Thanks for the tip!
On Sun, Mar 28, 2021 at 8:41 PM John Mayfield <john.wilkinson...@gmail.com>
wrote:
> You should use the *CircularFingerprinter* for similarity.
>
> On Sun, 28 Mar 2021 at 08:39, Sub Jae Shin <cnb.mons...@gmail.com> wrote:
>
>> To John Mayfield
>>
>> Hi, I found the drugbank id property from AtomContainer's getproperties
>> method, so that I could specify which atom container indicates which drug.
>>
>> I think my goal to get drug-drug similarity has been achieved in my guess.
>>
>> package com.company;
>> import org.openscience.cdk.ChemFile;
>> import org.openscience.cdk.exception.CDKException;
>> import org.openscience.cdk.fingerprint.Fingerprinter;
>> import org.openscience.cdk.fingerprint.IBitFingerprint;
>> import org.openscience.cdk.fingerprint.IFingerprinter;
>> import org.openscience.cdk.graph.rebond.Bspt;
>> import org.openscience.cdk.interfaces.IAtomContainer;
>> import org.openscience.cdk.interfaces.IChemFile;
>> import org.openscience.cdk.io.MDLV2000Reader;
>> import org.openscience.cdk.similarity.Tanimoto;
>> import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
>>
>> import java.io.*;
>> import java.lang.reflect.Array;
>> import java.util.ArrayList;
>> import java.util.List;
>> import java.util.Map;
>>
>> public class Main {
>>
>> public static void main(String[] args) {
>> try {
>>
>> InputStream structures = new
>> FileInputStream("../data/drugbank/structures.sdf");
>> MDLV2000Reader reader = new MDLV2000Reader(structures);
>> IChemFile file = reader.read(new ChemFile());
>> //Where can I find drugbank id?
>>
>> Fingerprinter finger = new Fingerprinter();
>> List<IAtomContainer> AtomData =
>> ChemFileManipulator.getAllAtomContainers(file);
>> int count = AtomData.size();
>> ArrayList<ArrayList> df = new ArrayList<>();
>>
>> for(int i = 0; i < count; ++i) {
>> ArrayList<Object> list = new ArrayList<>();
>> IAtomContainer acReference = AtomData.get(i);
>> Map refProperties = acReference.getProperties();
>> list.add(refProperties.get("DATABASE_ID"));
>> for(int j = 0; j < count; ++j) {
>> IAtomContainer acStructure = AtomData.get(j);
>> Map structProperties = acStructure.getProperties();
>> System.out.println("REF DATABASE_ID : " +
>> refProperties.get("DATABASE_ID") +
>> "-" + "COMP DATABASE_ID" +
>> structProperties.get("DATABASE_ID") + " similarity is now calculating....");
>> double similarity = cdkCalculateTanimotoCoef(finger,
>> acReference, acStructure);
>> list.add(similarity);
>> }
>> df.add(list);
>> }
>> FileWriter result_csv = new
>> FileWriter("../data/drugbank/drug_drug_sim.csv");
>>
>> for(ArrayList a : df){
>> String row = "";
>> for(int i = 0; i < a.size(); ++i) {
>> if(i == a.size() - 1) {
>> row = row + a.get(i).toString() + "\n";
>> }
>> else {
>> row = row + a.get(i).toString() + ",";
>> }
>> }
>> // System.out.println(row);
>> result_csv.write(row);
>> }
>>
>> result_csv.close();
>>
>> //System.out.println(acReference.toString());
>>
>>
>> } catch (FileNotFoundException | CDKException e) {
>> System.out.println(e.getMessage());
>> } catch (IOException e) {
>> e.printStackTrace();
>> }
>> }
>>
>> public static double cdkCalculateTanimotoCoef(IFingerprinter
>> fingerprinter, IAtomContainer acReference, IAtomContainer acStructure ) {
>>
>> double ret = 0.0;
>>
>> try {
>>
>> IBitFingerprint fpReference =
>> fingerprinter.getBitFingerprint(acReference);
>>
>> //Tanimoto-score
>> IBitFingerprint fpStructure =
>> fingerprinter.getBitFingerprint(acStructure);
>> ret = Tanimoto.calculate(fpReference, fpStructure);
>>
>> } catch (Exception ex) {
>> //...
>> }
>>
>> return ret;
>> }
>> }
>>
>>
>> I hope this code result matches with my goal.
>>
>> I always thank you all, cdk developers.
>>
>> Sincerely
>> Seopjae Shin
>>
>>
>> On Fri, Mar 26, 2021 at 6:36 PM John Mayfield <
>> john.wilkinson...@gmail.com> wrote:
>>
>>> Do you have a mol2 file or a SMILES file? It's not clear. Mol2 support
>>> isn't great in the CDK mainly because it's more a compchem/modelling format
>>> than cheminformations which primarily use SMILES or MOLfile.
