Package schrodinger :: Package pipeline :: Module stage
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Module stage


Base classes for Pipeline stages.

To create a stage instance:

    stageobj = YourStage(<stagename>)

    # Add keywords:

    stageobj['NUM_RINGS'] = 2
    stageobj['UNIQUEFIELD'] = 's_m_title'

    # Add input objects:
    # ligand_files is list of file names
    ligandsobj = pipeio.Structures(ligand_files)
    stageobj.setInput(1, 'INPUT1', ligandsobj)
    
    # Tell the stage where to save it's output:
    stageobj.setOutputName(1, 'OUTPUT')
    
    # Integers (1) are position numbers.
    # INPUT1 is the name of the input object
    
    # Run the stage:
    
    outputs = stageobj.run()
    
    # outputs is now a dictionary of output objects


Copyright Schrodinger, LLC. All rights reserved.


Version: 40023

Classes [hide private]
  DotPrinter
Class for printing a progress period or percentage every N number of iterations.
  StageInput
Class defining a stage input
  StageOutput
Class defining a stage output
  Stage
Functions [hide private]
 
get_time(t1, t2=0)
Returns a string of the time difference between t2 and t1 in human readable format.
 
_host_is_queue(hostname)
Return True if specified host is a queue
 
Restart(restart_file, ignored=None)
Run this function in order to recover a saved Stage instance.
Variables [hide private]
  __doc__ = ...
  _version = '$Revision: 1.119 $'
  logger = log.get_logger("schrodinger.pipeline.stage")
  handler = logging.StreamHandler(sys.stdout)
  DEBUG = False
  __package__ = 'schrodinger.pipeline'
Function Details [hide private]

get_time(t1, t2=0)

 

Returns a string of the time difference between t2 and t1 in human readable format. t2 and t1 are times, as returned by time.time()


Variables Details [hide private]

__doc__

Value:
"""
Base classes for Pipeline stages.

To create a stage instance:

    stageobj = YourStage(<stagename>)

    # Add keywords:
...