/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2008 Egon Willighagen <egonw@users.sf.net>
* 2010 Brian Gilman <gilmanb@gmail.com>
*
* Contact: cdk-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.io.pubchemxml;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import javax.vecmath.Point2d;
import javax.vecmath.Point3d;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IElement;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.xmlpull.v1.XmlPullParser;
/**
* Helper class to parse PubChem XML documents.
*
* @cdk.module io
* @cdk.githash
*
* @author Egon Willighagen <egonw@users.sf.net>
* @cdk.created 2008-05-05
*/
public class PubChemXMLHelper {
private IChemObjectBuilder builder;
private IsotopeFactory factory;
/**
* @throws java.io.IOException if there is error in getting the {@link IsotopeFactory}
*/
public PubChemXMLHelper(IChemObjectBuilder builder) throws IOException {
this.builder = builder;
factory = IsotopeFactory.getInstance(builder);
}
// general elements
public final static String EL_PCCOMPOUND = "PC-Compound";
public final static String EL_PCCOMPOUNDS = "PC-Compounds";
public final static String EL_PCSUBSTANCE = "PC-Substance";
public final static String EL_PCSUBSTANCE_SID = "PC-Substance_sid";
public final static String EL_PCCOMPOUND_ID = "PC-Compound_id";
public final static String EL_PCCOMPOUND_CID = "PC-CompoundType_id_cid";
public final static String EL_PCID_ID = "PC-ID_id";
// atom block elements
public final static String EL_ATOMBLOCK = "PC-Atoms";
public final static String EL_ATOMSELEMENT = "PC-Atoms_element";
public final static String EL_ATOMSCHARGE = "PC-Atoms_charge";
public final static String EL_ATOMINT = "PC-AtomInt";
public final static String EL_ATOMINT_AID = "PC-AtomInt_aid";
public final static String EL_ATOMINT_VALUE = "PC-AtomInt_value";
public final static String EL_ELEMENT = "PC-Element";
// coordinate block elements
public final static String EL_COORDINATESBLOCK = "PC-Compound_coords";
public final static String EL_COORDINATES_AID = "PC-Coordinates_aid";
public final static String EL_COORDINATES_AIDE = "PC-Coordinates_aid_E";
public final static String EL_ATOM_CONFORMER = "PC-Conformer";
public final static String EL_ATOM_CONFORMER_X = "PC-Conformer_x";
public final static String EL_ATOM_CONFORMER_XE = "PC-Conformer_x_E";
public final static String EL_ATOM_CONFORMER_Y = "PC-Conformer_y";
public final static String EL_ATOM_CONFORMER_YE = "PC-Conformer_y_E";
public final static String EL_ATOM_CONFORMER_Z = "PC-Conformer_z";
public final static String EL_ATOM_CONFORMER_ZE = "PC-Conformer_z_E";
// bond block elements
public final static String EL_BONDBLOCK = "PC-Bonds";
public final static String EL_BONDID1 = "PC-Bonds_aid1";
public final static String EL_BONDID2 = "PC-Bonds_aid2";
public final static String EL_BONDORDER = "PC-Bonds_order";
// property block elements
public final static String EL_PROPSBLOCK = "PC-Compound_props";
public final static String EL_PROPS_INFODATA = "PC-InfoData";
public final static String EL_PROPS_URNLABEL = "PC-Urn_label";
public final static String EL_PROPS_URNNAME = "PC-Urn_name";
public final static String EL_PROPS_SVAL = "PC-InfoData_value_sval";
public final static String EL_PROPS_FVAL = "PC-InfoData_value_fval";
public final static String EL_PROPS_BVAL = "PC-InfoData_value_binary";
