schrodinger.pipeline.stages.phase module¶
Stages for running Phase jobs.
Copyright Schrodinger, LLC. All rights reserved.
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class
schrodinger.pipeline.stages.phase.
DBConfSitesStage
(*args, **kwargs)¶ Bases:
schrodinger.pipeline.stage.Stage
Stage for generating conformations for structures in a Phase database.
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createSubsetForCompsWithoutSites
(db, jobname)¶ Run a “subset” task to create a subset of compounds in the database that don’t already have sites. Must run on the host that has access to the database.
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operate
()¶ Perform an operation on the input files. There are setup, running, and post-processing steps, and the stage records its current status so that it can be restarted in that step if there is a failure. Raises a RuntimeError if the JobDJ run() method fails, or if the stage finishes with an improper status.
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class
schrodinger.pipeline.stages.phase.
DBExportStage
(*args, **kwargs)¶ Bases:
schrodinger.pipeline.stage.Stage
Stage for exporting structures from a Phase database.
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findManageOutfiles
(out_basename, outext)¶
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operate
()¶ Perform an operation on the input files.
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class
schrodinger.pipeline.stages.phase.
DBManageStage
(*args, **kwargs)¶ Bases:
schrodinger.pipeline.stage.Stage
Stage for creating a Phase database.
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operate
()¶ Perform an operation on the input files. There are setup, running, and post-processing steps, and the stage records its current status so that it can be restarted in that step if there is a failure. Raises a RuntimeError if the JobDJ run() method fails, or if the stage finishes with an improper status.
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runAddJob
(cmd)¶ Run a phase_database job. Will also check the log file and exit the stage if the Phase job failed.
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class
schrodinger.pipeline.stages.phase.
PhaseShapeStage
(*args, **kwargs)¶ Bases:
schrodinger.pipeline.stage.Stage
Stage for running Phase Shape on the input ligands.
This stage is used by Data Fusion workflow (data_fusion_backend.py).
Input 1: Shape query structure Input 2: Ligand structures Output 1: Resulting poses
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operate
()¶ The only overridden & required method in this class. Called by the Pipeline to run this stage’s main code.
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schrodinger.pipeline.stages.phase.
check_subset_existence
(dbpath, subsetname)¶ 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.
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schrodinger.pipeline.stages.phase.
extract_properties
(db, stage, jobname)¶ Run phase_database extract in CWD for the specified database.
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schrodinger.pipeline.stages.phase.
run_phase_database_job
(cmd, stage)¶ Run the given phase_database job. On failure, exits the stage.