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"
|
|
|
|
|
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
|
|
|
_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
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)
|
_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.
...
|
|