>>>
>>> Presume you know how to read line by line from a file here is an example
>>> from SMILES:
>>>
>>> IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
>>>> // load from SMILES and compute the ECFP (circular) fingerprint
>>>> IFingerprinter fpr = new CircularFingerprinter();
>>>> SmilesParser smipar = new SmilesParser(bldr);
>>>> List<String> smiles = Arrays.asList("Clc1ccccc1",
>>>> "Fc1ccccc1",
>>>> "Ic1ccccc1",
>>>> "Clc1ncccc1");
>>>> List<BitSet> fps = new ArrayList<>();
>>>> for (String smi : smiles) {
>>>> IAtomContainer mol = smipar.parseSmiles(smi);
>>>> fps.add(fpr.getBitFingerprint(mol).asBitSet());
>>>> }
>>>> // print N^2 comparison table
>>>> for (int j = 0; j < fps.size(); j++)
>>>> System.out.print("," + smiles.get(j));
>>>> System.out.print('\n');
>>>> for (int i = 0; i < fps.size(); i++) {
>>>> System.out.print(smiles.get(i));
>>>> for (int j = 0; j < fps.size(); j++) {
>>>> System.out.printf(",%.3f", Tanimoto.calculate(fps.get(i),
>>>> fps.get(j)));
>>>> }
>>>> System.out.print('\n');
>>>> }
>>>
>>>
>>> ,Clc1ccccc1,Fc1ccccc1,Ic1ccccc1,Clc1ncccc1
>>> Clc1ccccc1,1.000,0.368,0.368,0.292
>>> Fc1ccccc1,0.368,1.000,0.368,0.192
>>> Ic1ccccc1,0.368,0.368,1.000,0.192
>>> Clc1ncccc1,0.292,0.192,0.192,1.000
>>>
>>> There are a lot more optimal ways of doing it and for a large comparison
>>> table use ChemFP: https://chemfp.com/.
>>>
>>> On Wed, 24 Mar 2021 at 06:42, Stesycki, Manuel <
>>> stesy...@mpi-muelheim.mpg.de> wrote:
>>>
>>>> Good morning,
>>>>
>>>> Use this class for Tanimoto calucations:
>>>> org.openscience.cdk.similarity.Tanimoto (see doc:
>>>> http://cdk.github.io/cdk/latest/docs/api/index.html)
>>>>
>>>> you could do something like this to calculate your tanimoto score:
>>>>
>>>> public static double cdkCalculateTanimotoCoef(IFingerprinter
>>>> fingerprinter, IAtomContainer acReference, IAtomContainer acStructure ) {
>>>>
>>>> double ret = 0.0;
>>>>
>>>> try {
>>>>
>>>> IBitFingerprint fpReference =
>>>> fingerprinter.getBitFingerprint(acReference);
>>>>
>>>> //Tanimoto-score
>>>> IBitFingerprint fpStructure =
>>>> fingerprinter.getBitFingerprint(acStructure);
>>>> ret = Tanimoto.calculate(fpReference, fpStructure);
>>>>
>>>> } catch (Exception ex) {
>>>> //...
>>>> }
>>>>
>>>> return ret;
>>>> }
>>>>
>>>>
>>>>
>>>> Viele Grüße,
>>>> Manuel Stesycki
>>>>
>>>> IT
>>>> 0208 / 306-2146
>>>> Physikbau, Büro 117
>>>> stesy...@mpi-muelheim.mpg.de
>>>>
>>>> Max-Planck-Institut für Kohlenforschung
>>>> Kaiser-Wilhelm-Platz 1
>>>> D-45470 Mülheim an der Ruhr
>>>> http://www.kofo.mpg.de/de
>>>>
>>>> Am 24.03.2021 um 04:55 schrieb Sub Jae Shin <cnb.mons...@gmail.com>:
>>>>
>>>> To CDK developers.
>>>>
>>>> Hello, I'm trying to get drug-drug similarity by Tanimoto score.
>>>>
>>>> I'm a beginner of cdk and java, so I'm stuck in the process of changing
>>>> smiles file to Tanimoto score's calculate method's variable.
>>>>
>>>> package com.company;
>>>> import org.openscience.cdk.ChemFile;
>>>> import org.openscience.cdk.exception.CDKException;
>>>> import org.openscience.cdk.interfaces.IChemFile;
>>>> import org.openscience.cdk.io.SMILESReader;
>>>> import java.io.*;
>>>>
>>>> public class Main {
>>>>
>>>> public static void main(String[] args) {
>>>> try {
>>>>
>>>> InputStream mol2DataStream = new
>>>> FileInputStream("../data/drugbank/structure.smiles");
>>>> SMILESReader reader = new SMILESReader(mol2DataStream);
>>>> IChemFile file = reader.read(new ChemFile());
>>>>
>>>> } catch (FileNotFoundException | CDKException e) {
>>>> System.out.println(e.getMessage());
>>>> }
>>>> }
>>>> }
>>>>
>>>> Sincerely
>>>> Seopjae Shin.
>>>>
>>>>
>>>> _______________________________________________
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>>>> Cdk-user@lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>>>
>>>>
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>>>>
>>>
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