API docs#

class openfe.SmallMoleculeComponent(*args, **kwargs)#

A molecule wrapper suitable for small molecules

Note

This class is a read-only representation of a molecule, if you want to edit the molecule do this in an appropriate toolkit before creating an instance from this class.

This wrapper uses SMILES as the primary hash, so is best suited to smaller molecules. It also supports reading/writing to .sdf format, which again is suited to smaller molecules. A small molecule can have a name associated with it, which is needed to distinguish two molecules with the same SMILES representation, or is simply useful to help identify ligand molecules later. The name can be explicitly set by the name attribute, or implicitly set based on the tags in the input molecular representation (if supported, as with RDKit). If not explicitly set on creation, the molecule will first look for an OpenFE-specific tag ofe-name, and if that doesn’t exist, for a commonly-used naming tag (e.g., the _Name property for RDKit molecules). If no name is found, the empty string is used.

Parameters:

  • rdkit (rdkit.Chem.rdchem.Mol) – rdkit representation of the molecule

  • name (str, optional) – if multiple Molecules with identical SMILES but differing positions are used, a name must be given to differentiate these. This name will be used in the hash.

class openfe.LigandAtomMapping(*args, **kwargs)#

Simple container with the mapping between two Molecules

class openfe.LigandNetwork(edges: Iterable[LigandAtomMapping], nodes: Iterable[SmallMoleculeComponent] | None = None)#

A directed graph connecting many ligands according to their atom mapping

Parameters:
class openfe.setup.atom_mapping.LigandAtomMapper#

Suggests AtomMappings for a pair of SmallMoleculeComponents.

Subclasses will typically implement the _mappings_generator method, which returns an iterable of LigandAtomMapping suggestions.