MDK Apps Service

pom.xml

<dependency>
    <groupId>uk.ac.ebi.mdk</groupId>
    <artifactId>mdk-apps-service</artifactId>
    <version>1.3.2-SNAPSHOT</version>
</dependency>

ServiceDemo.java

package demo;

import org.openscience.cdk.interfaces.IAtomContainer;
import uk.ac.ebi.mdk.domain.identifier.HMDBIdentifier;
import uk.ac.ebi.mdk.service.DefaultServiceManager;
import uk.ac.ebi.mdk.service.ServiceManager;
import uk.ac.ebi.mdk.service.query.data.MolecularFormulaService;
import uk.ac.ebi.mdk.service.query.name.IUPACNameService;
import uk.ac.ebi.mdk.service.query.name.PreferredNameService;
import uk.ac.ebi.mdk.service.query.name.SynonymService;
import uk.ac.ebi.mdk.service.query.structure.StructureSearch;
import uk.ac.ebi.mdk.service.query.structure.StructureService;

import java.util.Collection;

public class ServiceDemo {


    public static void main(String[] args) {

        ServiceManager manager = DefaultServiceManager.getInstance();

        {
            System.out.println("-- Retrieve/Search Names --");
            IUPACNameService<HMDBIdentifier> service = manager.getService(HMDBIdentifier.class,
                                                                          IUPACNameService.class);
            System.out.println(service.searchIUPACName("some long and tedious name", Boolean.FALSE));
        }
        {
            SynonymService<HMDBIdentifier> service = manager.getService(HMDBIdentifier.class,
                                                                        SynonymService.class);
            System.out.println(service.searchSynonyms("ATP", Boolean.FALSE));

            MolecularFormulaService<HMDBIdentifier> formula = manager.getService(HMDBIdentifier.class,
                                                                                 MolecularFormulaService.class);

            System.out.println("-- Retrieve/Search Formula --");
            System.out.println("HMDB00538 formula " + formula.getMolecularFormula(new HMDBIdentifier("HMDB00538")));

        }
        {
            StructureService<HMDBIdentifier> service = manager.getService(HMDBIdentifier.class,
                                                                          StructureService.class);
            IAtomContainer container = service.getStructure(new HMDBIdentifier("HMDB00538"));
            System.out.println("-- Retrieve Structures --");
            System.out.println("Loaded container: " + container.getAtomCount() + " atoms");

            StructureSearch<HMDBIdentifier> search = manager.getService(HMDBIdentifier.class,
                                                                        StructureSearch.class);

            // custom service construction (service is declared at the bottom of this file)
            MultinameService names = manager.createService(HMDBIdentifier.class,
                                                           MultinameService.class);


            System.out.println("-- Search Structures --");
            search.setMaxResults(5); // limit our search
            Collection<HMDBIdentifier> similar = search.structureSearch(container, Boolean.FALSE);
            for (HMDBIdentifier identifier : similar) {
                System.out.println(identifier + "\t"
                                           + names.getPreferredName(identifier) + "\t"
                                           + names.getIUPACName(identifier));
            }


        }


    }


    static interface MultinameService
            extends PreferredNameService<HMDBIdentifier>,
                    IUPACNameService<HMDBIdentifier> {

    }

}

stdout.txt

-- Retrieve/Search Names --
[]
[HMDB03665, HMDB00538]
-- Retrieve/Search Formula --
HMDB00538 formula C10H16N5O13P3
-- Retrieve Structures --
Loaded container: 31 atoms
-- Search Structures --
ERROR uk.ac.ebi.mdk.service.query.structure.AbstractStructureQueryService - Approximate variable not used!
HMDB00538	Adenosine triphosphate	[[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxyphosphonic acid
HMDB01155	Diadenosine triphosphate	[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl hydrogen phosphate
HMDB01192	Diadenosine pentaphosphate	[[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl hydrogen phosphate
HMDB01211	Diadenosine tetraphosphate	[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-tetrahydrofuran-2-yl]methyl hydrogen phosphate
HMDB01282	Diadenosine hexaphosphate	[[[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl hydrogen phosphate