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

Class SystemBuilder

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

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

_set_csb(self)

_postbuild(self, job)

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

hook_captured_successful_job(self, job)

prestage(self)

poststage(self)

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

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]

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

gen_restraint(model, setting, job)
Generates restraints.

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

merge_atom_group(model, group_key)

set_atom_group(model, group, permanent_group=None)

Class Variables

[hide private]

NAME = "system_builder"

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

SB_CMD = os.path.join(envir.CONST.SCHRODINGER_UTILITIES, "syst...

PARAM = cmj._create_param_when_needed(...

CROSS_LINK = {}

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

Class Variable Details

[hide private]

SOLVENT

Value:

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

SB_CMD

Value:

os.path.join(envir.CONST.SCHRODINGER_UTILITIES, "system_builder")

PARAM

Value:

cmj._create_param_when_needed("""
    DATA = {
    csb_file          = ""
    distil_solute     = true
    solvate_system    = true
    neutralize_system = true
    assign_forcefield = true
    buffer_width      = 10.0
...

Class SystemBuilder

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

crunch(self)

hook_captured_successful_job(self, job)

prestage(self)

poststage(self)

SOLVENT

SB_CMD

PARAM

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