atom_mapping#
Mappings from atoms in one molecule to those in another.
LigandAtomMapper defines the interface of atom mappers, and is
implemented by LomapAtomMapper and PersesAtomMapper.
LigandAtomMapping is a simple container for an atom maping. It
describes which atoms in one molecule should be transformed into which atoms
in the other, and which atoms should be destroyed or created over the
transformation.
The perses_scorers and lomap_scorers modules provide scoring
functions used for both atom mappings and transformations. A scorer takes
a mapping.LigandAtomMapping and possibly some other parameters and
returns a score between 0 and 1. Higher scores represent better mappings. These
scores are used by LigandNetwork
planners to select the best mapping for a given transformation and also to
compare different transformations while optimising network topologies.
Modules
Functions from Perses for scoring atom mappings. |
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Functions from LOMAP for scoring atom mappings. |
Classes
Simple container for an atom mapping between two small molecule components. |
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Suggest atom mappings between two |
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Suggest atom mappings with the MCS atom mapper from Lomap. |
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Suggest atom mappings with the Perses atom mapper. |