openforcefield.topology.FrozenMolecule

class openforcefield.topology.FrozenMolecule(other=None, file_format=None, toolkit_registry=<openforcefield.utils.toolkits.ToolkitRegistry object>, allow_undefined_stereo=False)[source]

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

Examples

Create a molecule from a sdf file

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

Convert to OpenEye OEMol object

>>> oemol = molecule.to_openeye()

Create a molecule from an OpenEye molecule

>>> molecule = FrozenMolecule.from_openeye(oemol)

Convert to RDKit Mol object

>>> rdmol = molecule.to_rdkit()

Create a molecule from an RDKit molecule

>>> molecule = FrozenMolecule.from_rdkit(rdmol)

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

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

Create a molecule from SMILES

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

Warning

This API is experimental and subject to change.

Attributes:
angles

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

atoms

Iterate over all Atom objects.

bonds

Iterate over all Bond objects.

conformers

Iterate over all conformers in this molecule.

impropers

Iterate over all proper torsions in the molecule

n_angles

int: number of angles in the Molecule.

n_atoms

The number of Atom objects.

n_bonds

The number of Bond objects.

n_conformers

Iterate over all Atom objects.

n_impropers

int: number of improper torsions in the Molecule.

n_particles

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

n_propers

int: number of proper torsions in the Molecule.

n_virtual_sites

The number of VirtualSite objects.

name

The name (or title) of the molecule

partial_charges

Returns the partial charges (if present) on the molecule

particles

Iterate over all Particle objects.

propers

Iterate over all proper torsions in the molecule

properties

The properties dictionary of the molecule

torsions

Get an iterator over all i-j-k-l torsions.

total_charge

Return the total charge on the molecule

virtual_sites

Iterate over all VirtualSite objects.

Methods

chemical_environment_matches(query[, …]) Retrieve all matches for a given chemical environment query.
compute_partial_charges([toolkit_registry]) Warning! Not Implemented! Calculate partial atomic charges for this molecule using an underlying toolkit
compute_partial_charges_am1bcc([…]) Calculate partial atomic charges for this molecule using AM1-BCC run by an underlying toolkit
compute_wiberg_bond_orders([charge_model, …]) Calculate wiberg bond orders for this molecule using an underlying toolkit
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(filename[, file_format, …]) Create one or more molecules from a file
from_iupac(iupac_name, **kwargs) Generate a molecule from IUPAC or common name
from_json(serialized) Instantiate an object from a JSON serialized representation.
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_pickle(serialized) Instantiate an object from a pickle serialized representation.
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 openforcefield Topology containing a single Molecule object.
from_xml(serialized) Instantiate an object from an XML serialized representation.
from_yaml(serialized) Instantiate from a YAML serialized representation.
generate_conformers([toolkit_registry, …]) Generate conformers for this molecule using an underlying toolkit
get_fractional_bond_orders([method, …]) Get fractional bond orders.
is_isomorphic(other[, …]) Determines whether the molecules are isomorphic by comparing their graphs.
to_bson() Return a BSON serialized representation.
to_dict() Return a dictionary representation of the molecule.
to_file(outfile, outfile_format[, …]) Write the current molecule to a file or file-like object
to_iupac() Generate IUPAC name from Molecule
to_json([indent]) Return a JSON serialized representation.
to_messagepack() Return a MessagePack representation.
to_networkx() Generate a NetworkX undirected graph from the Molecule.
to_openeye([aromaticity_model]) Create an OpenEye molecule
to_pickle() Return a pickle serialized representation.
to_rdkit([aromaticity_model]) Create an RDKit molecule
to_smiles([toolkit_registry]) Return a canonical isomeric SMILES representation of the current molecule
to_toml() Return a TOML serialized representation.
to_topology() Return an openforcefield Topology representation containing one copy of this molecule
to_xml([indent]) Return an XML representation.
to_yaml() Return a YAML serialized representation.
__init__(other=None, file_format=None, toolkit_registry=<openforcefield.utils.toolkits.ToolkitRegistry object>, allow_undefined_stereo=False)[source]

