On 22 May 2013 16:29, John May <[email protected]> wrote:
> The aromaticity and atom types are automatically added before the
> fingerprint.
>
>
> https://github.com/johnmay/cdk/blob/master/src/main/org/openscience/cdk/fingerprint/Fingerprinter.java#L173
>
OK, I think it was not so in 1.4.x versions (at least the one I am still
using).
(and yes, hydrogens matter as well )
>
> This will likely be changed in future as the fingerprinter should not have
> this responsibility
>
Indeed, it may be redundant if already done.
> but I think the issue is more subtle.
>
Nina
>
> J
>
> On 22 May 2013, at 14:14, Nina Jeliazkova <[email protected]>
> wrote:
>
> 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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