Module phase

Stages for running Phase jobs.

Classes

DBManageStage
Stage for creating a Phase database.

DBConfSitesStage
Stage for generating conformations for structures in a Phase database.

DBExportStage
Stage for exporting structures from a Phase database.

PhaseShapeStage
Stage for running Phase Shape on the input ligands.

Functions

check_subset_existence(dbpath, subsetname)
If the subset exists, returns a full subset path (absolute file path w/o the "_phase.inp" extension).

run_phase_database_job(cmd, stage)
Run the given phase_database job.

extract_properties(db, stage, jobname)
Run phase_database extract in CWD for the specified database.

Variables

__doc__ = ...

PHASE_DATABASE_EXE = '/scr/buildbot/savedbuilds/2017-2/NB/buil...

phase_shape = '/scr/buildbot/savedbuilds/2017-2/NB/build-142/s...

MMSHARE_DATA_DIR = '/scr/buildbot/savedbuilds/2017-2/NB/build-...

ALT_FILES = ['/scr/buildbot/savedbuilds/2017-2/NB/build-142/mm...

__package__ = 'schrodinger.pipeline.stages'

Function Details

If the subset exists, returns a full subset path (absolute file path w/o the "_phase.inp" extension). If it does not exist, raises RuntimeError.

Run the given phase_database job. On failure, exits the stage.

Variables Details

Value:

"""
Stages for running Phase jobs.

Copyright Schrodinger, LLC. All rights reserved.

"""

Value:

'/scr/buildbot/savedbuilds/2017-2/NB/build-142/phase_database'

Value:

'/scr/buildbot/savedbuilds/2017-2/NB/build-142/shape_screen'

Value:

'/scr/buildbot/savedbuilds/2017-2/NB/build-142/mmshare-v3.8/data'

Value:

['/scr/buildbot/savedbuilds/2017-2/NB/build-142/mmshare-v3.8/data/proj
_AD_feature.ini']