schrodinger.pipeline.stages.phase module

Stages for running Phase jobs.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.pipeline.stages.phase.DBConfSitesStage(*args, **kwargs)

Bases: schrodinger.pipeline.stage.Stage

Stage for generating conformations for structures in a Phase database.

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.

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.

class schrodinger.pipeline.stages.phase.DBExportStage(*args, **kwargs)

Bases: schrodinger.pipeline.stage.Stage

Stage for exporting structures from a Phase database.

findManageOutfiles(out_basename, outext)
operate()

Perform an operation on the input files.

class schrodinger.pipeline.stages.phase.DBManageStage(*args, **kwargs)

Bases: schrodinger.pipeline.stage.Stage

Stage for creating a Phase database.

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.

runAddJob(cmd)

Run a phase_database job. Will also check the log file and exit the stage if the Phase job failed.

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

operate()

The only overridden & required method in this class. Called by the Pipeline to run this stage’s main code.

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.

schrodinger.pipeline.stages.phase.extract_properties(db, stage, jobname)

Run phase_database extract in CWD for the specified database.

schrodinger.pipeline.stages.phase.run_phase_database_job(cmd, stage)

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