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

Class Simulate

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

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_model(self, job, fname)

_write_cms(self, jobname, model)

_write_cfg(self, jobname, task, add_tag=config.tag_md, tag="MD", param=None)

_create_job(self, pre_job=[], job_param=[])

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

restart_subjobs(self, jobs)
Subclass should override this if it supports subjob restarting.

hook_captured_successful_job(self, job)

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]

check_cms_file(fname)

Class Variables

[hide private]

NAME = "simulate"

DESMOND_CMD = os.path.join(envir.CONST.SCHRODINGER, "desmond")

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

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)

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

Overrides: cmj.StageBase.crunch

restart_subjobs(self, jobs)

Subclass should override this if it supports subjob restarting.

Overrides: cmj.StageBase.restart_subjobs: (inherited documentation)

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.MD, """
    DATA = {
    jobname    = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"
    dir        = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$[
_lambda$LAMBDA$]"
    host       = "$SUBHOST"
    fep.model_file = []
    jin_file   = []
...

Class Simulate

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

crunch(self)

restart_subjobs(self, jobs)

hook_captured_successful_job(self, job)

PARAM

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