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.
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class
schrodinger.application.phase.packages.shape_generator.
AtomTypes
¶ Bases:
enum.Enum
An enumeration.
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element
= 2¶
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mmod
= 1¶
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qsar
= 3¶
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class
schrodinger.application.phase.packages.shape_generator.
ShapeGenerator
(args)¶ Bases:
object
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__init__
(args)¶ Initializes shape generation options.
Parameters: args (argparser.Namespace) – argument namespace with command line options
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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
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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
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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
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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
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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)
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class
schrodinger.application.phase.packages.shape_generator.
SerializableShapeGenerator
(params)¶ Bases:
schrodinger.application.phase.packages.shape_generator.ShapeGenerator
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__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.
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fromDict
(data)¶ Configures the instance using data from
data
.Parameters: data (dict) – Dictionary representation of the instance configuration.
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toDict
()¶ Returns dictionary representation intended for JSON serialization.
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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)
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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
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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
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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
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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
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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
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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
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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)
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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)