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

Copyright Schrodinger, LLC. All rights reserved.

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.

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.

processJobOutputs()

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

setupJobs()

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

setupQSiteJob(complex_st, qsite_jobname)

Setup the QSite job(s)