Package schrodinger :: Package pipeline :: Package stages :: Module phase :: Class PhaseShapeStage

Class PhaseShapeStage

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

Stage for running Phase Shape on the input ligands.

This stage is used by Data Fusion workflow (data_fusion_backend.py).

Input 1: Shape query structure Input 2: Ligand structures Output 1: Resulting poses

Instance Methods

[hide private]

__init__(self, *args, **kwargs)
Creates the stage instance, and passes the <args> and <kwargs> to the stage.Stage's constructor.

operate(self)
The only overridden & required method in this class.

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)

Creates the stage instance, and passes the <args> and <kwargs> to the stage.Stage's constructor.

Overrides: UserDict.UserDict.__init__

operate(self)

The only overridden & required method in this class. Called by the Pipeline to run this stage's main code.

Overrides: stage.Stage.operate

Class PhaseShapeStage

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

operate(self)

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