/
Convertor.java
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/
Convertor.java
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/* Copyright (C) 2009 Egon Willighagen <egonw@users.sf.net>
*
* Contact: jchempaint-devel@lists.sourceforge.net
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
* All we ask is that proper credit is given for our work, which includes
* - but is not limited to - adding the above copyright notice to the beginning
* of your source code files, and to any copyright notice that you may distribute
* with programs based on this work.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*/
package org.openscience.cdk.libio.jena;
import java.util.HashMap;
import java.util.Map;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IElement;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IAtomType.Hybridization;
import org.openscience.cdk.interfaces.IBond.Order;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.ResIterator;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.vocabulary.RDF;
/**
* Helper class that converts a CDK {@link IChemObject} into RDF using a
* Jena model and the CDK data model ontology.
*
* @cdk.module iordf
* @cdk.githash
* @cdk.keyword Resource Description Framework
* @cdk.keyword Jena
* @cdk.keyword RDF
* @cdk.keyword Web Ontology Language
* @cdk.keyword OWL
*/
public class Convertor {
public static Model molecule2Model(IMolecule molecule) {
Model model = createCDKModel();
Resource subject = model.createResource(
createIdentifier(model, molecule)
);
model.add(subject, RDF.type, CDK.Molecule);
Map<IAtom,Resource> cdkToRDFAtomMap = new HashMap<IAtom, Resource>();
for (IAtom atom : molecule.atoms()) {
Resource rdfAtom = model.createResource(
createIdentifier(model, atom)
);
cdkToRDFAtomMap.put(atom, rdfAtom);
model.add(rdfAtom, RDF.type, CDK.Atom);
model.add(rdfAtom, CDK.symbol, atom.getSymbol());
model.add(subject, CDK.hasAtom, rdfAtom);
serializeAtomTypeFields(model, rdfAtom, atom);
}
for (IBond bond : molecule.bonds()) {
Resource rdfBond = model.createResource(
createIdentifier(model, bond)
);
model.add(rdfBond, RDF.type, CDK.Bond);
for (IAtom atom : bond.atoms()) {
model.add(rdfBond, CDK.bindsAtom, cdkToRDFAtomMap.get(atom));
}
if (bond.getOrder() == IBond.Order.SINGLE) {
model.add(rdfBond, CDK.hasOrder, CDK.SingleBond);
} else if (bond.getOrder() == IBond.Order.DOUBLE) {
model.add(rdfBond, CDK.hasOrder, CDK.DoubleBond);
} else if (bond.getOrder() == IBond.Order.TRIPLE) {
model.add(rdfBond, CDK.hasOrder, CDK.TripleBond);
} else if (bond.getOrder() == IBond.Order.QUADRUPLE) {
model.add(rdfBond, CDK.hasOrder, CDK.QuadrupleBond);
}
model.add(subject, CDK.hasBond, rdfBond);
}
return model;
}
private static void serializeChemObjectFields(Model model,
Resource rdfObject, IChemObject object) {
if (object.getID() != null)
model.add(rdfObject, CDK.identfier, object.getID());
}
private static void deserializeChemObjectFields(
Resource rdfObject, IChemObject object) {
Statement id = rdfObject.getProperty(CDK.identfier);
if (id != null) object.setID(id.getString());
}
private static void serializeElementFields(Model model,
Resource rdfObject, IElement element) {
serializeChemObjectFields(model, rdfObject, element);
if (element.getSymbol() != null)
model.add(rdfObject, CDK.symbol, element.getSymbol());
if (element.getAtomicNumber() != null)
model.add(rdfObject, CDK.hasAtomicNumber,
element.getAtomicNumber().toString());
}
private static void deserializeElementFields(
Resource rdfObject, IElement element) {
deserializeChemObjectFields(rdfObject, element);
Statement symbol = rdfObject.getProperty(CDK.symbol);
if (symbol != null) element.setSymbol(symbol.getString());
Statement atomicNumber = rdfObject.getProperty(CDK.hasAtomicNumber);
if (atomicNumber != null)
element.setAtomicNumber(atomicNumber.getInt());
}
private static void serializeAtomTypeFields(Model model,
Resource rdfObject, IAtomType type) {
serializeElementFields(model, rdfObject, type);
if (type.getHybridization() != null) {
Hybridization hybrid = type.getHybridization();
if (hybrid == Hybridization.S) {
model.add(rdfObject, CDK.hasHybridization, CDK.S);
} else if (hybrid == Hybridization.SP1) {
model.add(rdfObject, CDK.hasHybridization, CDK.SP1);
} else if (hybrid == Hybridization.SP2) {
model.add(rdfObject, CDK.hasHybridization, CDK.SP2);
} else if (hybrid == Hybridization.SP3) {
model.add(rdfObject, CDK.hasHybridization, CDK.SP3);
} else if (hybrid == Hybridization.PLANAR3) {
model.add(rdfObject, CDK.hasHybridization, CDK.PLANAR3);
} else if (hybrid == Hybridization.SP3D1) {
model.add(rdfObject, CDK.hasHybridization, CDK.SP3D1);
} else if (hybrid == Hybridization.SP3D2) {
model.add(rdfObject, CDK.hasHybridization, CDK.SP3D2);
