openff.toolkit.utils.toolkits.RDKitToolkitWrapper
- class openff.toolkit.utils.toolkits.RDKitToolkitWrapper[source]
RDKit toolkit wrapper
Warning
This API is experimental and subject to change.
- __init__()[source]
Methods
__init__
()apply_elf_conformer_selection
(molecule[, ...])Applies the ELF method to select a set of diverse conformers which have minimal electrostatically strongly interacting functional groups from a molecules conformers.
assign_partial_charges
(molecule[, ...])Compute partial charges with RDKit, and assign the new values to the partial_charges attribute.
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_rings
(molecule)Find the rings in a given 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 openff.toolkit.topology.Molecule from a file using this toolkit.
from_file_obj
(file_obj, file_format[, ...])Return an openff.toolkit.topology.Molecule from a file-like object using this toolkit.
from_inchi
(inchi[, allow_undefined_stereo, _cls])Construct a Molecule from a InChI representation
from_object
(obj[, allow_undefined_stereo, _cls])If given an rdchem.Mol (or rdchem.Mol-derived object), this function will load it into an openff.toolkit.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.
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
List of file formats that this toolkit can read.
List of file formats that this toolkit can write.
Instructions on how to install the wrapped toolkit.
Return the name of the toolkit wrapped by this class as a str
Return the version of the wrapped toolkit as a str
- classmethod is_available()[source]
Check whether the RDKit toolkit can be imported
- Returns
- is_installedbool
True if RDKit is installed, False otherwise.
- from_object(obj, allow_undefined_stereo=False, _cls=None)[source]
If given an rdchem.Mol (or rdchem.Mol-derived object), this function will load it into an openff.toolkit.topology.molecule. Otherwise, it will return False.
- Parameters
- objA rdchem.Mol-derived object
An object to be type-checked and converted into a Molecule, if possible.
- allow_undefined_stereobool, default=False
Whether to accept molecules with undefined stereocenters. If False, an exception will be raised if a molecule with undefined stereochemistry is passed into this function.
- _clsclass
Molecule constructor
- Returns
- Molecule or False
An openff.toolkit.topology.molecule Molecule.
- Raises
- NotImplementedError
If the object could not be converted into a Molecule.
- from_pdb_and_smiles(file_path, smiles, allow_undefined_stereo=False, _cls=None)[source]
Create a Molecule from a pdb file and a SMILES string using RDKit.
Requires RDKit to be installed.
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.
- _clsclass
Molecule constructor
- Returns
- moleculeopenff.toolkit.Molecule (or _cls() type)
An OFFMol instance with ordering the same as used in the PDB file.
- Raises
- InvalidConformerErrorif the SMILES and PDB molecules are not isomorphic.
- from_file(file_path, file_format, allow_undefined_stereo=False, _cls=None)[source]
Create an openff.toolkit.topology.Molecule from a file using this toolkit.
- Parameters
- file_pathstr
The file to read the molecule from
- file_formatstr
Format specifier, usually file suffix (eg. ‘MOL2’, ‘SMI’) Note that not all toolkits support all formats. Check ToolkitWrapper.toolkit_file_read_formats for details.
- allow_undefined_stereobool, default=False
If false, raises an exception if oemol contains undefined stereochemistry.
- _clsclass
Molecule constructor
- Returns
- ——-
- moleculesiterable of Molecules
a list of Molecule objects is returned.
- from_file_obj(file_obj, file_format, allow_undefined_stereo=False, _cls=None)[source]
Return an openff.toolkit.topology.Molecule from a file-like object using this toolkit.
A file-like object is an object with a “.read()” method.
Warning
This API is experimental and subject to change.
- Parameters
- file_objfile-like object
The file-like object to read the molecule from
- file_formatstr
Format specifier, usually file suffix (eg. ‘MOL2’, ‘SMI’) Note that not all toolkits support all formats. Check ToolkitWrapper.toolkit_file_read_formats for details.
- allow_undefined_stereobool, default=False
If false, raises an exception if oemol contains undefined stereochemistry.
- _clsclass
Molecule constructor
- Returns
- ——-
- moleculesMolecule or list of Molecules
a list of Molecule objects is returned.
- to_file_obj(molecule, file_obj, file_format)[source]
Writes an OpenFF Molecule to a file-like object
- Parameters
- moleculean OpenFF Molecule
The molecule to write
- file_obj
The file-like object to write to
- file_format
The format for writing the molecule data
- to_file(molecule, file_path, file_format)[source]
Writes an OpenFF Molecule to a file-like object
- Parameters
- moleculean OpenFF Molecule
The molecule to write
- file_path
The file path to write to
- file_format
The format for writing the molecule data
- Returns
- ——
- enumerate_stereoisomers(molecule, undefined_only=False, max_isomers=20, rationalise=True)[source]
Enumerate the stereocenters and bonds of the current molecule.
