Sir John , Actually i'm storing the bits from a substructure bit file into an arraylist and in another arraylist i'm storing the common bits of all sdf molecules ,, and then comparing to find out uncommon bits . i'm trying it using remove and retain methods in arraylist.
Sir, can you please tell how to get bits as 1 0 1 0 format instead of the bits as 0,1,2,3,4,,, and so on Thanks Gauri John May-4 wrote: > > 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. >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> 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. 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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 >>> >>> >> -- >> 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-tp35424370p35596445.html >> Sent from the cdk-user mailing list archive at Nabble.com. >> >> >> ------------------------------------------------------------------------------ >> How ServiceNow helps IT people transform IT departments: >> 1. A cloud service to automate IT design, transition and operations >> 2. Dashboards that offer high-level views of enterprise services >> 3. 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