} else if (hybrid == Hybridization.SP3D3) {
model.add(rdfObject, CDK.hasHybridization, CDK.SP3D3);
} else if (hybrid == Hybridization.SP3D4) {
model.add(rdfObject, CDK.hasHybridization, CDK.SP3D4);
} else if (hybrid == Hybridization.SP3D5) {
model.add(rdfObject, CDK.hasHybridization, CDK.SP3D5);
}
}
if (type.getAtomTypeName() != null) {
model.add(rdfObject, CDK.hasAtomTypeName, type.getAtomTypeName());
}
if (type.getMaxBondOrder() != null) {
model.add(
rdfObject, CDK.hasMaxBondOrder,
order2Resource(type.getMaxBondOrder())
);
}
}
private static void deserializeAtomTypeFields(
Resource rdfObject, IAtomType element) {
deserializeElementFields(rdfObject, element);
Statement hybrid = rdfObject.getProperty(CDK.hasHybridization);
if (hybrid != null) {
Resource rdfHybrid = (Resource)hybrid.getObject();
if (rdfHybrid.equals(CDK.S)) {
element.setHybridization(Hybridization.S);
} else if (rdfHybrid.equals(CDK.SP1)) {
element.setHybridization(Hybridization.SP1);
} else if (rdfHybrid.equals(CDK.SP2)) {
element.setHybridization(Hybridization.SP2);
} else if (rdfHybrid.equals(CDK.SP3)) {
element.setHybridization(Hybridization.SP3);
} else if (rdfHybrid.equals(CDK.PLANAR3)) {
element.setHybridization(Hybridization.PLANAR3);
} else if (rdfHybrid.equals(CDK.SP3D1)) {
element.setHybridization(Hybridization.SP3D1);
} else if (rdfHybrid.equals(CDK.SP3D2)) {
element.setHybridization(Hybridization.SP3D2);
} else if (rdfHybrid.equals(CDK.SP3D3)) {
element.setHybridization(Hybridization.SP3D3);
} else if (rdfHybrid.equals(CDK.SP3D4)) {
element.setHybridization(Hybridization.SP3D4);
} else if (rdfHybrid.equals(CDK.SP3D5)) {
element.setHybridization(Hybridization.SP3D5);
}
}
Statement name = rdfObject.getProperty(CDK.hasAtomTypeName);
if (name != null) {
element.setAtomTypeName(name.getString());
}
Statement order = rdfObject.getProperty(CDK.hasMaxBondOrder);
if (order != null) {
Resource maxOrder = (Resource)order.getResource();
element.setMaxBondOrder(resource2Order(maxOrder));
}
}
public static Order resource2Order(Resource rdfOrder) {
if (rdfOrder.equals(CDK.SingleBond)) {
return Order.SINGLE;
} else if (rdfOrder.equals(CDK.DoubleBond)) {
return Order.DOUBLE;
} else if (rdfOrder.equals(CDK.TripleBond)) {
return Order.TRIPLE;
} else if (rdfOrder.equals(CDK.QuadrupleBond)) {
return Order.QUADRUPLE;
}
return null;
}
public static Resource order2Resource(Order order) {
if (order == Order.SINGLE) {
return CDK.SingleBond;
} else if (order == Order.DOUBLE) {
return CDK.DoubleBond;
} else if (order == Order.TRIPLE) {
return CDK.TripleBond;
} else if (order == Order.QUADRUPLE) {
return CDK.QuadrupleBond;
}
return null;
}
private static String createIdentifier(Model model, IChemObject object) {
StringBuilder result = new StringBuilder();
result.append("http://example.com/");
result.append(model.hashCode()).append('/');
result.append(object.getClass().getSimpleName()).append('/');
result.append(object.hashCode());
return result.toString();
}
public static IMolecule model2Molecule(Model model,
IChemObjectBuilder builder) {
ResIterator mols =
model.listSubjectsWithProperty(RDF.type, CDK.Molecule);
IMolecule mol = null;
if (mols.hasNext()) {
Resource rdfMol = mols.next();
mol = builder.newMolecule();
Map<Resource,IAtom> rdfToCDKAtomMap = new HashMap<Resource,IAtom>();
StmtIterator atoms = rdfMol.listProperties(CDK.hasAtom);
while (atoms.hasNext()) {
Resource rdfAtom = atoms.nextStatement().getResource();
IAtom atom = builder.newAtom();
rdfToCDKAtomMap.put(rdfAtom, atom);
Statement symbol = rdfAtom.getProperty(CDK.symbol);
if (symbol != null) atom.setSymbol(symbol.getString());
deserializeAtomTypeFields(rdfAtom, atom);
mol.addAtom(atom);
}
StmtIterator bonds = rdfMol.listProperties(CDK.hasBond);
while (bonds.hasNext()) {
Statement rdfBond = bonds.nextStatement();
IBond bond = builder.newBond();
StmtIterator bondAtoms = rdfBond.getResource()
.listProperties(CDK.bindsAtom);
int atomCounter = 0;
while (bondAtoms.hasNext()) {
Statement rdfAtom = bondAtoms.nextStatement();
IAtom atom = rdfToCDKAtomMap.get(rdfAtom.getResource());
bond.setAtom(atom, atomCounter);
atomCounter++;
}
Resource order = rdfBond.
getProperty(CDK.hasOrder).getResource();
if (order.equals(CDK.SingleBond)) {
bond.setOrder(IBond.Order.SINGLE);
} else if (order.equals(CDK.DoubleBond)) {
bond.setOrder(IBond.Order.DOUBLE);
} else if (order.equals(CDK.TripleBond)) {
bond.setOrder(IBond.Order.TRIPLE);
} else if (order.equals(CDK.QuadrupleBond)) {
bond.setOrder(IBond.Order.QUADRUPLE);
}
mol.addBond(bond);
}
}
return mol;
}
private static Model createCDKModel() {
Model model = ModelFactory.createOntologyModel();
model.setNsPrefix("cdk", "http://cdk.sourceforge.net/model.owl#");
return model;
}
}