README

This repository contains base classes that help manage the surprisingly complex
task of input-file management in protein specificity / multistate design particularly
on UNC's MPI cluster, dogwood.

The goal of the functionality provided in these classes is to make the work
requried to write the script for preparing and launching a set of multistate
design jobs relatively easy.

The "setup_jobs.py" script will look something like this:

    import (some things)

    si = ServerIdentifier()
    opts = OptHolder()
    with blargs.Parser(opts) as p:
        DerivedMSDJob.add_options(p)
        JobExecutionOptions.add_options(p)

    msd_job = DerivedMSDJob(opts)
    msd_job_manager = MSDJobManager(msd_job, opts, si)
    msd_job_manager.prepare_job()

and that's it.

The programmer will define a class DerivedMSDJob, derived from either
the IsolateBBInterfaceMSDJob class or the MergeBBInterfaceMSDJob, and
with the DerivedMSDJob, a DerivedDesignSpecies class, derived from
either the IsolateBBDesignSpecies or the MergeBBDesignSpecies classes,
and a DerivedStateVersion class, derived from either the 
IsolateBBStateVersion or MergeBBStateVersion classes. These three
classes will specify how the design job should proceed in broad
strokes, where their base classes will do the heavy lifting.