org.opencb.cellbase.lib.builders.DrugParser Maven / Gradle / Ivy
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/*
* Copyright 2015-2020 OpenCB
*
* 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 org.opencb.cellbase.lib.builders;
import org.opencb.cellbase.core.serializer.CellBaseSerializer;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.nio.file.Path;
//import org.opencb.commons.bioformats.drug.drugbank.DrugbankParser;
//import org.opencb.commons.bioformats.drug.drugbank.v201312jaxb.*;
//import drugbank.drugbank.*;
//import drugbank.drugbank.DrugPartnerInteraction;
//import drugbank.xjc20131209.*;
/**
* Created with IntelliJ IDEA.
* User: mbleda
* Date: 12/9/13
* Time: 4:43 PM
* To change this template use File | Settings | File Templates.
*/
@Deprecated
public class DrugParser {
private final Path drugbankPath;
protected Logger logger = LoggerFactory.getLogger(this.getClass());
public DrugParser(Path drugbankPath, CellBaseSerializer serializer) {
// super(serializer);
this.drugbankPath = drugbankPath;
}
// public void parse() throws JAXBException, IOException {
//
//// System.out.println("Number of drugs: "+ drugs.getDrug().size());
//// System.out.println("Number of partners: "+ drugs.getPartners().getPartner().size());
//
// DrugbankParser dxp = new DrugbankParser();
// Drugs drugs = (Drugs) dxp.loadXMLInfo(drugbankPath.toString());
//
// /**
// * Store all Partner Uniprot ID into a Map to speed up searching
// * Partner ID --> Uniprot ID
// */
// Map partnersMap = new HashMap<>(20000);
// for (PartnerType partner: drugs.getPartners().getPartner()){
// partnersMap.put(partner.getId(), partner);
// }
//
//// BufferedWriter bw = Files.newBufferedWriter(drugbankPath, Charset.defaultCharset());
//
// // Setting drug paramenters
// //=================================================
// for (DrugType dt : drugs.getDrug()){
// Drug drug = new Drug();
// List xRefList = new ArrayList<>();
//
// // ID
// drug.setId(dt.getDrugbankId());
//
// // Name
// drug.setName(dt.getName());
//
// // Type
// drug.setType(dt.getType());
//
// // ATC codes
// drug.setAtcCode(dt.getAtcCodes().getAtcCode());
// for (String atc : dt.getAtcCodes().getAtcCode()){
// xRefList.add(new XRef(atc, "ATC"));
// }
//
// // Indication
// drug.setIndication(dt.getIndication());
//
// // Pharmacology
// drug.setPharmacology(dt.getPharmacology());
//
// // Mechanism of action
// drug.setMechanismOfAction(dt.getMechanismOfAction());
//
// // Toxicity
// drug.setToxicity(dt.getToxicity());
//
// // Route of elimination
// drug.setRouteOfElimination(dt.getRouteOfElimination());
//
// // Volume of distribution
// drug.setVolumeOfDistribution(dt.getVolumeOfDistribution());
//
// // Half life
// drug.setHalfLife(dt.getHalfLife());
//
// // Clearance
// drug.setClearance(dt.getClearance());
//
// // Category
// drug.setCategory(dt.getCategories().getCategory());
//
// // Groups
// drug.setGroup(dt.getGroups().getGroup());
//
// // Description
// drug.setDescription(dt.getDescription());
//
// // Absorption
// drug.setAbsorption(dt.getAbsorption());
//
// // Food interactions
// List foodInteractionList = new ArrayList<>();
// for (String food : dt.getFoodInteractions().getFoodInteraction()){
// Interactor interactor = new Interactor(food);
// foodInteractionList.add(interactor);
// }
// drug.setFoodInteractor(foodInteractionList);
//
// // Drug interactions
// List drugInteractorList = new ArrayList<>();
// for (DrugInteraction drugInt : dt.getDrugInteractions().getDrugInteraction()){
// Interactor drugInterator = new Interactor(drugInt.getName(), drugInt.getDrug(), drugInt.getDescription());
// drugInteractorList.add(drugInterator);
// }
// drug.setDrugInteractor(drugInteractorList);
//
// // Xrefs
// xRefList.add(new XRef(dt.getDrugbankId(), "Drugbank"));
//
// xRefList.add(new XRef(dt.getName(), "name"));
//
// for ( String sa : dt.getSecondaryAccessionNumbers().getSecondaryAccessionNumber()){
// xRefList.add(new XRef(sa, "Drugbank Secondary Accession"));
// }
//
// for ( String synonym : dt.getSynonyms().getSynonym()){
// xRefList.add(new XRef(synonym, "Synonym"));
// }
//
// for (IdentifiersType.ExternalIdentifier xr : dt.getExternalIdentifiers().getExternalIdentifier()){
// xRefList.add(new XRef(xr.getIdentifier(), xr.getResource()));
// }
//
// for (String xr : dt.getAhfsCodes().getAhfsCode()){
// xRefList.add(new XRef(xr, "AHFS"));
// }
//
// xRefList.add(new XRef(dt.getCasNumber(), "CAS number"));
//
// for (String brand : dt.getBrands().getBrand()){
