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