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

Class SolvatePocket

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

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_spd(self)

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 = "solvate_pocket"

SOLVATE_POCKET_CMD = os.path.join(envir.CONST.SCHRODINGER_UTIL...

PARAM = cmj._create_param_when_needed([...

DEFAULT_SPD = ...

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]

SOLVATE_POCKET_CMD

Value:

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

PARAM

Value:

cmj._create_param_when_needed(["""
    DATA = {
    jobname     = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"
    dir         = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$
[_lambda$LAMBDA$]"
    host        = "$SUBHOST"
    spd_file    = ""
    ligand_file = "$MASTERJOBNAME-ligand.mae"
...

DEFAULT_SPD

Value:

"""
    name                    = "standard solvate_pocket command file"
    chemical_potential      = -7.17
    init_chemical_potential = -6.2
    temperature             = 300.0
    cut_off                 = 9.0
    init_num_passes         = 7500
    num_passes              = 100000
...

Class SolvatePocket

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

crunch(self)

hook_captured_successful_job(self, job)

SOLVATE_POCKET_CMD

PARAM

DEFAULT_SPD

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