schrodinger.application.phase.packages.shape_generator module¶

Supplies consistent means of generating shape structures via ligand and pharmacophore command line options.

class schrodinger.application.phase.packages.shape_generator.AtomTypes(value)¶

Bases: enum.Enum

An enumeration.

mmod = 1¶

element = 2¶

qsar = 3¶

class schrodinger.application.phase.packages.shape_generator.ShapeGenerator(args)[source]¶

Bases: object

__init__(args)[source]¶

Initializes shape generation options.

Parameters: args (argparser.Namespace) – argument namespace with command line options

getFeatureDefinitions(args)[source]¶

Collects the feature definitions to use for generating pharmacophore hypothesis shapes from ligands.

Parameters: args (argparser.Namespace) – argument namespace with command line options
Returns: list of pharmacophore feature definitions
Return type: list of phase.PhpFeatureDefinition

getHypothesisFeatureRadii(radii_file)[source]¶

Collects user specified pharmacophore feature radii to use for generating pharmacophore hypothesis shapes from ligands.

Parameters: radii_file (str) – user supplied .rad filename
Returns: Data for feature specific radii
Return type: phase.PhpFeatureData

getHypothesisSitesShape(sites)[source]¶

Returns a shape structure created from the given Phase hypothesis.

Parameters: sites (list(phase.PhpSite)) – pharmacophore sites source
Returns: shape structure derived from the given hypothesis
Return type: shape.ShapeStructure

getShape(st, atom_weight_property=None)[source]¶

Creates a shape structure from the given ligand structure.

Parameters: st (structure.Structure) – ligand source structure
Returns: shape structure derived from the given structure
Return type: shape.ShapeStructure

getConformerShapes(conformers)[source]¶

Creates a list of shape structure from the given ligand conformers.

Parameters: conformers (list(structure.Structure)) – ligand source conformers of the same structure
Returns: shape structures derived from the given conformers
Return type: list(shape.ShapeStructure)

class schrodinger.application.phase.packages.shape_generator.SerializableShapeGenerator(params)[source]¶

Bases: schrodinger.application.phase.packages.shape_generator.ShapeGenerator

__init__(params)[source]¶

Accept either command line arguments or dictionary representation.

Parameters: params (namespace or dict) – Command line arguments or dictionary representation similar to the one returned by the toDict method.

fromDict(data)[source]¶

Configures the instance using data from data.

Parameters: data (dict) – Dictionary representation of the instance configuration.

toDict()[source]¶: Returns dictionary representation intended for JSON serialization.

getConformerShapes(conformers)¶

Creates a list of shape structure from the given ligand conformers.

Parameters: conformers (list(structure.Structure)) – ligand source conformers of the same structure
Returns: shape structures derived from the given conformers
Return type: list(shape.ShapeStructure)

getFeatureDefinitions(args)¶

Collects the feature definitions to use for generating pharmacophore hypothesis shapes from ligands.

Parameters: args (argparser.Namespace) – argument namespace with command line options
Returns: list of pharmacophore feature definitions
Return type: list of phase.PhpFeatureDefinition

getHypothesisFeatureRadii(radii_file)¶

Collects user specified pharmacophore feature radii to use for generating pharmacophore hypothesis shapes from ligands.

Parameters: radii_file (str) – user supplied .rad filename
Returns: Data for feature specific radii
Return type: phase.PhpFeatureData

getHypothesisSitesShape(sites)¶

Returns a shape structure created from the given Phase hypothesis.

Parameters: sites (list(phase.PhpSite)) – pharmacophore sites source
Returns: shape structure derived from the given hypothesis
Return type: shape.ShapeStructure

getShape(st, atom_weight_property=None)¶

Creates a shape structure from the given ligand structure.

Parameters: st (structure.Structure) – ligand source structure
Returns: shape structure derived from the given structure
Return type: shape.ShapeStructure

schrodinger.application.phase.packages.shape_generator.add_shape_generation_options(parser)[source]¶

Adds ligand-based screening options to the provided parser.

Parameters: parser (argparser.ArgumentParser) – Argument parser object

schrodinger.application.phase.packages.shape_generator.validate_shape_gen_options(args)[source]¶

Validates command-line argument pharmacophore option compatibility.

Parameters: args (argparse.Namespace) – argument namespace with command line options
Returns: tuple of validation success, and error message
Return type: bool, str

schrodinger.application.phase.packages.shape_generator.validate_shape_generator_dict(data)[source]¶

Validates “serialized” (as dictionary) representation of ShapeGenerator.

Parameters: data (dict) – Dictionary representation of the instance configuration.
Returns: Validation outcome and complain (if any).
Return type: (bool, str)

schrodinger.application.phase.packages.shape_generator.validate_shape_generator_dict_compatibility(meta1, meta2)[source]¶

Validates shape generators compatibility.

Parameters

meta1 (dict) – Validated shape generator dict #1.
meta2 (dict) – Validated shape generator dict #2.

Returns

Validation outcome and complain (if any).

Return type

(bool, str)