Sir John , I'm using Substructure fingerprinter
John May-4 wrote: > > 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 > > -- 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-tp35424370p35556643.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