public IMoleculeSet parseCompoundsBlock(XmlPullParser parser) throws Exception {
IMoleculeSet set = builder.newMoleculeSet();
// assume the current element is PC-Compounds
if (!parser.getName().equals(EL_PCCOMPOUNDS)) {
return null;
}
while (parser.next() != XmlPullParser.END_DOCUMENT) {
if (parser.getEventType() == XmlPullParser.END_TAG) {
if (EL_PCCOMPOUNDS.equals(parser.getName())) {
break; // done parsing compounds block
}
} else if (parser.getEventType() == XmlPullParser.START_TAG) {
if (EL_PCCOMPOUND.equals(parser.getName())) {
IMolecule molecule = parseMolecule(parser, builder);
if (molecule.getAtomCount() > 0) {
// skip empty PC-Compound's
set.addMolecule(molecule);
}
}
}
}
return set;
}
public IChemModel parseSubstance(XmlPullParser parser) throws Exception {
IChemModel model = builder.newChemModel();
// assume the current element is PC-Compound
if (!parser.getName().equals("PC-Substance")) {
return null;
}
while (parser.next() != XmlPullParser.END_DOCUMENT) {
if (parser.getEventType() == XmlPullParser.END_TAG) {
if (EL_PCSUBSTANCE.equals(parser.getName())) {
break; // done parsing the molecule
}
} else if (parser.getEventType() == XmlPullParser.START_TAG) {
if (EL_PCCOMPOUNDS.equals(parser.getName())) {
IMoleculeSet set = parseCompoundsBlock(parser);
model.setMoleculeSet(set);
} else if (EL_PCSUBSTANCE_SID.equals(parser.getName())) {
String sid = getSID(parser);
model.setProperty(CDKConstants.TITLE, sid);
}
}
}
return model;
}
public String getSID(XmlPullParser parser) throws Exception {
String sid = "unknown";
while (parser.next() != XmlPullParser.END_DOCUMENT) {
if (parser.getEventType() == XmlPullParser.END_TAG) {
if (EL_PCSUBSTANCE_SID.equals(parser.getName())) {
break; // done parsing the atom block
}
} else if (parser.getEventType() == XmlPullParser.START_TAG) {
if (EL_PCID_ID.equals(parser.getName())) {
sid = parser.nextText();
}
}
}
return sid;
}
public String getCID(XmlPullParser parser) throws Exception {
String cid = "unknown";
while (parser.next() != XmlPullParser.END_DOCUMENT) {
if (parser.getEventType() == XmlPullParser.END_TAG) {
if (EL_PCCOMPOUND_ID.equals(parser.getName())) {
break; // done parsing the atom block
}
} else if (parser.getEventType() == XmlPullParser.START_TAG) {
if (EL_PCCOMPOUND_CID.equals(parser.getName())) {
cid = parser.nextText();
}
}
}
return cid;
}
public void parseAtomElements(XmlPullParser parser, IMolecule molecule) throws Exception {
while (parser.next() != XmlPullParser.END_DOCUMENT) {
if (parser.getEventType() == XmlPullParser.END_TAG) {
if (EL_ATOMSELEMENT.equals(parser.getName())) {
break; // done parsing the atom elements
}
} else if (parser.getEventType() == XmlPullParser.START_TAG) {
if (EL_ELEMENT.equals(parser.getName())) {
int atomicNumber = Integer.parseInt(parser.nextText());
IElement element = factory.getElement(atomicNumber);
if (element == null) {
IAtom atom = molecule.getBuilder().newPseudoAtom();
molecule.addAtom(atom);
} else {
IAtom atom = molecule.getBuilder().newAtom(element.getSymbol());
atom.setAtomicNumber(element.getAtomicNumber());
molecule.addAtom(atom);
}
}
}
}
}
public void parserAtomBlock(XmlPullParser parser, IMolecule molecule) throws Exception {
while (parser.next() != XmlPullParser.END_DOCUMENT) {
if (parser.getEventType() == XmlPullParser.END_TAG) {
