Package schrodinger :: Package pipeline :: Package stages :: Module filtering :: Class GeneratePropsStage

Class GeneratePropsStage

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

Ev:85070

For each structure in the input set, runs: $SCHRODINGER/run generate_ligfilter_properties.py, which generates properties specified via the ligfilter.predefined_function_dict.

Instance Methods

[hide private]

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

setupJobs(self)
Sets up subjobs, which are distributed via JobDJ.

processJobOutputs(self)
Analyzes the output files from the subjobs.

operate(self)
Perform an operation on the input files.

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, getNJobs, getName, getOutput, getOutputName, getOutputNames, getRuntimePath, getStageDirectory, getVerbosity, hasCompleted, hasStarted, info, iterInputs, log, lognoret, mainProduct, outputRequested, productsInstalled, reportParameters, requiredProduct, requiredProductRuntime, run, runJobDJ, setInput, setJobDJOptions, setJobOptions, setMainProduct, setOutput, setOutputName, updateJobdj, validateValues, waitForFileStatus, waitForFiles, warning

Inherited from stage.Stage (private): _adjustNJobs, _calcStsPerJob, _getNCpus, _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__

setupJobs(self)

Sets up subjobs, which are distributed via JobDJ. There will be one subjob per each input file.

processJobOutputs(self)

Analyzes the output files from the subjobs. Raises a RuntimeError if there are any errors with the subjobs.

operate(self)

Perform an operation on the input files. There are setup, running, and post-processing steps, and the stage records its current status so that it can be restarted in that step if there is a failure. Raises a RuntimeError if the JobDJ run() method fails, or if the stage finishes with an improper status.

Overrides: stage.Stage.operate

Class GeneratePropsStage

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

setupJobs(self)

processJobOutputs(self)

operate(self)

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