schrodinger.pipeline.stages.prime module

A stage for running Prime jobs.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.pipeline.stages.prime.PrimeStage(*args, **kwargs)

Bases: schrodinger.pipeline.stage.Stage

Prime Active Site Optimization stage: Performs the familiar sidechain prediction plus minimization, used by IFD jobs. The residues used are those in RESIDUE_LIST.

__init__(*args, **kwargs)

See class docstring.

setupJobs()

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

processJobOutputs()

Checks for failure of any subjobs (by reading the .log file). Renames the Prime 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.

class schrodinger.pipeline.stages.prime.MMGBSAStage(*args, **kwargs)

Bases: schrodinger.pipeline.stage.Stage

Stage for running Prime MM-GBSA on input structures. First structure in the input set is assumed to be the receptor.

There are no keywords specific to the stage.

The stage takes one input structure file set and generates one set of corresponding output structure files (also in PV format).

__init__(*args, **kwargs)

See class docstring.

mainProduct()

Product string identifying the job type. Used for running different job types with different host sets.

setupJobs()

Sets up Prime MM-GBSA jobs, which are distributed via JobDJ. There will be one MMGBSA job for each input PV file. This method clears the working directory of previous input file symlinks, output files, and log files (if any).

processJobOutputs()

Process the MMGBSA output. Returns with an error if any of the output files are missing.

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.