Package schrodinger :: Package pipeline :: Package stages :: Module convert :: Class ConvertStage

Class ConvertStage

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


Stage for converting structure files from one format to another
Each file is converted using Schrodingers specific conversion utility
and the number of files is not changed.

Input file format is determined from the extension of each file.

Supported conversions:
  smiles <-> maestro
  smilescsv <-> maestro
  sd <-> maestro

Files with unrecognized extensions are treated as SD (Ev:62575)

Instance Methods

[hide private]

__init__(self, *args, **kwargs)
See class docstring.

operate(self)
Combine all the input files from all input sets into one set, optionally labelling each structure according to the set from which it originated.

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)

See class docstring.

Overrides: UserDict.UserDict.__init__

operate(self)

Combine all the input files from all input sets into one set, optionally labelling each structure according to the set from which it originated. Raises a RuntimeError if there is a problem reading an input file or writing an output file.

Overrides: stage.Stage.operate

Class ConvertStage

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

operate(self)

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