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.

__class__

alias of enum.EnumMeta

__members__ = mappingproxy(OrderedDict([('mmod', <AtomTypes.mmod: 1>), ('element', <AtomTypes.element: 2>), ('qsar', <AtomTypes.qsar: 3>)]))

__module__ = 'schrodinger.application.phase.packages.shape_generator'

element = 2

mmod = 1

qsar = 3

class schrodinger.application.phase.packages.shape_generator.ShapeGenerator(args)

Bases: object

required_constructor_arguments = ('atomtypes', 'color', 'fd', 'hydrogens', 'pharm', 'rad', 'screen', 'shape')

__init__(args)

Initializes shape generation options.

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

getGenerationOptions()

Populates ShapeGenerationOptions object from ShapeGenerator members

Returns:shape generation options object Return type:shape.ShapeGenerationOptions

getGenerationOptionsDict()

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)

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__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.phase.packages.shape_generator', 'required_constructor_arguments': ('atomtypes', 'color', 'fd', 'hydrogens', 'pharm', 'rad', 'screen', 'shape'), '__init__': <function ShapeGenerator.__init__>, 'getGenerationOptions': <function ShapeGenerator.getGenerationOptions>, 'getGenerationOptionsDict': <function ShapeGenerator.getGenerationOptionsDict>, 'getFeatureDefinitions': <function ShapeGenerator.getFeatureDefinitions>, 'getHypothesisFeatureRadii': <function ShapeGenerator.getHypothesisFeatureRadii>, 'getHypothesisSitesShape': <function ShapeGenerator.getHypothesisSitesShape>, 'getShape': <function ShapeGenerator.getShape>, 'getConformerShapes': <function ShapeGenerator.getConformerShapes>, '__dict__': <attribute '__dict__' of 'ShapeGenerator' objects>, '__weakref__': <attribute '__weakref__' of 'ShapeGenerator' objects>, '__doc__': None})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.phase.packages.shape_generator'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

schrodinger.application.phase.packages.shape_generator.add_ligand_options(parser)

Adds ligand-based screening options to the provided parser.

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

schrodinger.application.phase.packages.shape_generator.add_pharmacophore_options(parser)

Adds pharmacophore-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