if (EL_ATOMBLOCK.equals(parser.getName())) {
break; // done parsing the atom block
}
} else if (parser.getEventType() == XmlPullParser.START_TAG) {
if (EL_ATOMSELEMENT.equals(parser.getName())) {
parseAtomElements(parser, molecule);
} else if (EL_ATOMSCHARGE.equals(parser.getName())) {
parseAtomCharges(parser, molecule);
}
}
}
}
public void parserCompoundInfoData(XmlPullParser parser, IMolecule molecule) throws Exception {
String urn_label = null;
String urn_name = null;
String sval = null;
while (parser.next() != XmlPullParser.END_DOCUMENT) {
if (parser.getEventType() == XmlPullParser.END_TAG) {
if (EL_PROPS_INFODATA.equals(parser.getName())) {
break; // done parsing the atom block
}
} else if (parser.getEventType() == XmlPullParser.START_TAG) {
if (EL_PROPS_URNNAME.equals(parser.getName())) {
urn_name = parser.nextText();
} else if (EL_PROPS_URNLABEL.equals(parser.getName())) {
urn_label = parser.nextText();
} else if (EL_PROPS_SVAL.equals(parser.getName())) {
sval = parser.nextText();
} else if(EL_PROPS_FVAL.equals(parser.getName())){
sval = parser.nextText();
} else if(EL_PROPS_BVAL.equals(parser.getName())){
sval = parser.nextText();
}
}
}
if (urn_label != null & sval != null) {
String property = urn_label + (urn_name == null ? "" : " (" + urn_name + ")");
molecule.setProperty(property, sval);
}
}
public void parseAtomCharges(XmlPullParser parser, IMolecule molecule) throws Exception {
while (parser.next() != XmlPullParser.END_DOCUMENT) {
if (parser.getEventType() == XmlPullParser.END_TAG) {
if (EL_ATOMSCHARGE.equals(parser.getName())) {
break; // done parsing the molecule
}
} else if (parser.getEventType() == XmlPullParser.START_TAG) {
if (EL_ATOMINT.equals(parser.getName())) {
int aid = 0;
int charge = 0;
while (parser.next() != XmlPullParser.END_DOCUMENT) {
if (parser.getEventType() == XmlPullParser.END_TAG) {
if (EL_ATOMINT.equals(parser.getName())) {
molecule.getAtom(aid-1).setFormalCharge(charge);
break; // done parsing an atoms charge
}
} else if (parser.getEventType() == XmlPullParser.START_TAG) {
if (EL_ATOMINT_AID.equals(parser.getName())) {
aid = Integer.parseInt(parser.nextText());
} else if (EL_ATOMINT_VALUE.equals(parser.getName())) {
charge = Integer.parseInt(parser.nextText());
}
}
}
}
}
}
}
public IMolecule parseMolecule(XmlPullParser parser, IChemObjectBuilder builder) throws Exception {
IMolecule molecule = builder.newMolecule();
// assume the current element is PC-Compound
if (!parser.getName().equals("PC-Compound")) {
return null;
}
while (parser.next() != XmlPullParser.END_DOCUMENT) {
if (parser.getEventType() == XmlPullParser.END_TAG) {
if (EL_PCCOMPOUND.equals(parser.getName())) {
break; // done parsing the molecule
}
} else if (parser.getEventType() == XmlPullParser.START_TAG) {
if (EL_ATOMBLOCK.equals(parser.getName())) {
parserAtomBlock(parser, molecule);
} else if (EL_BONDBLOCK.equals(parser.getName())) {
parserBondBlock(parser, molecule);
} else if (EL_COORDINATESBLOCK.equals(parser.getName())) {
parserCoordBlock(parser, molecule);
} else if (EL_PROPS_INFODATA.equals(parser.getName())) {
parserCompoundInfoData(parser, molecule);
} else if (EL_PCCOMPOUND_ID.equals(parser.getName())) {
String cid = getCID(parser);
molecule.setProperty("PubChem CID", cid);
}
}
}
return molecule;
}
public void parserBondBlock(XmlPullParser parser, IMolecule molecule) throws Exception {