Create a new FrozenMolecule object

Parameters:
other : optional, default=None

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

  • a Molecule object
  • a file that can be used to construct a Molecule object
  • an openeye.oechem.OEMol
  • an rdkit.Chem.rdchem.Mol
  • a serialized Molecule object
file_format : str, 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_registry : a ToolkitRegistry or ToolkitWrapper object, optional, default=GLOBAL_TOOLKIT_REGISTRY

ToolkitRegistry or ToolkitWrapper to use for I/O operations

allow_undefined_stereo : bool, default=False

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

Examples

Create an empty molecule:

>>> empty_molecule = FrozenMolecule()

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

>>> from openforcefield.utils import get_data_filename
>>> sdf_filepath = get_data_filename('molecules/ethanol.sdf')
>>> molecule = FrozenMolecule(sdf_filepath)
>>> molecule = FrozenMolecule(open(sdf_filepath, 'r'), file_format='sdf')
>>> import gzip
>>> mol2_gz_filepath = get_data_filename('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
chemical_environment_matches(query[, …]) Retrieve all matches for a given chemical environment query.
compute_partial_charges([toolkit_registry]) Warning! Not Implemented! Calculate partial atomic charges for this molecule using an underlying toolkit
compute_partial_charges_am1bcc([…]) Calculate partial atomic charges for this molecule using AM1-BCC run by an underlying toolkit
compute_wiberg_bond_orders([charge_model, …]) Calculate wiberg bond orders for this molecule using an underlying toolkit
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(filename[, file_format, …]) Create one or more molecules from a file
from_iupac(iupac_name, **kwargs) Generate a molecule from IUPAC or common name
from_json(serialized) Instantiate an object from a JSON serialized representation.
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_pickle(serialized) Instantiate an object from a pickle serialized representation.
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 openforcefield Topology containing a single Molecule object.
from_xml(serialized) Instantiate an object from an XML serialized representation.
from_yaml(serialized) Instantiate from a YAML serialized representation.
generate_conformers([toolkit_registry, …]) Generate conformers for this molecule using an underlying toolkit
get_fractional_bond_orders([method, …]) Get fractional bond orders.
is_isomorphic(other[, …]) Determines whether the molecules are isomorphic by comparing their graphs.
to_bson() Return a BSON serialized representation.
to_dict() Return a dictionary representation of the molecule.
to_file(outfile, outfile_format[, …]) Write the current molecule to a file or file-like object
to_iupac() Generate IUPAC name from Molecule
to_json([indent]) Return a JSON serialized representation.
to_messagepack() Return a MessagePack representation.
to_networkx() Generate a NetworkX undirected graph from the Molecule.
to_openeye([aromaticity_model]) Create an OpenEye molecule
to_pickle() Return a pickle serialized representation.
to_rdkit([aromaticity_model]) Create an RDKit molecule
to_smiles([toolkit_registry]) Return a canonical isomeric SMILES representation of the current molecule
to_toml() Return a TOML serialized representation.
to_topology() Return an openforcefield Topology representation containing one copy of this molecule
to_xml([indent]) Return an XML representation.
to_yaml() Return a YAML serialized representation.

Attributes

angles Get an iterator over all i-j-k angles.
atoms Iterate over all Atom objects.
bonds Iterate over all Bond objects.
conformers Iterate over all conformers in this molecule.
impropers Iterate over all proper torsions in the molecule
n_angles int: number of angles in the Molecule.
n_atoms The number of Atom objects.
n_bonds The number of Bond objects.
n_conformers Iterate over all Atom objects.
n_impropers int: number of improper torsions in the Molecule.
n_particles The number of Particle objects, which corresponds to how many positions must be used.
n_propers int: number of proper torsions in the Molecule.
n_virtual_sites The number of VirtualSite objects.
name The name (or title) of the molecule
partial_charges Returns the partial charges (if present) on the molecule
particles Iterate over all Particle objects.
propers Iterate over all proper torsions in the molecule
properties The properties dictionary of the molecule
torsions Get an iterator over all i-j-k-l torsions.
total_charge Return the total charge on the molecule
virtual_sites Iterate over all VirtualSite objects.
to_dict()[source]

Return a dictionary representation of the molecule.

