Package schrodinger :: Package application :: Package desmond :: Module stage :: Class ProteinMutationGenerator

Class ProteinMutationGenerator

         object --+        
                  |        
picklejar.Picklable --+    
                      |    
          cmj.StageBase --+
                          |
                         ProteinMutationGenerator

Nested Classes

[hide private]

Inherited from cmj.StageBase: __metaclass__

Instance Methods

[hide private]

__init__(self, *arg, **kwarg)
x.__init__(...) initializes x; see help(type(x)) for signature

crunch(self)
We will either read the mutations from a file or directly from the msj where mutations are defined as a list of space seperated strings

create_mutation_file(self)

Inherited from cmj.StageBase: __getstate__, __setstate__, capture, check_param, describe, determine, hook_captured_successful_job, pack_stage, poststage, prestage, push, release, restart_subjobs

Inherited from cmj.StageBase (private): _effect, _gen_unique_jobname, _get_jobname_and_dir, _get_macro_dict, _log, _param_jlaunch_opt_check, _print, _reg_param_postcheck, _reg_param_precheck, _set

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

Class Variables

[hide private]

NAME = "protein_mutation_generator"

PARAM = cmj._create_param_when_needed([...

Inherited from cmj.StageBase: count, stage_cls, stage_obj

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, *arg, **kwarg)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__

crunch(self)

We will either read the mutations from a file or directly from the msj where mutations are defined as a list of space seperated strings

mutations = ["C:23->ALA" "C:23->SER"]

Overrides: cmj.StageBase.crunch

Class Variable Details

[hide private]

PARAM

Value:

cmj._create_param_when_needed(["""
    DATA = {
    mutation_file = ""
    cpu = 1
    mutations = []
    }
    VALIDATE = {
    mutation_file = {type = str}
...

Class ProteinMutationGenerator

__init__(self, *arg, **kwarg) (Constructor)

crunch(self)

PARAM

init(self, *arg, **kwarg)
(Constructor)