msk.drugbank4.DrugBankParser.java Source code

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Here is the source code for msk.drugbank4.DrugBankParser.java

Source

// Copyright 2015 mkutmon
//
//   Licensed under the Apache License, Version 2.0 (the "License");
//   you may not use this file except in compliance with the License.
//   You may obtain a copy of the License at
//
//       http://www.apache.org/licenses/LICENSE-2.0
//
//   Unless required by applicable law or agreed to in writing, software
//   distributed under the License is distributed on an "AS IS" BASIS,
//   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
//   See the License for the specific language governing permissions and
//   limitations under the License.

package msk.drugbank4;

import java.io.File;
import java.io.IOException;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.jdom2.Namespace;
import org.jdom2.input.SAXBuilder;

/**
 * Download XML file from Drugbank (http://www.drugbank.ca/downloads)
 * Version 4
 * for version 4.1 at least 2g memory required
 * 
 * @author msk
 *
 */
public class DrugBankParser {

    private Namespace nsDrugBank;

    public DrugBankParser() {
        nsDrugBank = Namespace.getNamespace("http://www.drugbank.ca");
    }

    /**
     * return a set of drugs
     * DrugModel contains also the list of targets
     */
    public Set<DrugModel> parse(File drugBankXml) throws JDOMException, IOException {
        SAXBuilder builder = new SAXBuilder();

        Document document = (Document) builder.build(drugBankXml);
        Element rootNode = document.getRootElement();

        Set<DrugModel> drugs = new HashSet<DrugModel>();

        List<Element> list = rootNode.getChildren("drug", nsDrugBank);
        for (Element drug : list) {
            DrugModel model = new DrugModel();

            Element id = drug.getChild("drugbank-id", nsDrugBank);
            model.setDrugbankID(id.getValue());

            Element name = drug.getChild("name", nsDrugBank);
            model.setName(name.getValue());

            Element cas = drug.getChild("cas-number", nsDrugBank);
            model.setCasNumber(cas.getValue());

            model.setInChiKey(getInchiKey(drug));
            model.getGroups().addAll(getGroups(drug));
            model.getCategories().addAll(getCategories(drug));
            model.getTargets().addAll(getTargets(drug));

            drugs.add(model);
        }

        return drugs;
    }

    /**
     * reads targets for current drug
     */
    private Set<TargetModel> getTargets(Element drug) {
        Set<TargetModel> set = new HashSet<TargetModel>();
        Element targets = drug.getChild("targets", nsDrugBank);
        if (targets != null) {
            List<Element> targetList = targets.getChildren("target", nsDrugBank);
            for (Element target : targetList) {
                TargetModel targetModel = new TargetModel();

                Element targetId = target.getChild("id", nsDrugBank);
                targetModel.setDrugbankId(targetId.getValue());

                Element targetName = target.getChild("name", nsDrugBank);
                targetModel.setName(targetName.getValue());

                Element targetOrganism = target.getChild("organism", nsDrugBank);
                targetModel.setOrganism(targetOrganism.getValue());

                Element polypeptide = target.getChild("polypeptide", nsDrugBank);
                if (polypeptide != null) {
                    Element polypeptideGeneName = polypeptide.getChild("gene-name", nsDrugBank);
                    targetModel.setGeneName(polypeptideGeneName.getValue());

                    Element xrefs = polypeptide.getChild("external-identifiers", nsDrugBank);
                    List<Element> xrefList = xrefs.getChildren("external-identifier", nsDrugBank);
                    for (Element xref : xrefList) {
                        Element res = xref.getChild("resource", nsDrugBank);
                        if (res.getValue().equals("UniProtKB")) {
                            Element uniprot = xref.getChild("identifier", nsDrugBank);
                            targetModel.setUniprotId(uniprot.getValue());
                        }
                    }
                }
                set.add(targetModel);
            }
        }
        return set;
    }

    /**
     * reads categories for current drug
     */
    private Set<String> getCategories(Element drug) {
        Set<String> set = new HashSet<String>();
        Element categories = drug.getChild("categories", nsDrugBank);
        if (categories != null) {
            List<Element> categoryList = categories.getChildren("category", nsDrugBank);
            for (Element category : categoryList) {
                Element cat = category.getChild("category", nsDrugBank);
                set.add(cat.getValue());
            }
        }
        return set;
    }

    /**
     * reads groups for current drug
     */
    private Set<String> getGroups(Element drug) {
        Set<String> set = new HashSet<String>();
        Element groups = drug.getChild("groups", nsDrugBank);
        if (groups != null) {
            List<Element> groupList = groups.getChildren("group", nsDrugBank);
            for (Element group : groupList) {
                set.add(group.getValue());
            }
        }
        return set;
    }

    /**
     * reads inchikey for current drug
     */
    private String getInchiKey(Element drug) {
        Element props = drug.getChild("calculated-properties", nsDrugBank);
        if (props != null) {
            List<Element> typeList = props.getChildren("property", nsDrugBank);
            for (Element type : typeList) {
                Element kind = type.getChild("kind", nsDrugBank);
                if (kind.getValue().equals("InChIKey")) {
                    Element value = type.getChild("value", nsDrugBank);
                    return value.getValue().substring(9);

                }
            }
        }
        return "";
    }
}