Returns:
molecule_dict : OrderedDict

A dictionary representation of the molecule.

classmethod from_dict(molecule_dict)[source]

Create a new Molecule from a dictionary representation

Parameters:
molecule_dict : OrderedDict

A dictionary representation of the molecule.

Returns:
molecule : Molecule

A Molecule created from the dictionary representation

to_smiles(toolkit_registry=<openforcefield.utils.toolkits.ToolkitRegistry object>)[source]

Return a canonical isomeric SMILES representation of the current molecule

Note

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

Parameters:
toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None

ToolkitRegistry or ToolkitWrapper to use for SMILES conversion

Returns:
smiles : str

Canonical isomeric explicit-hydrogen SMILES

Examples

>>> from openforcefield.utils import get_data_filename
>>> sdf_filepath = get_data_filename('molecules/ethanol.sdf')
>>> molecule = Molecule(sdf_filepath)
>>> smiles = molecule.to_smiles()
static from_smiles(smiles, hydrogens_are_explicit=False, toolkit_registry=<openforcefield.utils.toolkits.ToolkitRegistry object>)[source]

Construct a Molecule from a SMILES representation

Parameters:
smiles : str

The SMILES representation of the molecule.

hydrogens_are_explicit : bool, default = False

If False, the cheminformatics toolkit will perform hydrogen addition

toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None

ToolkitRegistry or ToolkitWrapper to use for SMILES-to-molecule conversion

Returns:
molecule : openforcefield.topology.Molecule

Examples

>>> molecule = Molecule.from_smiles('Cc1ccccc1')
is_isomorphic(other, compare_atom_stereochemistry=True, compare_bond_stereochemistry=True)[source]

Determines whether the molecules are isomorphic by comparing their graphs.

Parameters:
other : an openforcefield.topology.molecule.FrozenMolecule

The molecule to test for isomorphism.

compare_atom_stereochemistry : bool, optional

If False, atoms’ stereochemistry is ignored for the purpose of determining equality. Default is True.

compare_bond_stereochemistry : bool, optional

If False, bonds’ stereochemistry is ignored for the purpose of determining equality. Default is True.

Returns:
molecules_are_isomorphic : bool
generate_conformers(toolkit_registry=<openforcefield.utils.toolkits.ToolkitRegistry object>, num_conformers=10, clear_existing=True)[source]

Generate conformers for this molecule using an underlying toolkit

Parameters:
toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None

ToolkitRegistry or ToolkitWrapper to use for SMILES-to-molecule conversion

num_conformers : int, default=1

The maximum number of conformers to produce

clear_existing : bool, default=True

Whether to overwrite existing conformers for the molecule

Raises:
InvalidToolkitError

If an invalid object is passed as the toolkit_registry parameter

Examples

>>> molecule = Molecule.from_smiles('CCCCCC')
>>> molecule.generate_conformers()
compute_partial_charges_am1bcc(toolkit_registry=<openforcefield.utils.toolkits.ToolkitRegistry object>)[source]

Calculate partial atomic charges for this molecule using AM1-BCC run by an underlying toolkit

Parameters:
toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None

ToolkitRegistry or ToolkitWrapper to use for the calculation

Raises:
InvalidToolkitError

If an invalid object is passed as the toolkit_registry parameter

Examples

>>> molecule = Molecule.from_smiles('CCCCCC')
>>> molecule.generate_conformers()
>>> molecule.compute_partial_charges_am1bcc()
compute_partial_charges(toolkit_registry=<openforcefield.utils.toolkits.ToolkitRegistry object>)[source]

Warning! Not Implemented! Calculate partial atomic charges for this molecule using an underlying toolkit

Parameters:
quantum_chemical_method : string, default=’AM1-BCC’

