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

Class FepVrun

         object --+            
                  |            
picklejar.Picklable --+        
                      |        
          cmj.StageBase --+    
                          |    
                   Simulate --+
                              |
                             FepVrun

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

_get_parent(self, parent)

_write_cfg(self, jobname, task, add_tag=config.tag_vrun, tag="VRUN", param=None)

_create_job(self, job_request)

crunch(self)
This is where jobs of this stage are created.

hook_captured_successful_job(self, job)

Inherited from Simulate: restart_subjobs

Inherited from Simulate (private): _get_model, _write_cms

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

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__

Static Methods

[hide private]

Inherited from Simulate: check_cms_file

Class Variables

[hide private]

NAME = "fep_vrun"

PARAM = cmj._create_param_when_needed([config.VRUN, ...

Inherited from Simulate: DESMOND_CMD

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__

_write_cfg(self, jobname, task, add_tag=config.tag_vrun, tag="VRUN", param=None)

Overrides: Simulate._write_cfg

_create_job(self, job_request)

Overrides: Simulate._create_job

crunch(self)

This is where jobs of this stage are created. This function should be overriden by the subclass.

Overrides: cmj.StageBase.crunch

hook_captured_successful_job(self, job)

Overrides: cmj.StageBase.hook_captured_successful_job

Class Variable Details

[hide private]

PARAM

Value:

cmj._create_param_when_needed([config.VRUN, """
    DATA = {
    trajectory   = off
    checkpt      = off
    simbox       = off
    maeff_output = off
    eneseq.interval     = 0.0
    fep.output.interval = 0.0
...

Class FepVrun

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

_write_cfg(self, jobname, task, add_tag=config.tag_vrun, tag="VRUN", param=None)

_create_job(self, job_request)

crunch(self)

hook_captured_successful_job(self, job)

PARAM

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