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

Class WaterMap

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

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

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

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__

Class Variables

[hide private]

NAME = "watermap"

WATERMAP_CMD = os.path.join(envir.CONST.WATERMAP_EXEC_DIR, "wa...

PARAM = cmj._create_param_when_needed([...

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

hook_captured_successful_job(self, job)

Overrides: cmj.StageBase.hook_captured_successful_job

Class Variable Details

[hide private]

WATERMAP_CMD

Value:

os.path.join(envir.CONST.WATERMAP_EXEC_DIR, "watermap_analysis")

PARAM

Value:

cmj._create_param_when_needed(["""
    DATA = {
    ligand_file       = "$MASTERJOBNAME-ligand.mae"
    protein_file      = "$MASTERJOBNAME-protein.mae"
    output            = "$JOBNAME_wm.mae"
    tpi               = true
    keep_trajectory   = true
    probe_radius      = 1.0
...

Class WaterMap

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

crunch(self)

hook_captured_successful_job(self, job)

WATERMAP_CMD

PARAM

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