LigandAtomMapping

class openfe.setup.atom_mapping.LigandAtomMapping(componentA: SmallMoleculeComponent, componentB: SmallMoleculeComponent, componentA_to_componentB: dict[int, int], annotations: dict[str, Any] | None = None)

Bases: AtomMapping

Simple container for an atom mapping between two small molecule components.

Parameters:

• componentA (SmallMoleculeComponent) – the ligand molecules on either end of the mapping

• componentB (SmallMoleculeComponent) – the ligand molecules on either end of the mapping

• componentA_to_componentB (dict[int, int]) – correspondence of indices of atoms between the two ligands; the keys are indices in componentA and the values are indices in componentB

• annotations (dict[str, Any]) – Mapping of annotation identifier to annotation data. Annotations may contain arbitrary JSON-serializable data. Annotation identifiers starting with ofe- may have special meaning in other parts of OpenFE. score is a reserved annotation identifier.

Methods

draw_to_file	Save atom map visualization to disk
get_distances	Return the distances between pairs of atoms in the mapping
with_annotations	Create an new mapping based on this one with extra annotations.

Attributes

annotations
componentA_to_componentB	Maps the index of an item from Component A onto Component B
componentA_unique	Indices of atoms in component A that aren't mappable to B
componentB_to_componentA	Similar to A to B, but reversed.
componentB_unique	Indices of atoms in component B that aren't mappable to A

property annotations

property componentA: Component

A copy of the first Component in the mapping

property componentA_to_componentB: dict[int, int]

Maps the index of an item from Component A onto Component B

Keys are indices from Component A, values are indices from Component B.

Not all indices will be resolvable, these items have no corresponding entity in the other component (e.g. the atom disappears), therefore resulting in a KeyError on query

property componentA_unique

Indices of atoms in component A that aren’t mappable to B

property componentB: Component

A copy of the second Component in the mapping

property componentB_to_componentA: dict[int, int]

Similar to A to B, but reversed.

property componentB_unique

Indices of atoms in component B that aren’t mappable to A

draw_to_file(fname: str, d2d=None)

Save atom map visualization to disk

Parameters:

• d2d (rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D) – If desired specify an instance of a MolDraw2D object. Default None will write a .png file using the MolDraw2DCairo backend.

• fname (str) – Name of file to save atom map

get_distances() → ndarray[Any, dtype[float64]]

Return the distances between pairs of atoms in the mapping

with_annotations(annotations: dict[str, Any])

Create an new mapping based on this one with extra annotations.

Parameters:

annotations (dict[str, Any]) – Annotation update for this mapping. New annotation keys will be added to the annotations dict; existing keys will be replaced by the data provided here.