Package schrodinger :: Package application :: Package canvas :: Module cluster :: Class CanvasFingerprintClusterCLI

Class CanvasFingerprintClusterCLI

              object --+    
                       |    
CanvasFingerprintCluster --+
                           |
                          CanvasFingerprintClusterCLI

A subclass of the canvas fingerprint cluster manager which is to be used from a program with a command line interface. This class has methods for defining options in an option parser and for applying those options once they've been parsed. The idea is to provide a standard command line interface for setting the clustering options

Instance Methods

[hide private]

__init__(self, logger)
Initialize the instance of the cluster class

addOptions(self, parser)
Add options for cluster linkage

parseOptions(self, options)
Examine the options and set the internal state to reflect them

getLinkageDescription(self)
Return a string which contains a description of the linkage methods available for cluster linkage

Inherited from CanvasFingerprintCluster: __del__, clusterDM, clusterFP, debug, generateDM, getAverageDistanceFromCentroid, getBestNumberOfClusters, getClusterContents, getClusterOrderMap, getClusterTime, getClusterVariance, getClusteringMap, getCurrentLinkage, getDendrogramData, getDescription, getDistanceMatrixFile, getDistanceToCentroid, getGroupTime, getIsFarthestFromCentroid, getIsNearestToCentroid, getKelleyPenaltyList, getMatrixTime, getMaxDistanceFromCentroid, getMergeDistanceList, getNumberOfClustersList, getRSquaredList, getSemiPartialRSquaredList, getSeparationRatioList, group, setLinkage

Inherited from CanvasFingerprintCluster (private): _createTempFile, _deleteIfExists, _getLine, _readClusterStatistics, _readGroupFile

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables

[hide private]

Inherited from CanvasFingerprintCluster: LINKAGE_TYPES

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, logger)
(Constructor)

Initialize the instance of the cluster class

Overrides: object.__init__: (inherited documentation)

Class CanvasFingerprintClusterCLI

__init__(self, logger) (Constructor)

init(self, logger)
(Constructor)