds with two atom indices, bond order, stereochemistry, and aromaticity flags
Examples
Retrieve the bond graph for imatinib (OpenEye toolkit required)
>>> molecule = Molecule.from_iupac('imatinib') >>> nxgraph = molecule.to_networkx()
- find_rotatable_bonds(ignore_functional_groups=None, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)[source]
Find all bonds classed as rotatable ignoring any matched to the
ignore_functional_groups
list.- Parameters
- ignore_functional_groups: optional, List[str], default=None,
A list of bond SMARTS patterns to be ignored when finding rotatable bonds.
- toolkit_registry: openff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, optional, default=None
ToolkitRegistry
orToolkitWrapper
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.
- 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 n_particles
The number of Particle objects, which corresponds to how many positions must be used.
- property n_rings
Return the number of rings found in the Molecule
Requires the RDKit to be installed.
Note
For systems containing some special cases of connected rings, this function may not be well-behaved and may report a different number rings than expected. Some problematic cases include networks of many (5+) rings or bicyclic moieties (i.e. norbornane).
- property 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.
- 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 impropers
Iterate over all improper torsions in the molecule.
- Returns
- impropersset of tuple
An iterator of tuples, each containing the indices of atoms making up a possible improper torsion.
See also
- 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
- 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
- nth_degree_neighbors(n_degrees)[source]
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.
- to_hill_formula() str [source]
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.
- chemical_environment_matches(query, unique=False, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)[source]
Retrieve all matches for a given chemical environment query.
- Parameters
- querystr or ChemicalEnvironment
SMARTS string (with one or more tagged atoms) or
ChemicalEnvironment
query. Query will internally be resolved to SMIRKS usingquery.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
orToolkitWrapper
to use for chemical environment matches
- Returns
- matcheslist of atom index tuples
A list of tuples, containing the indices of the matching atoms.
Examples
Retrieve all the carbon-carbon bond matches in a molecule
>>> molecule = Molecule.from_iupac('imatinib') >>> matches = molecule.chemical_environment_matches('[#6X3:1]~[#6X3:2]')
- classmethod from_iupac(iupac_name, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit, allow_undefined_stereo=False, **kwargs)[source]
Generate a molecule from IUPAC or common name
- Parameters
- iupac_namestr
IUPAC name of molecule to be generated
- toolkit_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, optional, default=GLOBAL_TOOLKIT_REGISTRY
ToolkitRegistry
orToolkitWrapper
to use for chemical environment matches- allow_undefined_stereobool, default=False
If false, raises an exception if molecule contains undefined stereochemistry.
- Returns
- moleculeMolecule
The resulting molecule with position
Note
This method requires the OpenEye toolkit to be installed. ..
Examples
Create a molecule from an IUPAC name
>>> molecule = Molecule.from_iupac('4-[(4-methylpiperazin-1-yl)methyl]-N-(4-methyl-3-{[4-(pyridin-3-yl)pyrimidin-2-yl]amino}phenyl)benzamide')
Create a molecule from a common name
>>> molecule = Molecule.from_iupac('imatinib')
- to_iupac(toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)[source]
Generate IUPAC name from Molecule
- Returns
- iupac_namestr
IUPAC name of the molecule
Note
This method requires the OpenEye toolkit to be installed. ..
Examples
>>> from 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()
- classmethod from_topology(topology)[source]
Return a Molecule representation of an OpenFF Topology containing a single Molecule object.
- Parameters
- 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)
- to_topology()[source]
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()
- classmethod from_file(file_path, file_format=None, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit, allow_undefined_stereo=False)[source]
Create one or more molecules from a file
- Parameters
- file_pathstr or file-like object
The path to the file or file-like object to stream one or more molecules from.
- file_formatstr, optional, default=None
Format specifier, usually file suffix (eg. ‘MOL2’, ‘SMI’) Note that not all toolkits support all formats. Check ToolkitWrapper.toolkit_file_read_formats for your loaded toolkits for details.
- toolkit_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper,
- optional, default=GLOBAL_TOOLKIT_REGISTRY
ToolkitRegistry
orToolkitWrapper
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)
- to_file(file_path, file_format, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)[source]
Write the current molecule to a file or file-like object
- Parameters
- file_pathstr or file-like object
A file-like object or the path to the file to be written.
