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

Class SampleRingsStage

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

Stage for sampling rings with 7 or more members using MacroModel

Instance Methods

[hide private]

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

prepareInputLigands(self)

setupJobs(self)
Built up the MacroModel command for each subjob, and add it to JobDJ

processJobOutputs(self)
Is run after all subjobs are complete to recombine the output ligands

operate(self)
Perform an 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__

operate(self)

Perform an operation on the input files.

Overrides: stage.Stage.operate

Class SampleRingsStage

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

operate(self)

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