openforcefield.utils.toolkits.OpenEyeToolkitWrapper

class openforcefield.utils.toolkits.OpenEyeToolkitWrapper

OpenEye 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

assign_fractional_bond_orders(molecule[, …])	Update and store list of bond orders this molecule.
assign_partial_charges(molecule[, …])	Compute partial charges with OpenEye quacpac, and assign the new values to the partial_charges attribute.
canonical_order_atoms(molecule)	Canonical order the atoms in the molecule using the OpenEye toolkit.
compute_partial_charges_am1bcc(molecule[, …])	Compute AM1BCC partial charges with OpenEye quacpac.
enumerate_protomers(molecule[, max_states])	Enumerate the formal charges of a molecule to generate different protomoers.
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[, …])	Return 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 OEMol (or OEMol-derived object), this function will load it into an openforcefield.topology.molecule
from_openeye(oemol[, allow_undefined_stereo])	Create a Molecule from an OpenEye molecule.
from_smiles(smiles[, …])	Create a Molecule from a SMILES string using the OpenEye toolkit.
generate_conformers(molecule[, …])	Generate molecule conformers using OpenEye Omega.
get_tagged_smarts_connectivity(smarts)	Returns a tuple of tuples indicating connectivity between tagged atoms in a SMARTS string.
is_available([oetools])	Check if the given OpenEye toolkit components are available.
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_openeye(molecule[, aromaticity_model])	Create an OpenEye molecule using the specified aromaticity model
to_smiles(molecule[, isomeric, …])	Uses the OpenEye toolkit to convert a Molecule into a SMILES string.

__init__()

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

Methods

__init__()	Initialize self.
assign_fractional_bond_orders(molecule[, …])	Update and store list of bond orders this molecule.
assign_partial_charges(molecule[, …])	Compute partial charges with OpenEye quacpac, and assign the new values to the partial_charges attribute.
canonical_order_atoms(molecule)	Canonical order the atoms in the molecule using the OpenEye toolkit.
compute_partial_charges_am1bcc(molecule[, …])	Compute AM1BCC partial charges with OpenEye quacpac.
enumerate_protomers(molecule[, max_states])	Enumerate the formal charges of a molecule to generate different protomoers.
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[, …])	Return 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 OEMol (or OEMol-derived object), this function will load it into an openforcefield.topology.molecule
from_openeye(oemol[, allow_undefined_stereo])	Create a Molecule from an OpenEye molecule.
from_smiles(smiles[, …])	Create a Molecule from a SMILES string using the OpenEye toolkit.
generate_conformers(molecule[, …])	Generate molecule conformers using OpenEye Omega.
get_tagged_smarts_connectivity(smarts)	Returns a tuple of tuples indicating connectivity between tagged atoms in a SMARTS string.
is_available([oetools])	Check if the given OpenEye toolkit components are available.
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_openeye(molecule[, aromaticity_model])	Create an OpenEye molecule using the specified aromaticity model
to_smiles(molecule[, isomeric, …])	Uses the OpenEye 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.