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(value)¶ Bases:
enum.EnumAn enumeration.
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mmod= 1¶
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element= 2¶
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qsar= 3¶
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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
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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-
__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
toDictmethod.
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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)