Package schrodinger :: Package pipeline :: Package stages :: Module macromodel :: Class ConfSearchStage

Class ConfSearchStage

    UserDict.UserDict --+        
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UserDict.IterableUserDict --+    
                            |    
                  stage.Stage --+
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                               ConfSearchStage

Stage for running MacroModel calculations

Instance Methods

[hide private]

__init__(self, *args, **kwargs)
This is the Stage class.

recombineInputLigands(self)
Read all input structure files, and write them to separate subjob input files.

setupJobs(self)
Build up command to use to launch each subjob, and add that command to JobDJ.

processJobOutputs(self)
After subjobs are complete, they are combined into a few output files

splitJobOutputs(self)

operate(self)
Run MacroModel conformer serch operation on the input files

writeSIFFile(self, ligfile, inpfile, outfile)

Inherited from stage.Stage: JobDJOptions, __getitem__, __getstate__, addExpectedInput, addExpectedOutput, addOutputFile, checkFile, checkFiles, checkInputs, checkParameters, checkProducts, debug, dump, error, exit, genFileName, genOutputFileName, getAdjustedNJobs, getCleanupRequested, getHostList, getHostStr, getInput, getInputNames, getJobDJ, getLocal, getMaxRetries, getNCpus, getNJobs, getName, getOutput, getOutputName, getOutputNames, getRuntimePath, getStageDirectory, getVerbosity, hasCompleted, hasStarted, info, iterInputs, log, lognoret, mainProduct, outputRequested, reportParameters, requiredProduct, requiredProductRuntime, run, runJobDJ, setInput, setJobDJOptions, setJobOptions, setMainProduct, setOutput, setOutputName, updateJobdj, validateValues, waitForFileStatus, waitForFiles, warning

Inherited from stage.Stage (private): _adjustNJobs, _calcStsPerJob, _inputCheck, _minVersionPresent, _readMessageFromDriver

Inherited from UserDict.IterableUserDict: __iter__

Inherited from UserDict.UserDict: __cmp__, __contains__, __delitem__, __len__, __repr__, __setitem__, clear, copy, get, has_key, items, iteritems, iterkeys, itervalues, keys, pop, popitem, setdefault, update, values

Class Methods

[hide private]

Inherited from UserDict.UserDict: fromkeys

Class Variables

[hide private]

Inherited from UserDict.UserDict: __hash__

Method Details

[hide private]

init(self, *args, **kwargs)
(Constructor)


This is the Stage class. Derive your own class from it.
  stagename - full name for this stage (<jobname>-<stagename>)
  specs - ConfigObj specification for the supported keywords
  allow_extra_keywords - Whether to allow keywords that are not in the specification.
  cleanup - Whether to remove intermediate files
  inpipeline - Whether the state is running within a Python Pipeline.
               If the stage is manually created, do NOT set this flag.
               Python Pipeline will set it as needed.

Overrides: UserDict.UserDict.__init__

recombineInputLigands(self)

Read all input structure files, and write them to separate subjob input files. The number of subjobs is determined by the Pipeline and adjusted so that the subjob size is within a good limit, if requested by the user.

operate(self)

Run MacroModel conformer serch operation on the input files

Overrides: stage.Stage.operate

Class ConfSearchStage

__init__(self, *args, **kwargs) (Constructor)

recombineInputLigands(self)

operate(self)

init(self, *args, **kwargs)
(Constructor)