schrodinger.pipeline.stages.semiemp module

Stage for running semi-empirical jobs.

Input structure file - maestro file of one or more ligands (it does not

yet have an QM/MM mode for processing complexes).

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.pipeline.stages.semiemp.SemiEmpStage(*args, **kwargs)

Bases: schrodinger.pipeline.stage.Stage

Stage for running semi-empirical jobs.

Input is a structure file of one or more ligands.

__init__(*args, **kwargs)

Creates the stage instance, and passes the <args> and <kwargs> to the stage.Stage’s constructor.

recombineInputLigands()

Split/recombine the input ligand files into the desired number of subsets/subjobs.

setupJobs()

Sets up the semi-empirical jobs, which are distributed via JobDJ.

processJobOutputs()

Renames the semi-empirical output files and does a final check for their existence.

operate()

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

If the stage has crashed, Pipeline will restart it from the last dump() point and call this method again.

Perform the operation on the input files. There are preparing, 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.