Yep you need to take the complement of the bits. If your working on the binary
it's the unary '~' operator on the BitSet it's the method named flip.
BitSet set = fingerprint.asBitSet(); // 1.5.x
set.flip();
J
On 6 Jun 2013, at 10:49, Gauri S <[email protected]> wrote:
>
> 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:
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> --
> View this message in context:
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> Sent from the cdk-user mailing list archive at Nabble.com.
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