Chem.Fingerprints.ClusterMols

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]
GetDistanceMatrix(data, metric, isSimilarity=1) data should be a list of tuples with fingerprints in position 1... | 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: ClusterMols.py 778 2008-07-30 09:51:55Z gl``...``
| idx1 = `4`
| idx2 = `54`
| __VERSION_STRING = ``'``ClusterMols.py 778 2008-07-30 09:51:55Z g``...``
| _usageDoc = ``'``\nUsage: ClusterMols.py [args] <fName>\n\n If <f``...``

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)

### ClusterFromDetails(details) | source code
    Returns the cluster tree

Variables Details | [hide private]

  ### _cvsVersion Value:
      '$Id: ClusterMols.py 778 2008-07-30 09:51:55Z glandrum $'

  ### __VERSION_STRING Value:
      ' ClusterMols.py 778 2008-07-30 09:51:55Z glandrum '

  ### _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.

      ...