mmtfPyspark.interactions.interactionFingerprinter module¶

interactionFingerprinter.py

This class creates dataset of ligand - macromolecule and macromolecule - macromolecule interaction information. Criteria to select interactions are specified by the InteractionFilter.

class InteractionFingerprinter[source]¶

Bases: object

Methods

get_ligand_polymer_interactions(…)	Returns a dataset of ligand - macromolecule interacting residues.
get_polymer_interactions(interactionFilter)	Returns a dataset of ligand - macromolecule interacting information.

get_ligand_polymer_interactions(interactionFilter)[source]¶

Returns a dataset of ligand - macromolecule interacting residues.

The dataset contains the following columns: - structureChainId - pdbId.chainName of chain that interacts with ligand - queryLigandId - id of ligand from PDB chemical component dictionary - queryLigandNumber - group number of ligand including insetion code - queryLigandChainId - chain name of ligand - targetChainId - name of chain for which the interaction data are listed - groupNumbers - array of residue number of interacting groups including insertion code (e.g. 101A) - sequenceIndices - array of zero-based index of interaction groups (residues) mapped onto target sequence - sequence - interacting polymer sequence - interactingChains - total number of chains that interact with ligand

Parameters:	structures : PythonRDD a set of PDB structures interactionFilter : InteractionFilter interaction criteria
Returns:	dataset dataset with interacting residue information

get_polymer_interactions(interactionFilter)[source]¶

Returns a dataset of ligand - macromolecule interacting information.

The dataset contains the following columns:

structureChainId - pdbId.chainName for which the interaction data are listed queryChainId - name of chain that interacts with target chain targetChainId - name of chain for which the interaction data are listed groupNumbers - array of residue number of interacting groups including insertion code (e.g. 101A) sequenceIndices - array of zero-based index of interaction groups (residues) mapped onto target sequence sequence - target polymer sequence

Parameters:	structures : PythonRDD a set of PDB structures interactionFilter : InteractionFilter interaction criteria
Returns:	dataset dataset with interacting residue information