Package schrodinger :: Package pipeline :: Module stage

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: 55012

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
hash(x)

__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:
...