mmtfPyspark.interactions.groupInteractionExtractor module¶

groupInteractionExtractor.py

Creates a dataset of noncovalent interactions of specified groups (residues) in macromolecular structures. The criteria for interactions are specified using an InteractionFilter. The interactions can be returned as interacting atom pairs or as one row per interacting atom.

Typical use cases include: - Find interactions between a metal ion and protein/DNA/RNA - Find interactions between a small molecule and protein/DNA/RNA

class GroupInteractionExtractor[source]¶

Bases: object

Methods

`get_interactions`(structures, interactionFilter)	Returns a dataset of interactions that satisfy the criteria of the InteractionFilter.
`get_pair_interactions`(structures, …)	Returns a Dataset of pairwise interactions that satisfy the criteria of the InteractionFilter.

get_interactions(structures, interactionFilter)[source]¶

Returns a dataset of interactions that satisfy the criteria of the InteractionFilter. each atom and its interacting neightbor atoms are represented as a row in a Dataset. In addition, geometric freatures of the interactions, such as distances, angles, and orientation order parameters are returned in each row.

Parameters:

Parameters:	structures : PythonRDD a set of PDB structures interactionFilter : InteractionFilter filter criteria for determing noncovalent interactions
Returns:	dataset Dataset of pairwise interactions

structures : PythonRDD

a set of PDB structures

interactionFilter : InteractionFilter

filter criteria for determing noncovalent interactions

Returns:

dataset

Dataset of pairwise interactions

get_pair_interactions(structures, interactionFilter)[source]¶

Returns a Dataset of pairwise interactions that satisfy the criteria of the InteractionFilter. Each atom, its interacting neightbor atom, and the interacting distance is represented as a row.