schrodinger :: application :: desmond :: stage :: SystemBuilder :: Class SystemBuilder

Class SystemBuilder

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

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

_postbuild(self, job)

_set_csb(self)

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

hook_captured_successful_job(self, job)

poststage(self)

prestage(self)

Inherited from cmj.StageBase: __getstate__, __setstate__, capture, check_param, describe, determine, pack_stage, 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]

gen_restraint(model, setting, job)
Generates restraints.

merge_atom_group(model, group_key)

merge_restrain(model, res, new_restr, old_restr)
`res' is a `sea.Sea' object.

set_atom_group(model, group, permanent_group=None)

set_restrain(model, setting, permanent_restr=None, job=None)
`restr' is a `sea.Sea' object.

Class Variables

[hide private]

CROSS_LINK = {}

NAME = 'system_builder'

SB_CMD = '/scr/buildbot/savedbuilds/NB/2016-4/build-126/utilit...

SOLVENT = {'SPC': 'spc.box.mae', 'SPCFW': 'spcfw.box.mae', 'TI...

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

Class Variable Details

[hide private]

SB_CMD

Value:

'/scr/buildbot/savedbuilds/NB/2016-4/build-126/utilities/system_builde
r'

SOLVENT

Value:

{'SPC': 'spc.box.mae',
 'SPCFW': 'spcfw.box.mae',
 'TIP3P': 'tip3p.box.mae',
 'TIP4P': 'tip4p.box.mae',
 'TIP4PEW': 'tip4pew.box.mae'}

Class SystemBuilder

PARAM(...)

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

crunch(self)

hook_captured_successful_job(self, job)

poststage(self)

prestage(self)

SB_CMD

SOLVENT

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