The quantum chemical method to use for partial charge calculation.

partial_charge_method : string, default=’None’

The partial charge calculation method to use for partial charge calculation.

toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None

ToolkitRegistry or ToolkitWrapper to use for SMILES-to-molecule conversion

Raises:
InvalidToolkitError

If an invalid object is passed as the toolkit_registry parameter

Examples

>>> molecule = Molecule.from_smiles('CCCCCC')
>>> molecule.generate_conformers()
>>> molecule.compute_partial_charges()
compute_wiberg_bond_orders(charge_model=None, toolkit_registry=<openforcefield.utils.toolkits.ToolkitRegistry object>)[source]

Calculate wiberg bond orders for this molecule using an underlying toolkit

Parameters:
toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=None

ToolkitRegistry or ToolkitWrapper to use for SMILES-to-molecule conversion

charge_model : string, optional

The charge model to use for partial charge calculation

Raises:
InvalidToolkitError

If an invalid object is passed as the toolkit_registry parameter

Examples

>>> molecule = Molecule.from_smiles('CCCCCC')
>>> molecule.generate_conformers()
>>> molecule.compute_wiberg_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:
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()
partial_charges

Returns the partial charges (if present) on the molecule

Returns:
partial_charges : a simtk.unit.Quantity - wrapped numpy array [1 x n_atoms]

The partial charges on this Molecule’s atoms.

n_particles

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

n_atoms

The number of Atom objects.

n_virtual_sites

The number of VirtualSite objects.

n_bonds

The number of Bond objects.

n_angles

int: number of angles in the Molecule.

n_propers

int: number of proper torsions in the Molecule.

n_impropers

int: number of improper torsions in the Molecule.

particles

Iterate over all Particle objects.

atoms

Iterate over all Atom objects.

conformers

Iterate over all conformers in this molecule.

n_conformers

Iterate over all Atom objects.

virtual_sites

Iterate over all VirtualSite objects.

bonds

Iterate over all Bond objects.

angles

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

torsions

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
propers

Iterate over all proper torsions in the molecule

impropers

Iterate over all proper torsions in the molecule

total_charge

Return the total charge on the molecule

name

The name (or title) of the molecule

properties

The properties dictionary of the molecule

chemical_environment_matches(query, toolkit_registry=<openforcefield.utils.toolkits.ToolkitRegistry object>)[source]

Retrieve all matches for a given chemical environment query.

Parameters:
query : str or ChemicalEnvironment

SMARTS string (with one or more tagged atoms) or ChemicalEnvironment query Query will internally be resolved to SMIRKS using query.asSMIRKS() if it has an .asSMIRKS method.

toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper, optional, default=GLOBAL_TOOLKIT_REGISTRY

ToolkitRegistry or ToolkitWrapper to use for chemical environment matches

Returns:
matches : list of Atom tuples

A list of all matching Atom tuples

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, **kwargs)[source]

Generate a molecule from IUPAC or common name

Parameters:
iupac_name : str

IUPAC name of molecule to be generated

allow_undefined_stereo : bool, default=False

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

Returns:
molecule : Molecule

The resulting molecule with position

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

Examples

Create a molecule from a common 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()[source]

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 openforcefield.utils import get_data_filename
>>> sdf_filepath = get_data_filename('molecules/ethanol.sdf')
>>> molecule = Molecule(sdf_filepath)
>>> iupac_name = molecule.to_iupac()
static from_topology(topology)[source]

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

Parameters:
topology : openforcefield.topology.Topology

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

Returns:
molecule : openforcefield.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)  # doctest: +SKIP
to_topology()[source]

Return an openforcefield Topology representation containing one copy of this molecule

Returns:
topology : openforcefield.topology.Topology

A Topology representation of this molecule

Examples

>>> molecule = Molecule.from_iupac('imatinib')
>>> topology = molecule.to_topology()
static from_file(filename, file_format=None, toolkit_registry=<openforcefield.utils.toolkits.ToolkitRegistry object>, allow_undefined_stereo=False)[source]

