schrodinger.pipeline.stages.qsite module

A stage for running QSite jobs.

Input structure file - maestro file of one or more complexes OR a PV file

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class schrodinger.pipeline.stages.qsite.QSiteStage(*args, **kwargs)

Bases: schrodinger.pipeline.stage.Stage

Stage for running QSite jobs.

Input can be one of the following:

1. Complex maestro file

   QM region may be defined via molecule number or atom numbers

2. PV maestro file

   QM region will be set to the ligand

addExpectedKeyword(fullname, qsname, type, default=None, doc=None)

Used by constructor. Saves “QSite name” for specified keyword and returns ConfigObj validation string for it.

setupJobs()

Sets up the QSite jobs, which are distributed via JobDJ.

setupQSiteJob(complex_st, qsite_jobname)

Setup the QSite job(s)

processJobOutputs()

Checks for failure of any subjobs (by reading the .log file). Renames the QSite output files. Raises a RuntimeError if any subjob failed.

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.