Atom Mappings#

Tools for mapping atoms in one molecule to those in another. Used to generate efficient ligand networks.

Abstract Base Class

Suggest atom mappings between two SmallMoleculeComponent instances.

Implementations

`KartografAtomMapper`	Geometry Based Atom Mapper This mapper is a homebrew, that utilises rdkit in order to generate an atom-mapping based on the coordinates of two molecules.
`LomapAtomMapper`	Wraps the MCS atom mapper from Lomap.
`PersesAtomMapper`	Suggest atom mappings with the Perses atom mapper.

Data Types

Container for an atom mapping between two small molecule components.

Atom Map Scorers#

Scoring functions for a mapping between ligands. These are used as objective functions for Network Planners.

Scorers implemented by the LOMAP package.

`default_lomap_score`	The default score function from Lomap2
`ecr_score`	Equal charge rule (ECR) score.
`mcsr_score`	Maximum common substructure rule (MCSR) score.
`mncar_score`	Minimum number of common atoms rule (MNCAR) score.
`atomic_number_score`	A score on the elemental changes happening in the mapping
`hybridization_score`	Hybridization score — penalizes atom hybridization mismatches in the mapping.
`sulfonamides_score`	Sulfonamide score — penalizes mappings that mutate a sulfonamide group in or out.
`heterocycles_score`	Heterocycle score — penalizes mappings that form a heterocycle from a hydrogen.
`transmuting_methyl_into_ring_score`	Penalises having a non-mapped ring atoms become a non-ring
`transmuting_ring_sizes_score`	Ring size score — penalizes mappings that alter a ring size.

Scorers implemented by the Perses package.

Score an atom mapping with the default Perses score function.