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.BaseResidueFilter¶
Bases:
schrodinger.models.json.JsonableClassMixin
- toJsonImplementation()¶
Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.
- Returns
A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders
- classmethod fromJsonImplementation(json_dict)¶
Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.
- Parameters
json_dict (dict) – A dictionary loaded from a JSON string or file.
- Returns
An instance of the derived class.
- Return type
cls
- class schrodinger.application.bioluminate.pose_filtering.residue_filter.InterfaceResidueFilter(query_asl_1: str, query_asl_2: str, distance_cutoff: float)¶
Bases:
schrodinger.application.bioluminate.pose_filtering.residue_filter.BaseResidueFilter
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 ofdistance_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:
schrodinger.application.bioluminate.pose_filtering.residue_filter.BaseResidueFilter
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
- min_passing_residues: int¶
- __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) Tuple[List[schrodinger.structure._structure.Structure], List[str]] ¶
Return tuple that contains the poses that pass all filtering criteria defined in
filter_criteria
and the list of passing residue ids.- Parameters
poses – The poses to filter
filter_criteria – The criteria to use for filtering
- Returns
tuple that contains list of passing poses and corresponding residue ids.