No problem, Did you see the resolution? You need to add the implicit hydrogens, otherwise the matching isn't done correctly.
Thanks, J On 27 May 2013, at 08:31, Gauri S <[email protected]> wrote: > > 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 ------------------------------------------------------------------------------ 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
