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

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

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.

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

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables [hide private]
  NAME = "trajectory"
  TRAJ_CMD = [envir.CONST.SCHRODINGER+ "/run", "-FROM", "desmond...
  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

Class Variable Details [hide private]

TRAJ_CMD

Value:
[envir.CONST.SCHRODINGER+ "/run", "-FROM", "desmond", "manipulate_trj.\
py",]

PARAM

Value:
cmj._create_param_when_needed(["""
    DATA = {
    jobname     = "$MASTERJOBNAME_$STAGENO$[_lambda$LAMBDA$]"
    dir         = "$[$JOBPREFIX/$]$[$PREFIX/$]$MASTERJOBNAME_$STAGENO$\
[_lambda$LAMBDA$]"
    concatenate = 1
    save_trajectory = yes
    }
...