Package schrodinger :: Package pipeline :: Package stages :: Module canvas :: Class Canvas2DSimilarityStage

Class Canvas2DSimilarityStage

    UserDict.UserDict --+        
                        |        
UserDict.IterableUserDict --+    
                            |    
                  stage.Stage --+
                                |
                               Canvas2DSimilarityStage


This stage calculates a similarity score for each input ligand.
The simularity score is based on Canvas 2D fingerprints, and the
reference ligand is the "query" structure.

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

STAGE: Canvas 2D FingePrints stage
    Input 1: Query structure
    Input 2: Ligand structures to screen
    Output 1: Resulting structures with similarity scores

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 Canvas2DSimilarityStage

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

operate(self)

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