schrodinger :: application :: desmond :: stage :: Simulate :: Class Simulate

Class Simulate

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

Known Subclasses:

Nested Classes

[hide private]

Inherited from cmj.StageBase: __metaclass__

Instance Methods

[hide private]

PARAM(...)

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

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

_get_model(self, job, fname)

_get_snapcore_coordinates(self, job)
setting phase-aligned coordinates for both ref and mut molecules

_perform_snapcore(self, ct1, ct2)
Only snapcore for small molecule FEP simulations Guess protein mutations This should use API defined in DESMOND-6570 when it is done.

_write_cfg(self, jobname, task, add_tag=<function tag_md at 0x7f59555cb7d0>, tag='MD', param=None)

_write_cms(self, jobname, model)

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

hook_captured_successful_job(self, job)

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

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

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]

DESMOND_CMD = '/scr/buildbot/savedbuilds/NB/2016-4/build-126/d...

NAME = 'simulate'

Inherited from cmj.StageBase: count, stage_cls, stage_obj

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

PARAM(...)

Overrides: cmj.StageBase.PARAM

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

hook_captured_successful_job(self, job)

Overrides: cmj.StageBase.hook_captured_successful_job

restart_subjobs(self, jobs)

Subclass should override this if it supports subjob restarting.

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

Class Variable Details

[hide private]

DESMOND_CMD

Value:

'/scr/buildbot/savedbuilds/NB/2016-4/build-126/desmond'

Class Simulate

PARAM(...)

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

crunch(self)

hook_captured_successful_job(self, job)

restart_subjobs(self, jobs)

DESMOND_CMD

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