Create one or more molecules from a file

Parameters:
filename : str or file-like object

The name of 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 : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper,
optional, default=GLOBAL_TOOLKIT_REGISTRY

ToolkitRegistry or ToolkitWrapper to use for file loading. If a Toolkit is passed, only the highest-precedence toolkit is used

allow_undefined_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 openforcefield.tests.utils import get_monomer_mol2file
>>> mol2_filename = get_monomer_mol2file('cyclohexane')
>>> molecule = Molecule.from_file(mol2_filename)
to_file(outfile, outfile_format, toolkit_registry=<openforcefield.utils.toolkits.ToolkitRegistry object>)[source]

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

Parameters:
outfile : str or file-like object

A file-like object or the filename of the file to be written to

outfile_format : str

Format specifier, one of [‘MOL2’, ‘MOL2H’, ‘SDF’, ‘PDB’, ‘SMI’, ‘CAN’, ‘TDT’] Note that not all toolkits support all formats

toolkit_registry : openforcefield.utils.toolkits.ToolRegistry or openforcefield.utils.toolkits.ToolkitWrapper,
optional, default=GLOBAL_TOOLKIT_REGISTRY

ToolkitRegistry or ToolkitWrapper to use for file writing. If a Toolkit is passed, only the highest-precedence toolkit is used

Raises:
ValueError

If the requested outfile_format is not supported by one of the installed cheminformatics toolkits

Examples

>>> molecule = Molecule.from_iupac('imatinib')
>>> molecule.to_file('imatinib.mol2', outfile_format='mol2')  # doctest: +SKIP
>>> molecule.to_file('imatinib.sdf', outfile_format='sdf')  # doctest: +SKIP
>>> molecule.to_file('imatinib.pdb', outfile_format='pdb')  # doctest: +SKIP
static from_rdkit(rdmol, allow_undefined_stereo=False)[source]

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 oemol contains undefined stereochemistry.

Returns:
molecule : openforcefield.Molecule

An openforcefield molecule

Examples

Create a molecule from an RDKit molecule

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

Create an RDKit molecule

Requires the RDKit to be installed.

Parameters:
aromaticity_model : str, optional, default=DEFAULT_AROMATICITY_MODEL

The aromaticity model to use

Returns:
rdmol : rkit.RDMol

An RDKit molecule

Examples

Convert a molecule to RDKit

>>> from openforcefield.utils import get_data_filename
>>> sdf_filepath = get_data_filename('molecules/ethanol.sdf')
>>> molecule = Molecule(sdf_filepath)
>>> rdmol = molecule.to_rdkit()
static from_openeye(oemol, allow_undefined_stereo=False)[source]

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 : openforcefield.topology.Molecule

An openforcefield molecule

Examples

Create a Molecule from an OpenEye OEMol

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

Create an OpenEye molecule

Requires the OpenEye toolkit to be installed.

Parameters:
aromaticity_model : str, optional, default=DEFAULT_AROMATICITY_MODEL

The aromaticity model to use

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()
get_fractional_bond_orders(method='Wiberg', toolkit_registry=<openforcefield.utils.toolkits.ToolkitRegistry object>)[source]

Get fractional bond orders.

method : str, optional, default=’Wiberg’
The name of the charge method to use. Options are: * ‘Wiberg’ : Wiberg bond order
toolkit_registry : openforcefield.utils.toolkits ToolkitRegistry
The toolkit registry to use for molecule operations

Examples

Get fractional Wiberg bond orders

>>> molecule = Molecule.from_iupac('imatinib')
>>> molecule.generate_conformers()
>>> fractional_bond_orders = molecule.get_fractional_bond_orders(method='Wiberg')
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_json(serialized)

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_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_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_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_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

to_bson()

Return a BSON serialized representation.

Specification: http://bsonspec.org/

Returns:
serialized : bytes

A BSON serialized representation of the objecft

to_json(indent=None)

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_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_toml()

Return a TOML serialized representation.

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

Returns:
serialized : str

A TOML serialized representation of the object

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