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.
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.