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