Package rdkit :: Package Chem :: Package Fingerprints :: Module MolSimilarity
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Module MolSimilarity

source code

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
hash(x)
  _cvsVersion = '$Id$'
  idx1 = 0
  idx2 = 3
  __VERSION_STRING = '$Id'
  _usageDoc = '\nUsage: MolSimilarity.py [args] <fName>\n\n If ...
  __package__ = 'rdkit.Chem.Fingerprints'

Imports: RDConfig, Chem, DbConnect, DbModule, TopNContainer, sys, types, cPickle, FingerprintMols, DbFpSupplier, DataStructs


Variables Details [hide private]

_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
...