schrodinger.pipeline.stages.macromodel module

Stages for running MacroModel jobs.

ConfSearchStage - stage for running MacroModel conf-search calculations. SampleRingsStage - stage for sampling large rings

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.pipeline.stages.macromodel.ConfSearchStage(*args, **kwargs)

Bases: schrodinger.pipeline.stage.Stage

Stage for running MacroModel calculations

__init__(*args, **kwargs)

This is the Stage class. Derive your own class from it.

Parameters

  • stagename – full name for this stage (<jobname>-<stagename>)

  • specs – ConfigObj specification for the supported keywords

  • allow_extra_keywords – Whether to allow keywords that are not in the specification.

  • cleanup – Whether to remove intermediate files

  • inpipeline – Whether the state is running within a Python Pipeline. If the stage is manually created, do NOT set this flag. Python Pipeline will set it as needed.

  • driver_dir – Directory in which the driver is running.

recombineInputLigands()

Read all input structure files, and write them to separate subjob input files. The number of subjobs is determined by the Pipeline and adjusted so that the subjob size is within a good limit, if requested by the user.

setupJobs()

Build up command to use to launch each subjob, and add that command to JobDJ.

processJobOutputs()

After subjobs are complete, they are combined into a few output files

splitJobOutputs()
operate()

Run MacroModel conformer serch operation on the input files

writeSIFFile(ligfile, inpfile, outfile)
class schrodinger.pipeline.stages.macromodel.SampleRingsStage(*args, **kwargs)

Bases: schrodinger.pipeline.stage.Stage

Stage for sampling rings with 7 or more members using MacroModel

__init__(*args, **kwargs)

This is the Stage class. Derive your own class from it.

Parameters

  • stagename – full name for this stage (<jobname>-<stagename>)

  • specs – ConfigObj specification for the supported keywords

  • allow_extra_keywords – Whether to allow keywords that are not in the specification.

  • cleanup – Whether to remove intermediate files

  • inpipeline – Whether the state is running within a Python Pipeline. If the stage is manually created, do NOT set this flag. Python Pipeline will set it as needed.

  • driver_dir – Directory in which the driver is running.

prepareInputLigands()
setupJobs()

Built up the MacroModel command for each subjob, and add it to JobDJ

processJobOutputs()

Is run after all subjobs are complete to recombine the output ligands

operate()

Perform an operation on the input files.

writeSIFFile(ligfile, inpfile, outfile)