Hi Woon Yee, The method is correct, you can emit them at hexadecimal and pad with 0.
John On Mon, 25 Jul 2022 at 10:11, Egon Willighagen <egon.willigha...@gmail.com> wrote: > > Dear Woon Yee, > > you can use the getFingerprint() method instead. > > Egon > > On Mon, 25 Jul 2022 at 10:59, #NG WOON YEE# via Cdk-user < > cdk-user@lists.sourceforge.net> wrote: > >> Dear Helpdesk, >> >> >> >> I was using CDK (version 2.7) to generate FCFP4 and 6 for the compound >> butyramide ( >> https://www.ebi.ac.uk/chembl/api/data/molecule/CHEMBL1231396.sdf) and >> ethanol (https://www.ebi.ac.uk/chembl/api/data/molecule/CHEMBL545.sdf) >> from their MolFiles which I got from CHEMBL. I was using the following >> commands in CDK: >> >> >> --------------------------------------------------------------------------------------------------------------- >> >> package ecfp; >> >> import java.io.*; >> >> import com.opencsv.CSVReader; >> >> import com.opencsv.CSVReaderBuilder; >> >> import com.opencsv.CSVWriter; >> >> import com.opencsv.exceptions.CsvException; >> >> import java.util.Arrays; >> >> import java.util.List; >> >> import java.io.FileInputStream; >> >> import java.io.IOException; >> >> >> >> import org.openscience.cdk.exception.CDKException; >> >> import org.openscience.cdk.fingerprint.CircularFingerprinter; >> >> import org.openscience.cdk.fingerprint.ExtendedFingerprinter; >> >> import org.openscience.cdk.fingerprint.ICountFingerprint; >> >> import org.openscience.cdk.interfaces.IAtomContainer; >> >> import org.openscience.cdk.interfaces.IChemObjectBuilder; >> >> import org.openscience.cdk.io.MDLV2000Reader; >> >> import org.openscience.cdk.silent.SilentChemObjectBuilder; >> >> >> >> public class main{ >> >> public static void main(String[] args) throws CDKException, >> IOException { >> >> String filename = >> "C:\\Users\\NGWO0001\\Downloads\\CHEMBL545.sdf.txt"; >> >> FileInputStream in = new FileInputStream(filename); >> >> MDLV2000Reader reader = new MDLV2000Reader(in); >> >> IChemObjectBuilder bldr = >> SilentChemObjectBuilder.getInstance(); >> >> IAtomContainer mol = reader.read(bldr.newAtomContainer()); >> >> >> >> CircularFingerprinter fingerprinter0 = new >> CircularFingerprinter( >> >> CircularFingerprinter.CLASS_FCFP4 >> >> ); >> >> >> >> >> >> System.out.println("FCFP4 Ethanol:"); >> >> ICountFingerprint result0 = >> fingerprinter0.getCountFingerprint(mol); >> >> for (int k=0, n = result0.numOfPopulatedbins(); k < n; ++k) >> { >> >> String ans4 = ""; >> >> ans4 += result0.getHash(k); >> >> ans4 += " " + result0.getCount(k); >> >> System.out.printf("%s\n",ans4); >> >> } >> >> >> >> reader.close(); >> >> } >> >> } >> >> >> --------------------------------------------------------------------------------------------------------------- >> >> >> >> The results I got were: >> >> >> >> FCFP4 Butyramide: >> >> -1393198889 1 >> >> -1212393386 1 >> >> -1131767167 2 >> >> 0 4 >> >> 2 1 >> >> 3 1 >> >> 425233353 1 >> >> 785469695 1 >> >> 824716024 1 >> >> 994111779 1 >> >> 1429107614 1 >> >> >> >> FCFP6 Butyramide: >> >> -1393198889 1 >> >> -1212393386 1 >> >> -1131767167 2 >> >> 0 4 >> >> 2 1 >> >> 3 1 >> >> 425233353 1 >> >> 785469695 1 >> >> 824716024 1 >> >> 994111779 1 >> >> 1429107614 1 >> >> >> >> FCFP4 Ethanol: >> >> -1212393386 1 >> >> 0 2 >> >> 3 1 >> >> 629394235 1 >> >> 824716024 1 >> >> >> >> FCFP6 Ethanol: >> >> -1212393386 1 >> >> 0 2 >> >> 3 1 >> >> 629394235 1 >> >> 824716024 1 >> >> >> I think these results may not be right since I thought that fingerprints >> are supposed to be a series of hash and so they ought to be a series of >> fixed-length integers. However, as you see in the results I got, for >> example, for the FCFP6 for ethanol, one is 10-digits long while others are >> single digits and 9-digits long. >> >> >> >> Can you please tell me what I am doing wrong? >> >> >> >> Thanking you in advance for your assistance and time. >> >> >> >> Best regards, >> >> Woon Yee >> _______________________________________________ >> Cdk-user mailing list >> Cdk-user@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/cdk-user >> > > > -- > ---- > Super happy with this new eLife paper describing an Open Science project > where we discuss 260 thousand natural products and where they came from, > all 700 thousand pairs linked to their primary literature: "The LOTUS > initiative for open knowledge management in natural products research", > https://doi.org/10.7554/elife.70780 > > ----- > E.L. Willighagen > Department of Bioinformatics - BiGCaT > Maastricht University (http://www.bigcat.unimaas.nl/) > Twitter/Mastodon: @egonwillighagen <https://twitter.com/egonwillighagen> > / @egonw <https://scholar.social/@egonw> > Homepage: http://egonw.github.io/ > Blog: http://chem-bla-ics.blogspot.com/ > PubList: https://www.zotero.org/egonw > ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286> > ImpactStory: https://impactstory.org/u/egonwillighagen > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user >
_______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
