Package rdkit :: Package Chem :: Package Fingerprints :: Module ClusterMols

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# Module ClusterMols

source code

    utility functionality for clustering molecules using fingerprints
     includes a command line app for clustering

    Sample Usage:
      python ClusterMols.py  -d data.gdb -t daylight_sig     --idName="CAS_TF" -o clust1.pkl     --actTable="dop_test" --actName="moa_quant"

Functions | [hide private]

message(msg) | source code

error(msg) | source code

GetDistanceMatrix(data, metric, isSimilarity=1) data should be a list of tuples with fingerprints in position 1 (the rest of the elements of the tuple are not important) | source code

ClusterPoints(data, metric, algorithmId, haveLabels=False, haveActs=True, returnDistances=False) | source code

ClusterFromDetails(details) Returns the cluster tree | source code

Variables | [hide private]

| _cvsVersion = `"$Id$"`
| idx1 = `_cvsVersion.find(':')+ 1`
| idx2 = `_cvsVersion.rfind('$')`
| __VERSION_STRING = `"%s" %(_cvsVersion [idx1: idx2])`
| _usageDoc = ``...``

Imports: DbConnect, DbInfo, DbUtils, DataUtils, Clusters, Murtagh, sys, cPickle, FingerprintMols, MolSimilarity, DataStructs, numpy

Function Details | [hide private]

### GetDistanceMatrix(data, metric, isSimilarity=1)

source code

    data should be a list of tuples with fingerprints in position 1
    (the rest of the elements of the tuple are not important)

     Returns the symmetric distance matrix
     (see ML.Cluster.Resemblance for layout documentation)

Variables Details | [hide private]

### _usageDoc

Value:

      """
      Usage: ClusterMols.py [args] <fName>

        If <fName> is provided and no tableName is specified (see below),
        data will be read from the text file <fName>.  Text files delimited
        with either commas (extension .csv) or tabs (extension .txt) are
        supported.

      ...