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"
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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
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| ClusterPoints(data,
metric,
algorithmId,
haveLabels=False,
haveActs=True,
returnDistances=False) |
source code
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ClusterFromDetails(details)
Returns the cluster tree |
source code
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_cvsVersion = '$Id: ClusterMols.py 1528 2010-09-26 17:04:37Z g... |
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idx1 = 4
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idx2 = 55
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__VERSION_STRING = ' ClusterMols.py 1528 2010-09-26 17:04:37Z ... |
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_usageDoc = '\nUsage: ClusterMols.py [args] <fName>\n\n If <f... |
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__package__ = 'rdkit.Chem.Fingerprints' |
Imports:
DbConnect,
DbInfo,
DbUtils,
DataUtils,
Clusters,
Murtagh,
sys,
cPickle,
FingerprintMols,
MolSimilarity,
DataStructs,
numpy,
message,
error
GetDistanceMatrix(data,
metric,
isSimilarity=1)
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data should be a list of tuples with fingerprints in position 1
(the rest of the elements of the tuple are not important)
Returns the symmetric distance matrix
(see ML.Cluster.Resemblance for layout documentation)
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_cvsVersion
- Value:
'$Id: ClusterMols.py 1528 2010-09-26 17:04:37Z glandrum $'
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__VERSION_STRING
- Value:
' ClusterMols.py 1528 2010-09-26 17:04:37Z glandrum '
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_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.
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