openforcefield.utils.toolkits.RDKitToolkitWrapper

class openforcefield.utils.toolkits.RDKitToolkitWrapper[source]

RDKit toolkit wrapper

Warning

This API is experimental and subject to change.

Attributes
toolkit_file_read_formats

List of file formats that this toolkit can read.

toolkit_file_write_formats

List of file formats that this toolkit can write.

toolkit_installation_instructions

classmethod(function) -> method

toolkit_name

The name of the toolkit wrapped by this class.

Methods

canonical_order_atoms(molecule)

Canonical order the atoms in the molecule using the RDKit.

enumerate_stereoisomers(molecule[, …])

Enumerate the stereocenters and bonds of the current molecule.

enumerate_tautomers(molecule[, max_states])

Enumerate the possible tautomers of the current molecule.

find_smarts_matches(molecule, smarts[, …])

Find all SMARTS matches for the specified molecule, using the specified aromaticity model.

from_file(file_path, file_format[, …])

Create an openforcefield.topology.Molecule from a file using this toolkit.

from_file_obj(file_obj, file_format[, …])

Return an openforcefield.topology.Molecule from a file-like object (an object with a “.read()” method using this toolkit.

from_inchi(inchi[, allow_undefined_stereo])

Construct a Molecule from a InChI representation

from_object(object[, allow_undefined_stereo])

If given an rdchem.Mol (or rdchem.Mol-derived object), this function will load it into an openforcefield.topology.molecule.

from_pdb_and_smiles(file_path, smiles[, …])

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

from_rdkit(rdmol[, allow_undefined_stereo])

Create a Molecule from an RDKit molecule.

from_smiles(smiles[, …])

Create a Molecule from a SMILES string using the RDKit toolkit.

generate_conformers(molecule[, …])

Generate molecule conformers using RDKit.

get_tagged_smarts_connectivity(smarts)

Returns a tuple of tuples indicating connectivity between tagged atoms in a SMARTS string.

is_available()

Check whether the RDKit toolkit can be imported

requires_toolkit()

to_file(molecule, file_path, file_format)

Writes an OpenFF Molecule to a file-like object

to_file_obj(molecule, file_obj, file_format)

Writes an OpenFF Molecule to a file-like object

to_inchi(molecule[, fixed_hydrogens])

Create an InChI string for the molecule using the RDKit Toolkit.

to_inchikey(molecule[, fixed_hydrogens])

Create an InChIKey for the molecule using the RDKit Toolkit.

to_rdkit(molecule[, aromaticity_model])

Create an RDKit molecule

to_smiles(molecule[, isomeric, …])

Uses the RDKit toolkit to convert a Molecule into a SMILES string.

__init__()[source]

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__()

Initialize self.

canonical_order_atoms(molecule)

Canonical order the atoms in the molecule using the RDKit.

enumerate_stereoisomers(molecule[, …])

Enumerate the stereocenters and bonds of the current molecule.

enumerate_tautomers(molecule[, max_states])

Enumerate the possible tautomers of the current molecule.

find_smarts_matches(molecule, smarts[, …])

Find all SMARTS matches for the specified molecule, using the specified aromaticity model.

from_file(file_path, file_format[, …])

Create an openforcefield.topology.Molecule from a file using this toolkit.

from_file_obj(file_obj, file_format[, …])

Return an openforcefield.topology.Molecule from a file-like object (an object with a “.read()” method using this toolkit.

from_inchi(inchi[, allow_undefined_stereo])

Construct a Molecule from a InChI representation

from_object(object[, allow_undefined_stereo])

If given an rdchem.Mol (or rdchem.Mol-derived object), this function will load it into an openforcefield.topology.molecule.

from_pdb_and_smiles(file_path, smiles[, …])

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

from_rdkit(rdmol[, allow_undefined_stereo])

Create a Molecule from an RDKit molecule.

from_smiles(smiles[, …])

Create a Molecule from a SMILES string using the RDKit toolkit.

generate_conformers(molecule[, …])

Generate molecule conformers using RDKit.

get_tagged_smarts_connectivity(smarts)

Returns a tuple of tuples indicating connectivity between tagged atoms in a SMARTS string.

is_available()

Check whether the RDKit toolkit can be imported

requires_toolkit()

to_file(molecule, file_path, file_format)

Writes an OpenFF Molecule to a file-like object

to_file_obj(molecule, file_obj, file_format)

Writes an OpenFF Molecule to a file-like object

to_inchi(molecule[, fixed_hydrogens])

Create an InChI string for the molecule using the RDKit Toolkit.

to_inchikey(molecule[, fixed_hydrogens])

Create an InChIKey for the molecule using the RDKit Toolkit.

to_rdkit(molecule[, aromaticity_model])

Create an RDKit molecule

to_smiles(molecule[, isomeric, …])

Uses the RDKit toolkit to convert a Molecule into a SMILES string.

Attributes

toolkit_file_read_formats

List of file formats that this toolkit can read.

toolkit_file_write_formats

List of file formats that this toolkit can write.

toolkit_installation_instructions

classmethod(function) -> method

toolkit_name

The name of the toolkit wrapped by this class.