Package Chem :: Package Fingerprints :: Module ClusterMols

Module ClusterMols

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. 

...