Sir , can we find those bits which are missing,
eg suppose my molecule is giving me fingerprint like this
{0, 1, 2, 9, 10, 11, 12, 14, 18, 19, 20, 33, 143, 145, 146, 178, 182, 184,
185, 189, 192, 283, 284, 285, 286, 293, 299, 308, 332, 333, 337, 341, 344,
346, 349, 351, 352, 353, 355, 356, 366, 368, 370, 371, 374, 381, 382, 384,
390, 392, 393, 405, 406, 412, 416, 420, 430, 434, 439, 441, 443, 446, 451,
470, 476, 489, 490, 498, 507, 516, 520, 524, 535, 541, 542, 548, 552, 556,
564, 565, 567, 570, 573, 574, 578, 579, 582, 584, 586, 589, 590, 592, 594,
595, 599, 603, 604, 606, 608, 613, 614, 617, 618, 619, 620, 626, 632, 634,
637, 640, 641, 643, 645, 650, 651, 655, 660, 662, 664, 666, 667, 668, 677,
678, 679, 680, 681, 683, 684, 688, 689, 692, 696, 697, 698, 699, 704, 708,
709, 710, 712, 713, 714, 719, 734, 735, 755, 756, 776, 777, 782, 797, 798,
818, 819}
can i find the missing bits eg 3,4,5,6,7,8 ,,,,,, and so on ???
John May-4 wrote:
>
> 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.
>>>>
>>>>
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>> --
>> 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!
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>
>
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
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