schrodinger.application.bioluminate.pose_filtering.residue_filter module

class schrodinger.application.bioluminate.pose_filtering.residue_filter.ResidueFilter(*args, **kwargs)

Bases: Protocol

Protocol for classes that can filter a list of residue IDs pertaining to a structure.

filter_res_ids(st: schrodinger.structure._structure.Structure, res_ids: List[str]) → List[str]
__init__(*args, **kwargs)
class schrodinger.application.bioluminate.pose_filtering.residue_filter.InterfaceResidueFilter(query_asl_1: str, query_asl_2: str, distance_cutoff: float)

Bases: object

Class to filter residues by distance.

Variables

  • query_asl_1 – ASL for the first set of the interface

  • query_asl_2 – ASL for the second set of the interface

  • distance_cutoff – The maximum acceptable distance for two residues in an interaction

query_asl_1: str
query_asl_2: str
distance_cutoff: float
filter_res_ids(st: schrodinger.structure._structure.Structure, res_ids: List[str]) → List[str]

Return the residue IDs from res_ids that are found in protein interactions between ASL sets 1 and 2 with a maximum distance of distance_cutoff.

Note: Assumes res_ids is not empty.

Parameters

  • st – The structure to evaluate

  • res_ids – The residue IDs of the residues to evaluate with in the structure

__init__(query_asl_1: str, query_asl_2: str, distance_cutoff: float) → None
class schrodinger.application.bioluminate.pose_filtering.residue_filter.SasaResidueFilter(operator_name: str, percent_sasa_cutoff: float)

Bases: object

Class to filter residues by %SASA.

Variables

  • operator_name – The numeric operator to use. e.g. “>” or “<”

  • percent_sasa_cutoff – The %SASA cutoff value

operator_name: str
percent_sasa_cutoff: float
filter_res_ids(st: schrodinger.structure._structure.Structure, res_ids: List[str]) → List[str]

Return the residues from res_ids that are found to have an acceptable percent SASA. False otherwise.

Note: Assumes res_ids is not empty.

__init__(operator_name: str, percent_sasa_cutoff: float) → None
class schrodinger.application.bioluminate.pose_filtering.residue_filter.FilterCriteria(res_ids: List[str], min_passing_residues: int, filters: List[schrodinger.application.bioluminate.pose_filtering.residue_filter.ResidueFilter])

Bases: object

Variables

  • res_ids – Residue IDs to use for filtering

  • min_passing_residues – The minimum number of residues that must pass all filters

  • filters – All filters that should be run

res_ids: List[str]
min_passing_residues: int
filters: List[schrodinger.application.bioluminate.pose_filtering.residue_filter.ResidueFilter]
__init__(res_ids: List[str], min_passing_residues: int, filters: List[schrodinger.application.bioluminate.pose_filtering.residue_filter.ResidueFilter]) → None
schrodinger.application.bioluminate.pose_filtering.residue_filter.run_filters(poses: List[schrodinger.structure._structure.Structure], filter_criteria: schrodinger.application.bioluminate.pose_filtering.residue_filter.FilterCriteria) → List[schrodinger.structure._structure.Structure]

Return the poses that pass all filtering criteria defined in filter_criteria.

Parameters

poses – The poses to filter

Filter_criteria

The criteria to use for filtering