// xRefList.add(new XRef(brand, "Brand"));
// }
//
// for (Manufacturer manufacturer : dt.getManufacturers().getManufacturer()){
// xRefList.add(new XRef(manufacturer.getValue(), "Manufacturer"));
// }
// drug.setXrefs(xRefList);
//
//
// // Setting protein targets
// //=================================================
// for (TargetBondType target : dt.getTargets().getTarget()){
// Partner targetPartner = new Partner();
// PartnerType partner = partnersMap.get(target.getPartner());
// List targetXref = new ArrayList<>();
//
// targetPartner.setName(partner.getName());
// targetXref.add(new XRef(partner.getName(), "Name"));
//
// targetPartner.setGeneralFunction(partner.getGeneralFunction());
// targetPartner.setSpecificFunction(partner.getSpecificFunction());
// targetPartner.setCellularLocation(partner.getCellularLocation());
// targetPartner.setEssentiality(partner.getEssentiality());
// targetPartner.setReferences(partner.getReferences());
// if (partner.getProteinSequence() != null){
// targetPartner.setSequence(partner.getProteinSequence().getChain());
// }
//
// targetXref.add(new XRef(partner.getGeneName(), "Gene name"));
// for (IdentifiersType.ExternalIdentifier txr : partner.getExternalIdentifiers().getExternalIdentifier()){
// targetXref.add(new XRef(txr.getIdentifier(), txr.getResource()));
// if (txr.getResource().equals("UniProtKB")){
// targetPartner.setId(txr.getIdentifier());
// }
// }
// for (String txr : partner.getSynonyms().getSynonym()){
// targetXref.add(new XRef(txr, "Synonym"));
// }
// for (Pfam pfam : partner.getPfams().getPfam()){
// targetXref.add(new XRef(pfam.getIdentifier(), "Pfam", pfam.getName()));
// }
// for (GoClassifier go : partner.getGoClassifiers().getGoClassifier()){
// targetXref.add(new XRef(go.getDescription(), "GO", go.getDescription()));
// }
// targetPartner.setXrefs(targetXref);
//
//
// // Create drug-target protein interaction
// //=================================================
// DrugPartnerInteraction di = new DrugPartnerInteraction();
// di.setDrug(drug);
// di.setPartner(targetPartner);
// di.setKnownAction(target.getKnownAction());
// di.setAction(target.getActions().getAction());
// di.setType("target");
//
// // Add interaction
// //==================================================
// serializer.serialize(di);
//// bw.write(jsonMapper.writeValueAsString(di));
//// bw.write("\n");
//// drugInteractions.add(di);
// }
//
// // Setting protein enzymes
// //=================================================
// for (BondType enzyme : dt.getEnzymes().getEnzyme()){
// Partner enzymePartner = new Partner();
// PartnerType partner = partnersMap.get(enzyme.getPartner());
// List enzymeXref = new ArrayList<>();
//
// enzymePartner.setName(partner.getName());
// enzymeXref.add(new XRef(partner.getName(), "Name"));
//
// enzymePartner.setGeneralFunction(partner.getGeneralFunction());
// enzymePartner.setSpecificFunction(partner.getSpecificFunction());
// enzymePartner.setCellularLocation(partner.getCellularLocation());
// enzymePartner.setEssentiality(partner.getEssentiality());
// if (partner.getProteinSequence() != null){
// enzymePartner.setSequence(partner.getProteinSequence().getChain());
// }
// enzymePartner.setReferences(partner.getReferences());
//
// enzymeXref.add(new XRef(partner.getGeneName(), "Gene name"));
// for (IdentifiersType.ExternalIdentifier txr : partner.getExternalIdentifiers().getExternalIdentifier()){
// enzymeXref.add(new XRef(txr.getIdentifier(), txr.getResource()));
// if (txr.getResource().equals("UniProtKB")){
// enzymePartner.setId(txr.getIdentifier());
// }
// }
// for (String txr : partner.getSynonyms().getSynonym()){
// enzymeXref.add(new XRef(txr, "Synonym"));
// }
// for (Pfam pfam : partner.getPfams().getPfam()){
// enzymeXref.add(new XRef(pfam.getIdentifier(), "Pfam", pfam.getName()));
// }
// for (GoClassifier go : partner.getGoClassifiers().getGoClassifier()){
// enzymeXref.add(new XRef(go.getDescription(), "GO", go.getDescription()));
// }
// enzymePartner.setXrefs(enzymeXref);
//
//
// // Create drug-target protein interaction
// //=================================================
// DrugPartnerInteraction di = new DrugPartnerInteraction();
// di.setDrug(drug);
// di.setPartner(enzymePartner);
// di.setAction(enzyme.getActions().getAction());
// di.setType("enzyme");
//
// // Add interaction
// //==================================================
// serializer.serialize(di);
//// bw.write(jsonMapper.writeValueAsString(di));
//// bw.write("\n");
