Package schrodinger :: Package application :: Package desmond :: Module fep_protein_prep :: Class Workflow

Class Workflow

object --+
         |
        Workflow

Will take a list of proteins and a mutation dictionary and return a set of "lig" "rec" legs and msj for running the sims. Should also return a script that will fire all the jobs off.

Instance Methods

[hide private]

__init__(self, structure_fname, host_name, num_proc, mutation_fname, jobname)
Takes in parameters generated from the driver script

run(self)
Run the workflow

stage_one(self)
Run prime to generate mutants

stage_two(self)
Get mutation dictionary

stage_three(self)
Stage 3 build input files for FEP

stage_four(self)
tar it all up

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, structure_fname, host_name, num_proc, mutation_fname, jobname)
(Constructor)

Takes in parameters generated from the driver script

Overrides: object.__init__

Class Workflow

__init__(self, structure_fname, host_name, num_proc, mutation_fname, jobname) (Constructor)

init(self, structure_fname, host_name, num_proc, mutation_fname, jobname)
(Constructor)