- file_formatstr
Format specifier, one of [‘MOL2’, ‘MOL2H’, ‘SDF’, ‘PDB’, ‘SMI’, ‘CAN’, ‘TDT’] Note that not all toolkits support all formats
- toolkit_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper,
- optional, default=GLOBAL_TOOLKIT_REGISTRY
ToolkitRegistry
orToolkitWrapper
to use for file writing. If a Toolkit is passed, only the highest-precedence toolkit is used
- Raises
- ValueError
If the requested file_format is not supported by one of the installed cheminformatics toolkits
Examples
>>> molecule = Molecule.from_iupac('imatinib') >>> molecule.to_file('imatinib.mol2', file_format='mol2') >>> molecule.to_file('imatinib.sdf', file_format='sdf') >>> molecule.to_file('imatinib.pdb', file_format='pdb')
- enumerate_tautomers(max_states=20, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)[source]
Enumerate the possible tautomers of the current molecule
- Parameters
- max_states: int optional, default=20
The maximum amount of molecules that should be returned
- toolkit_registry: openff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, default=GLOBAL_TOOLKIT_REGISTRY
ToolkitRegistry
orToolkitWrapper
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.
- enumerate_stereoisomers(undefined_only=False, max_isomers=20, rationalise=True, toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)[source]
Enumerate the stereocenters and bonds of the current molecule.
- Parameters
- undefined_only: bool optional, default=False
If we should enumerate all stereocenters and bonds or only those with undefined stereochemistry
- max_isomers: int optional, default=20
The maximum amount of molecules that should be returned
- rationalise: bool optional, default=True
If we should try to build and rationalise the molecule to ensure it can exist
- toolkit_registry: openff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, default=GLOBAL_TOOLKIT_REGISTRY
ToolkitRegistry
orToolkitWrapper
to use to enumerate the stereoisomers.
- Returns
- molecules: List[openff.toolkit.topology.Molecule]
A list of
Molecule
instances not including the input molecule.
- enumerate_protomers(max_states=10)[source]
Enumerate the formal charges of a molecule to generate different protomoers.
- Parameters
- max_states: int optional, default=10,
The maximum number of protomer states to be returned.
- Returns
- molecules: List[openff.toolkit.topology.Molecule],
A list of the protomers of the input molecules not including the input.
- classmethod from_rdkit(rdmol, allow_undefined_stereo=False, hydrogens_are_explicit=False)[source]
Create a Molecule from an RDKit molecule.
Requires the RDKit to be installed.
- Parameters
- rdmolrkit.RDMol
An RDKit molecule
- allow_undefined_stereobool, default=False
If
False
, raises an exception ifrdmol
contains undefined stereochemistry.- hydrogens_are_explicitbool, default=False
If
False
, RDKit will perform hydrogen addition usingChem.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)
- to_rdkit(aromaticity_model=DEFAULT_AROMATICITY_MODEL)[source]
Create an RDKit molecule
Requires the RDKit to be installed.
- Parameters
- aromaticity_modelstr, optional, default=DEFAULT_AROMATICITY_MODEL
The aromaticity model to use
- Returns
- 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()
- classmethod from_openeye(oemol, allow_undefined_stereo=False)[source]
Create a
Molecule
from an OpenEye molecule.Requires the OpenEye toolkit to be installed.
- Parameters
- oemolopeneye.oechem.OEMol
An OpenEye molecule
- allow_undefined_stereobool, default=False
If
False
, raises an exception if oemol contains undefined stereochemistry.
- Returns
- 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])
- to_qcschema(multiplicity=1, conformer=0, extras=None)[source]
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()
- classmethod from_mapped_smiles(mapped_smiles, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit, allow_undefined_stereo=False)[source]
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
orToolkitWrapper
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_qcschema(qca_record, client=None, toolkit_registry=ToolkitRegistry containing The RDKit, AmberTools, Built-in Toolkit, allow_undefined_stereo=False)[source]
Create a Molecule from a QCArchive 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
orToolkitWrapper
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_pdb_and_smiles(file_path, smiles, allow_undefined_stereo=False)[source]
Create a Molecule from a pdb file and a SMILES string using RDKit.
Requires RDKit to be installed.
Warning
This API is experimental and subject to change.
The molecule is created and sanitised based on the SMILES string, we then find a mapping between this molecule and one from the PDB based only on atomic number and connections. The SMILES molecule is then 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.
- canonical_order_atoms(toolkit_registry=GLOBAL_TOOLKIT_REGISTRY)[source]
Canonical order the atoms in a copy of the molecule using a toolkit, returns a new copy.
Warning
This API is experimental and subject to change.
- Parameters
- toolkit_registryopenff.toolkit.utils.toolkits.ToolkitRegistry or openff.toolkit.utils.toolkits.ToolkitWrapper, optional
ToolkitRegistry
orToolkitWrapper
to use for SMILES-to-molecule conversion
- Returns
- moleculeopenff.toolkit.topology.Molecule
An new OpenFF style molecule with atoms in the canonical order.
