schrodinger.pipeline.stages.macromodel module

Stages for running MacroModel jobs.

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

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

Bases: schrodinger.pipeline.stage.Stage

Stage for running MacroModel calculations

operate()

Run MacroModel conformer serch operation on the input files

processJobOutputs()

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

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.

splitJobOutputs()

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

operate()

Perform an operation on the input files.

prepareInputLigands()

processJobOutputs()

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

setupJobs()

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

writeSIFFile(ligfile, inpfile, outfile)