- Parameters
- molecule: openff.toolkit.topology.Molecule
The molecule whose state we should enumerate
- 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
- Returns
- molecules: List[openff.toolkit.topology.Molecule]
A list of openff.toolkit.topology.Molecule instances
- enumerate_tautomers(molecule, max_states=20)[source]
Enumerate the possible tautomers of the current molecule.
- Parameters
- molecule: openff.toolkit.topology.Molecule
The molecule whose state we should enumerate
- max_states: int optional, default=20
The maximum amount of molecules that should be returned
- Returns
- molecules: List[openff.toolkit.topology.Molecule]
A list of openff.toolkit.topology.Molecule instances not including the input molecule.
- canonical_order_atoms(molecule)[source]
Canonical order the atoms in the molecule using the RDKit.
- Parameters
- molecule: openff.toolkit.topology.Molecule
The input molecule
- Returns
- moleculeopenff.toolkit.topology.Molecule
The input molecule, with canonically-indexed atoms and bonds.
- to_smiles(molecule, isomeric=True, explicit_hydrogens=True, mapped=False)[source]
Uses the RDKit toolkit to convert a Molecule into a SMILES string. A partially mapped smiles can also be generated for atoms of interest by supplying an atom_map to the properties dictionary.
- Parameters
- moleculeAn openff.toolkit.topology.Molecule
The molecule to convert into a SMILES.
- 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.
- Returns
- smilesstr
The SMILES of the input molecule.
- from_smiles(smiles, hydrogens_are_explicit=False, allow_undefined_stereo=False, _cls=None)[source]
Create a Molecule from a SMILES string using the RDKit toolkit.
Warning
This API is experimental and subject to change.
- Parameters
- smilesstr
The SMILES string to turn into a molecule
- hydrogens_are_explicitbool, default=False
If False, RDKit will perform hydrogen addition using Chem.AddHs
- 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.
- _clsclass
Molecule constructor
- Returns
- moleculeopenff.toolkit.topology.Molecule
An OpenFF style molecule.
- from_inchi(inchi, allow_undefined_stereo=False, _cls=None)[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.
- _clsclass
Molecule constructor
- Returns
- moleculeopenff.toolkit.topology.Molecule
- generate_conformers(molecule, n_conformers=1, rms_cutoff=None, clear_existing=True, _cls=None)[source]
Generate molecule conformers using RDKit.
Warning
This API is experimental and subject to change.
- Parameters
- moleculea
Molecule
The molecule to generate conformers for.
- n_conformersint, default=1
Maximum number of conformers to generate.
- rms_cutoffopenmm.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. If None, the cutoff is set to 1 Angstrom
- clear_existingbool, default=True
Whether to overwrite existing conformers for the molecule.
- _clsclass
Molecule constructor
- moleculea
- assign_partial_charges(molecule, partial_charge_method=None, use_conformers=None, strict_n_conformers=False, normalize_partial_charges=True, _cls=None)[source]
Compute partial charges with RDKit, and assign the new values to the partial_charges attribute.
Warning
This API is experimental and subject to change.
- Parameters
- moleculeopenff.toolkit.topology.Molecule
Molecule for which partial charges are to be computed
- partial_charge_methodstr, optional, default=None
The charge model to use. One of [‘mmff94’]. If None, ‘mmff94’ will be used.
- ‘mmff94’: Applies partial charges using the Merck Molecular Force Field
(MMFF). This method does not make use of conformers, and hence
use_conformers
andstrict_n_conformers
will not impact the partial charges produced.
- 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.
- 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.
- 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 generation method has low precision.
- _clsclass
Molecule constructor
- Raises
- ChargeMethodUnavailableError if the requested charge method can not be handled by this toolkit
- ChargeCalculationError if the charge method is supported by this toolkit, but fails
- apply_elf_conformer_selection(molecule: Molecule, percentage: float = 2.0, limit: int = 10, rms_tolerance: openmm.unit.quantity.Quantity = 0.05 * unit.angstrom)[source]
Applies the ELF method to select a set of diverse conformers which have minimal electrostatically strongly interacting functional groups from a molecules conformers.
The diverse conformer selection is performed by the
_elf_select_diverse_conformers
function, which attempts to greedily select conformers which are most distinct according to their RMS.- Parameters
- molecule
The molecule which contains the set of conformers to select from.