- remap(mapping_dict, current_to_new=True)[source]
Remap all of the indexes in the molecule to match the given mapping dict
Warning
This API is experimental and subject to change.
- Parameters
- mapping_dictdict,
A dictionary of the mapping between indexes, this should start from 0.
- current_to_newbool, default=True
If this is
True
, thenmapping_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.
- to_openeye(aromaticity_model=DEFAULT_AROMATICITY_MODEL)[source]
Create an OpenEye molecule
Requires the OpenEye toolkit to be installed.
- Parameters
- aromaticity_modelstr, optional, default=DEFAULT_AROMATICITY_MODEL
The aromaticity model to use
- Returns
- oemolopeneye.oechem.OEMol
An OpenEye molecule
Examples
Create an OpenEye molecule from a Molecule
>>> molecule = Molecule.from_smiles('CC') >>> oemol = molecule.to_openeye()
- get_bond_between(i, j)[source]
Returns the bond between two atoms
- Parameters
- i, jint or Atom
Atoms or atom indices to check
- Returns
- bondBond
The bond between i and j.
- property rings
Return the number of rings in this molecule.
Requires the RDKit to be installed.
Note
For systems containing some special cases of connected rings, this function may not be well-behaved and may report a different number rings than expected. Some problematic cases include networks of many (5+) rings or bicyclic moieties (i.e. norbornane).
- classmethod from_bson(serialized)
Instantiate an object from a BSON serialized representation.
Specification: http://bsonspec.org/
- Parameters
- serializedbytes
A BSON serialized representation of the object
- Returns
- instancecls
An instantiated object
- classmethod from_json(serialized)
Instantiate an object from a JSON serialized representation.
Specification: https://www.json.org/
- Parameters
- serializedstr
A JSON serialized representation of the object
- Returns
- instancecls
An instantiated object
- classmethod from_messagepack(serialized)
Instantiate an object from a MessagePack serialized representation.
Specification: https://msgpack.org/index.html
- Parameters
- serializedbytes
A MessagePack-encoded bytes serialized representation
- Returns
- instancecls
Instantiated object.
- classmethod from_pickle(serialized)
Instantiate an object from a pickle serialized representation.
Warning
This is not recommended for safe, stable storage since the pickle specification may change between Python versions.
- Parameters
- serializedstr
A pickled representation of the object
- Returns
- instancecls
An instantiated object
- classmethod from_toml(serialized)
Instantiate an object from a TOML serialized representation.
Specification: https://github.com/toml-lang/toml
- Parameters
- serlializedstr
A TOML serialized representation of the object
- Returns
- instancecls
An instantiated object
- classmethod from_xml(serialized)
Instantiate an object from an XML serialized representation.
Specification: https://www.w3.org/XML/
- Parameters
- serializedbytes
An XML serialized representation
- Returns
- instancecls
Instantiated object.
- classmethod from_yaml(serialized)
Instantiate from a YAML serialized representation.
Specification: http://yaml.org/
- Parameters
- serializedstr
A YAML serialized representation of the object
- Returns
- instancecls
Instantiated object
- to_bson()
Return a BSON serialized representation.
Specification: http://bsonspec.org/
- Returns
- serializedbytes
A BSON serialized representation of the objecft
- to_json(indent=None)
Return a JSON serialized representation.
Specification: https://www.json.org/
- Parameters
- indentint, optional, default=None
If not None, will pretty-print with specified number of spaces for indentation
- Returns
- serializedstr
A JSON serialized representation of the object
- to_messagepack()
Return a MessagePack representation.
Specification: https://msgpack.org/index.html
- Returns
- serializedbytes
A MessagePack-encoded bytes serialized representation of the object
- to_pickle()
Return a pickle serialized representation.
Warning
This is not recommended for safe, stable storage since the pickle specification may change between Python versions.
- Returns
- serializedstr
A pickled representation of the object
- to_toml()
Return a TOML serialized representation.
Specification: https://github.com/toml-lang/toml
- Returns
- serializedstr
A TOML serialized representation of the object
- to_xml(indent=2)
Return an XML representation.
Specification: https://www.w3.org/XML/
- Parameters
- indentint, optional, default=2
If not None, will pretty-print with specified number of spaces for indentation
- Returns
- serializedbytes
A MessagePack-encoded bytes serialized representation.
- to_yaml()
Return a YAML serialized representation.
Specification: http://yaml.org/
- Returns
- serializedstr
A YAML serialized representation of the object