Package Chem :: Package Fingerprints :: Module MolSimilarity

Module MolSimilarity

utility functionality for molecular similarity
 includes a command line app for screening databases


Sample Usage:

  python MolSimilarity.py  -d data.gdb -t daylight_sig --idName="Mol_ID"       --topN=100 --smiles='c1(C=O)ccc(Oc2ccccc2)cc1' --smilesTable=raw_dop_data       --smilesName="structure" -o results.csv

Functions

[hide private]

_ConstructSQL(details, extraFields='') source code

ScreenInDb(details, mol)

source code

GetFingerprints(details)
returns an iterable sequence of fingerprints each fingerprint will have a _fieldsFromDb member whose first entry is the id.

source code

ScreenFingerprints(details, data, mol=None, probeFp=None)
Returns a list of results...

source code

ScreenFromDetails(details, mol=None)
Returns a list of results...

source code

Variables

[hide private]

_dataSeq = None

_cvsVersion = '$Id: MolSimilarity.py 2 2006-05-06 22:54:39Z gl...

idx1 = 4

idx2 = 54

__VERSION_STRING = ' MolSimilarity.py 2 2006-05-06 22:54:39Z g...

_usageDoc = '\nUsage: MolSimilarity.py [args] <fName>\n\n If ...

Function Details

[hide private]

ScreenFingerprints(details, data, mol=None, probeFp=None)

source code

Returns a list of results

ScreenFromDetails(details, mol=None)

source code

Returns a list of results

Variables Details

[hide private]

_cvsVersion

Value:

'$Id: MolSimilarity.py 2 2006-05-06 22:54:39Z glandrum $'

__VERSION_STRING

Value:

' MolSimilarity.py 2 2006-05-06 22:54:39Z glandrum '

_usageDoc

Value:

'''
Usage: MolSimilarity.py [args] <fName>

  If <fName> is provided and no tableName is specified (see below),
  data will be read from the pickled file <fName>.  This file should
  contain a series of pickled (id,fingerprint) tuples.

  NOTE: at the moment the user is responsible for ensuring that the
...