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

classmethod fromJson(json_obj)¶

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters: json_obj (dict) – A json-loaded dictionary to create an object from.
Returns: An instance of this class.
Return type: cls

get_version()¶: Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

toJson(_mark_version=True)¶

Create and returns a data structure made up of jsonable items.

Return type: An instance of one the classes from NATIVE_JSON_DATATYPES

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 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¶

classmethod fromJson(json_obj)¶

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters: json_obj (dict) – A json-loaded dictionary to create an object from.
Returns: An instance of this class.
Return type: cls

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

get_version()¶: Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

toJson(_mark_version=True)¶

Create and returns a data structure made up of jsonable items.

Return type: An instance of one the classes from NATIVE_JSON_DATATYPES

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

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¶

classmethod fromJson(json_obj)¶

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters: json_obj (dict) – A json-loaded dictionary to create an object from.
Returns: An instance of this class.
Return type: cls

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

get_version()¶: Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

toJson(_mark_version=True)¶

Create and returns a data structure made up of jsonable items.

Return type: An instance of one the classes from NATIVE_JSON_DATATYPES

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

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