schrodinger.pipeline.stages.phase module¶

Stages for running Phase jobs.

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.run_phase_database_job(cmd, stage)¶: Run the given phase_database job. On failure, exits the stage.

schrodinger.pipeline.stages.phase.extract_properties(db, stage, jobname)¶: Run phase_database extract in CWD for the specified database.

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

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.DBConfSitesStage(*args, **kwargs)¶

Stage for generating conformations for structures in 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.

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.

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

Stage for exporting structures from a Phase database.

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

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

__init__(*args, **kwargs)¶: Creates the stage instance, and passes the <args> and <kwargs> to the stage.Stage’s constructor.

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