`kinoml.core.ligands`¶

MolecularComponent objects that represent ligand-like entities.

Module Contents¶

kinoml.core.ligands.logger¶

class kinoml.core.ligands.Ligand(molecule: Union[openff.toolkit.topology.Molecule, None] = None, smiles: str = '', name: str = '', metadata: Union[dict, None] = None, **kwargs)¶

Bases: kinoml.core.components.BaseLigand

Create a new Ligand object. An openff representation is accessible via the molecule attribute.

Examples

Create a ligand from file:

>>> ligand = Ligand.from_file("data/molecules/chloroform.sdf", name="chloroform")

Create a ligand from an openff molecule:

>>> from openff.toolkit.topology import Molecule
>>> molecule = Molecule.from_file("data/molecules/chloroform.sdf")
>>> ligand = Ligand(molecule=molecule, name="chloroform")

Create a ligand from SMILES:

>>> ligand = Ligand.from_smiles("C(Cl)(Cl)Cl", name="chloroform")

Create a ligand from SMILES with lazy instantiation:

>>> ligand = Ligand(smiles="C(Cl)(Cl)Cl", name="chloroform")

property molecule¶: Decorate molecule to modify setter and getter.

molecule()¶

Get the _molecule attribute. If the _smiles attribute is given and _molecule is None, a new openff molecule will be created from smiles, e.g. in case of lazy instantiation.

Returns: The openff molecular representation of the ligand.
Return type: openff.toolkit.topology.Molecule or None

classmethod from_smiles(smiles: str, name: str = '', allow_undefined_stereo: bool = True, **kwargs)¶

Create a Ligand from a SMILES representation.

Parameters

smiles (str) – smiles: str The SMILES representation of the ligand.
name (str, default="") – The name of the ligand.
allow_undefined_stereo (bool, default=True) – If undefined stereo centers should be allowed.
kwargs – Any keyword arguments allowed for the from_smiles method of the openff molecule class.

classmethod from_file(file_path: Union[pathlib.Path, str], name: str = '', allow_undefined_stereo: bool = True, **kwargs)¶

Create a Ligand from file.

Parameters

file_path (pathlib.Path or str) – The path to the molecular file. For supported formats see the openff molecule documentation.
name (str, default="") – The name of the ligand.
allow_undefined_stereo (bool, default=True) – If undefined stereo centers should be allowed.
kwargs – Any keyword arguments allowed for the from_file method of the openff molecule class.

kinoml.core.ligands¶

Module Contents¶

`kinoml.core.ligands`¶