Hi Gauri, Which fingerprinter are you using?
J On 22 May 2013, at 13:45, Gauri S <[email protected]> wrote: > > I have used SmilesParser to parse through the smile and generate the > fingerprint , it prints > fingerprints of query:{0, 1, 17, 87, 95, 142, 168, 273, 274, 294, 299, 300, > 301, 306} > > when i used sdf file of same molecule and generated fingerprint , it prints > bitsetarray: [{17, 87, 95, 142, 273, 274, 294, 301, 306}] > > even if it same molecule , still it does not consider 0,1,168,299,300 bits > > So, can anyone please tell me why is this difference and which method is > suitable to get the results properly? > > this is my small part of the code > > ArrayList<IMolecule> molList= new ArrayList< IMolecule >(); > ArrayList<BitSet> bitsetarray= new ArrayList< BitSet >(); > ArrayList<BitSet> bitsetarray1= new ArrayList< BitSet >(); > ArrayList<String> molidarray= new ArrayList< String >(); > ArrayList<String> molidarray1= new ArrayList< String >(); > //ArrayList<String> molidarray2= new ArrayList< String >(); > IMolecule molecule = null; > String query = > "CC1=C(C)C2=C(CCC(C)(COC3=CC=C(CC4SC(=O)NC4=O)C=C3)O2)C(C)=C1O"; > SmilesParser sp = new > SmilesParser(DefaultChemObjectBuilder.getInstance()); > > IAtomContainer mol1 = sp.parseSmiles(query); > mol1 = new AtomContainer(mol1); > BitSet fingerprint1 = fprinter.getFingerprint(mol1); > System.out.println("fingerprints of query:"+fingerprint1); > > > File sdfFile = new File("D:/gauri/cdk/Vasodilator/DB00197.sdf"); > > IteratingMDLReader reader = new IteratingMDLReader( > new FileInputStream(sdfFile), > DefaultIChemObjectBuilder.getInstance()); > > System.out.println("Reading the file..."); > while (reader.hasNext()) { > molecule = (IMolecule)reader.next(); > molList.add(molecule); > fingerprint = fprinter.getFingerprint(molecule); > // fprinter.getSize(); // returns 881 > //fingerprint.length(); // returns the highest set bit > bitsetarray.add(fingerprint); > > > molidarray.add(molecule.getProperty("DRUGBANK_ID").toString()); > // > molidarray2.add(molecule.getProperty("SMILES").toString()); > > } > -- > View this message in context: > http://old.nabble.com/fingerprints-generated-differently-for-same-molecules-using-different-methods---smileparser-and-reading-the-sdf-file-using-IteratingMDLReader-tp35424370p35424370.html > Sent from the cdk-user mailing list archive at Nabble.com. > > > ------------------------------------------------------------------------------ > Try New Relic Now & We'll Send You this Cool Shirt > New Relic is the only SaaS-based application performance monitoring service > that delivers powerful full stack analytics. Optimize and monitor your > browser, app, & servers with just a few lines of code. Try New Relic > and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user ------------------------------------------------------------------------------ Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_may _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
