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.
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class
schrodinger.application.phase.packages.bedroc_screener.
BedrocScreener
(hypo, match_options)¶ Bases:
object
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__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
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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
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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
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