schrodinger.application.phase.packages.bedroc_screener module

This module contains the BedrocScreener class, which performs in-process pharmacophore screens of zipped Phase projects containing actives and decoys. BedrocScreener provides a lightweight alternative to launching a phase_screen job with a .list file containing the names of the zipped projects.

class schrodinger.application.phase.packages.bedroc_screener.BedrocScreener(hypo, match_options)

Bases: object

__init__(hypo, match_options)

Constructor that takes a pharmacophore hypothesis and matching options.

Parameters:

• hypo (str) – Path to hypothesis file (.phypo)
• match_options (phase.PhpMatchOptions) – Hypothesis matching options

calcBEDROC(alpha=20.0)

Calculates the BEDROC score after a screen has been performed.

Parameters:alpha (float) – Early enrichment factor Returns:BEDROC score Return type:float

screen(actives, decoys, hit_file=None, zip_dir=None)

Performs screens. Projects are unzipped to a securely named temporary subdirectory that’s created in either a platform-dependent directory (/tmp, /var/tmp, etc.) or a specific named directory. The latter is recommended if the projects are large and/or if numerous screens will be run simultaneously. Unsorted hits are written to hit_file if that parameter is supplied.

Parameters:

• actives (str) – Path to zipped actives project (.phzip)
• decoys (str) – Path to zipped decoys project (.phzip)
• hit_file (str) – Maestro/SD file for unsorted hits
• zip_dir (str) – Overrides platform-dependent temporary directory

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.phase.packages.bedroc_screener', '__init__': <function BedrocScreener.__init__>, 'calcBEDROC': <function BedrocScreener.calcBEDROC>, 'screen': <function BedrocScreener.screen>, '_createCalculator': <function BedrocScreener._createCalculator>, '_doScreen': <function BedrocScreener._doScreen>, '_doScreens': <function BedrocScreener._doScreens>, '_sortHits': <function BedrocScreener._sortHits>, '_validateHypo': <function BedrocScreener._validateHypo>, '_validateScreenFiles': <function BedrocScreener._validateScreenFiles>, '__dict__': <attribute '__dict__' of 'BedrocScreener' objects>, '__weakref__': <attribute '__weakref__' of 'BedrocScreener' 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.bedroc_screener'

__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)