The differences are most probably due to missing atom type and aromaticity
recognition. The SmilesParser does atom typing automatically, the MDL
reader does not, before running the fingerprinter you would need to
explicitly invoke the atom typing and aromaticity recognition.
Best regards,
Nina
On 22 May 2013 16:06, John May <[email protected]> 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.
> >
> >
> >
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