- percentage
The percentage of conformers with the lowest electrostatic interaction energies to greedily select from.
- limit
The maximum number of conformers to select.
- rms_tolerance
Conformers whose RMS is within this amount will be treated as identical and the duplicate discarded.
Warning
Although this function is inspired by the OpenEye ELF10 method, this implementation may yield slightly different conformers due to potential differences in this and the OE closed source implementation.
See also
RDKitToolkitWrapper._elf_select_diverse_conformers
Notes
The input molecule should have a large set of conformers already generated to select the ELF10 conformers from.
The selected conformers will be retained in the molecule.conformers list while unselected conformers will be discarded.
Only heavy atoms are included when using the RMS to select diverse conformers.
- from_rdkit(rdmol, allow_undefined_stereo=False, hydrogens_are_explicit=False, _cls=None)[source]
Create a Molecule from an RDKit molecule.
Requires the RDKit to be installed.
Warning
This API is experimental and subject to change.
- Parameters
- rdmolrkit.RDMol
An RDKit molecule
- allow_undefined_stereobool, default=False
If false, raises an exception if rdmol contains undefined stereochemistry.
- hydrogens_are_explicitbool, default=False
If False, RDKit will perform hydrogen addition using Chem.AddHs
- _clsclass
Molecule constructor
- 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'))
>>> toolkit_wrapper = RDKitToolkitWrapper() >>> molecule = toolkit_wrapper.from_rdkit(rdmol)
- classmethod to_rdkit(molecule, aromaticity_model='OEAroModel_MDL')[source]
Create an RDKit molecule
Requires the RDKit to be installed.
Warning
This API is experimental and subject to change.
- Parameters
- aromaticity_modelstr, optional, default=DEFAULT_AROMATICITY_MODEL
The aromaticity model to use
- Returns
- rdmolrkit.RDMol
An RDKit molecule
Examples
Convert a molecule to RDKit
>>> from openff.toolkit.topology import Molecule >>> ethanol = Molecule.from_smiles('CCO') >>> rdmol = ethanol.to_rdkit()
- to_inchi(molecule, fixed_hydrogens=False)[source]
Create an InChI string for the molecule using the RDKit Toolkit. 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
- moleculeAn openff.toolkit.topology.Molecule
The molecule to convert into a SMILES.
- 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.
- Returns
- inchi: str
The InChI string of the molecule.
- to_inchikey(molecule, fixed_hydrogens=False)[source]
Create an InChIKey for the molecule using the RDKit Toolkit. 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
- moleculeAn openff.toolkit.topology.Molecule
The molecule to convert into a SMILES.
- 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.
- Returns
- inchi_key: str
The InChIKey representation of the molecule.
- get_tagged_smarts_connectivity(smarts)[source]
Returns a tuple of tuples indicating connectivity between tagged atoms in a SMARTS string. Does not return bond order.
- Parameters
- smartsstr
The tagged SMARTS to analyze
- Returns
- unique_tagstuple of int
A sorted tuple of all unique tagged atom map indices.
- tagged_atom_connectivitytuple of tuples of int, shape n_tagged_bonds x 2
- A tuple of tuples, where each inner tuple is a pair of tagged atoms (tag_idx_1, tag_idx_2)
which are bonded. The inner tuples are ordered smallest-to-largest, and the tuple of tuples is ordered lexically. So the return value for an improper torsion would be ((1, 2), (2, 3), (2, 4)).
- Raises
- SMIRKSParsingError
If RDKit was unable to parse the provided smirks/tagged smarts
- find_smarts_matches(molecule, smarts, aromaticity_model='OEAroModel_MDL', unique=False)[source]
Find all SMARTS matches for the specified molecule, using the specified aromaticity model.
Warning
This API is experimental and subject to change.
- Parameters
- moleculeopenff.toolkit.topology.Molecule
The molecule for which all specified SMARTS matches are to be located
- smartsstr
SMARTS string with optional SMIRKS-style atom tagging
- aromaticity_modelstr, optional, default=’OEAroModel_MDL’
Molecule is prepared with this aromaticity model prior to querying.
- .. note :: Currently, the only supported ``aromaticity_model`` is ``OEAroModel_MDL``
- find_rings(molecule)[source]
Find the rings in a given molecule.
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).
- Parameters
- moleculeopenff.toolkit.topology.Molecule
The molecule for which rings are to be found
- Returns
- ringstuple of tuples of atom indices
Nested tuples, each containing the indices of atoms in each ring