//// drugInteractions.add(di);
// }
//
// // Setting protein transporter
// //=================================================
// for (BondType transporter : dt.getTransporters().getTransporter()){
// Partner transporterPartner = new Partner();
// PartnerType partner = partnersMap.get(transporter.getPartner());
// List transporterXref = new ArrayList<>();
//
// transporterPartner.setName(partner.getName());
// transporterXref.add(new XRef(partner.getName(), "Name"));
//
// transporterPartner.setGeneralFunction(partner.getGeneralFunction());
// transporterPartner.setSpecificFunction(partner.getSpecificFunction());
// transporterPartner.setCellularLocation(partner.getCellularLocation());
// transporterPartner.setEssentiality(partner.getEssentiality());
// if (partner.getProteinSequence() != null){
// transporterPartner.setSequence(partner.getProteinSequence().getChain());
// }
// if (partner.getReferences() != null){
// transporterPartner.setReferences(partner.getReferences());
// }
//
// transporterXref.add(new XRef(partner.getGeneName(), "Gene name"));
// for (IdentifiersType.ExternalIdentifier txr : partner.getExternalIdentifiers().getExternalIdentifier()){
// transporterXref.add(new XRef(txr.getIdentifier(), txr.getResource()));
// if (txr.getResource().equals("UniProtKB")){
// transporterPartner.setId(txr.getIdentifier());
// }
// }
// for (String txr : partner.getSynonyms().getSynonym()){
// transporterXref.add(new XRef(txr, "Synonym"));
// }
// for (Pfam pfam : partner.getPfams().getPfam()){
// transporterXref.add(new XRef(pfam.getIdentifier(), "Pfam", pfam.getName()));
// }
// for (GoClassifier go : partner.getGoClassifiers().getGoClassifier()){
// transporterXref.add(new XRef(go.getDescription(), "GO", go.getDescription()));
// }
// transporterPartner.setXrefs(transporterXref);
//
//
// // Create drug-target protein interaction
// //=================================================
// DrugPartnerInteraction di = new DrugPartnerInteraction();
// di.setDrug(drug);
// di.setPartner(transporterPartner);
// di.setAction(transporter.getActions().getAction());
// di.setType("transporter");
//
// // Add interaction
// //==================================================
// serializer.serialize(di);
//// bw.write(jsonMapper.writeValueAsString(di));
//// bw.write("\n");
//// drugInteractions.add(di);
// }
//
// // Setting protein targets
// //=================================================
// for (BondType carrier : dt.getCarriers().getCarrier()){
// Partner carrierPartner = new Partner();
// PartnerType partner = partnersMap.get(carrier.getPartner());
// List carrierXref = new ArrayList<>();
//
// carrierPartner.setName(partner.getName());
// carrierXref.add(new XRef(partner.getName(), "Name"));
//
// carrierPartner.setGeneralFunction(partner.getGeneralFunction());
// carrierPartner.setSpecificFunction(partner.getSpecificFunction());
// carrierPartner.setCellularLocation(partner.getCellularLocation());
// carrierPartner.setEssentiality(partner.getEssentiality());
// carrierPartner.setSequence(partner.getProteinSequence().getChain());
// carrierPartner.setReferences(partner.getReferences());
//
// carrierXref.add(new XRef(partner.getGeneName(), "Gene name"));
// for (IdentifiersType.ExternalIdentifier txr : partner.getExternalIdentifiers().getExternalIdentifier()){
// carrierXref.add(new XRef(txr.getIdentifier(), txr.getResource()));
// if (txr.getResource().equals("UniProtKB")){
// carrierPartner.setId(txr.getIdentifier());
// }
// }
// for (String txr : partner.getSynonyms().getSynonym()){
// carrierXref.add(new XRef(txr, "Synonym"));
// }
// for (Pfam pfam : partner.getPfams().getPfam()){
// carrierXref.add(new XRef(pfam.getIdentifier(), "Pfam", pfam.getName()));
// }
// for (GoClassifier go : partner.getGoClassifiers().getGoClassifier()){
// carrierXref.add(new XRef(go.getDescription(), "GO", go.getDescription()));
// }
// carrierPartner.setXrefs(carrierXref);
//
//
// // Create drug-target protein interaction
// //=================================================
// DrugPartnerInteraction di = new DrugPartnerInteraction();
// di.setDrug(drug);
// di.setPartner(carrierPartner);
// di.setAction(carrier.getActions().getAction());
// di.setType("target");
//
// // Add interaction
// //==================================================
// serializer.serialize(di);
//// bw.write(jsonMapper.writeValueAsString(di));
//// bw.write("\n");
//// drugInteractions.add(di);
// }
// }
//// bw.close();
//
// }
}
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