Ligand Network Tools#

Ligand Network#

A network of mutations between ligands.

LigandNetwork

A directed graph connecting many ligands according to their atom mapping

Network Planners#

Functions that build a LigandNetwork from a collection of SmallMoleculeComponents by optimizing over a scoring function.

generate_radial_network

Plan a radial network with all ligands connected to a central node.

generate_maximal_network

Plan a network with all possible proposed mappings.

generate_minimal_spanning_network

Plan a network with as few edges as possible with maximum total score

generate_minimal_redundant_network

Plan a network with a specified amount of redundancy for each node

generate_lomap_network

Generate a LigandNetwork according to Lomap's network creation rules

Network Loaders#

Functions to load a LigandNetwork from equivalent classes in other packages, or to specify one by hand.

generate_network_from_names

Generate a LigandNetwork by specifying edges as tuples of names.

generate_network_from_indices

Generate a LigandNetwork by specifying edges as tuples of indices.

load_orion_network

Load a LigandNetwork from an Orion NES network file.

load_fepplus_network

Load a LigandNetwork from an FEP+ edges network file.

Atom Mappings#

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

Abstract Base Class

LigandAtomMapper

Suggest atom mappings between two SmallMoleculeComponent instances.

Implementations

LomapAtomMapper

Wraps the MCS atom mapper from Lomap.

PersesAtomMapper

Suggest atom mappings with the Perses atom mapper.

Data Types

LigandAtomMapping

Simple 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.

Lomap Scorers#

Scorers implemented by the LOMAP package.

default_lomap_score

The default score function from Lomap2

ecr_score

mcsr_score

Maximum command substructure rule

mncar_score

Minimum number of common atoms rule

atomic_number_score

A score on the elemental changes happening in the mapping

hybridization_score

Score calculated as:

sulfonamides_score

Checks if a sulfonamide appears and disallow this.

heterocycles_score

Checks if a heterocycle is formed from a -H

transmuting_methyl_into_ring_score

Penalises having a non-mapped ring atoms become a non-ring

transmuting_ring_sizes_score

Checks if mapping alters a ring size

Perses Scorers#

Scorers implemented by the Perses package.

default_perses_scorer

Score an atom mapping with the default Perses score function.