schrodinger :: application :: desmond :: stage :: AssignForcefield :: Class AssignForcefield

Class AssignForcefield

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

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

_constrained_water(self, ffio_constraints)
ffio_constraints: ffiostructure _FFIOConstraint instance return: set of atoms with constraint funct HOH

_get_hmr_sites(self, ffio)

_postbuild(self, job)

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

hook_captured_successful_job(self, job)

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

get_water_ct_indices(model)

Class Variables

[hide private]

CMD = '/scr/buildbot/savedbuilds/2017-2/NB/build-142/run'

NAME = 'assign_forcefield'

OPLS = ['OPLS_2005', 'OPLS2.1', 'OPLS3']

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

Class AssignForcefield

PARAM(...)

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

crunch(self)

hook_captured_successful_job(self, job)

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