schrodinger.application.phase.packages.shape_generator module

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

Copyright Schrodinger LLC, All Rights Reserved.

class schrodinger.application.phase.packages.shape_generator.AtomTypes

Bases: enum.Enum

An enumeration.

element = 2
mmod = 1
qsar = 3
class schrodinger.application.phase.packages.shape_generator.ShapeGenerator(args)

Bases: object

__init__(args)

Initializes shape generation options.

Parameters:args (argparser.Namespace) – argument namespace with command line options
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
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)
class schrodinger.application.phase.packages.shape_generator.SerializableShapeGenerator(params)

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

__init__(params)

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)

Configures the instance using data from data.

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

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)

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)

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)

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)

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)