List<String> id1s = new ArrayList<String>();
List<String> id2s = new ArrayList<String>();
List<String> orders = new ArrayList<String>();
while (parser.next() != XmlPullParser.END_DOCUMENT) {
if (parser.getEventType() == XmlPullParser.END_TAG) {
if (EL_BONDBLOCK.equals(parser.getName())) {
break; // done parsing the atom block
}
} else if (parser.getEventType() == XmlPullParser.START_TAG) {
if (EL_BONDID1.equals(parser.getName())) {
id1s = parseValues(parser, EL_BONDID1, "PC-Bonds_aid1_E");
} else if (EL_BONDID2.equals(parser.getName())) {
id2s = parseValues(parser, EL_BONDID2, "PC-Bonds_aid2_E");
} else if (EL_BONDORDER.equals(parser.getName())) {
orders = parseValues(parser, EL_BONDORDER, "PC-BondType");
}
}
}
// aggregate information
if (id1s.size() != id2s.size()) {
throw new CDKException("Inequal number of atom identifier in bond block.");
}
if (id1s.size() != orders.size()) {
throw new CDKException("Number of bond orders does not match number of bonds in bond block.");
}
for (int i=0; i<id1s.size(); i++) {
IAtom atom1 = molecule.getAtom(Integer.parseInt(id1s.get(i))-1);
IAtom atom2 = molecule.getAtom(Integer.parseInt(id2s.get(i))-1);
IBond bond = molecule.getBuilder().newBond(atom1, atom2);
int order = Integer.parseInt(orders.get(i));
if (order == 1) {
bond.setOrder(IBond.Order.SINGLE);
molecule.addBond(bond);
} else if (order == 2) {
bond.setOrder(IBond.Order.DOUBLE);
molecule.addBond(bond);
} if (order == 3) {
bond.setOrder(IBond.Order.TRIPLE);
molecule.addBond(bond);
} else {
// unknown bond order, skip
}
}
}
public void parserCoordBlock(XmlPullParser parser, IMolecule molecule) throws Exception {
List<String> ids = new ArrayList<String>();
List<String> xs = new ArrayList<String>();
List<String> ys = new ArrayList<String>();
List<String> zs = new ArrayList<String>();
boolean parsedFirstConformer = false;
while (parser.next() != XmlPullParser.END_DOCUMENT) {
if (parser.getEventType() == XmlPullParser.END_TAG) {
if (EL_COORDINATESBLOCK.equals(parser.getName())) {
break; // done parsing the atom block
} else if (EL_ATOM_CONFORMER.equals(parser.getName())) {
parsedFirstConformer = true;
}
} else if (parser.getEventType() == XmlPullParser.START_TAG &&
!parsedFirstConformer) {
if (EL_COORDINATES_AID.equals(parser.getName())) {
ids = parseValues(parser, EL_COORDINATES_AID, EL_COORDINATES_AIDE);
} else if (EL_ATOM_CONFORMER_X.equals(parser.getName())) {
xs = parseValues(parser, EL_ATOM_CONFORMER_X, EL_ATOM_CONFORMER_XE);
} else if (EL_ATOM_CONFORMER_Y.equals(parser.getName())) {
ys = parseValues(parser, EL_ATOM_CONFORMER_Y, EL_ATOM_CONFORMER_YE);
} else if (EL_ATOM_CONFORMER_Z.equals(parser.getName())) {
zs = parseValues(parser, EL_ATOM_CONFORMER_Z, EL_ATOM_CONFORMER_ZE);
}
}
}
// aggregate information
boolean has2dCoords = ids.size() == xs.size() && ids.size() == ys.size();
boolean has3dCoords = has2dCoords && ids.size() == zs.size();
for (int i=0; i<ids.size(); i++) {
IAtom atom = molecule.getAtom(Integer.parseInt(ids.get(i))-1);
if (has3dCoords) {
Point3d coord = new Point3d(
Double.parseDouble(xs.get(i)),
Double.parseDouble(ys.get(i)),
Double.parseDouble(zs.get(i))
);
atom.setPoint3d(coord);
} else if (has2dCoords) {
Point2d coord = new Point2d(
Double.parseDouble(xs.get(i)),
Double.parseDouble(ys.get(i))
);
atom.setPoint2d(coord);
}
}
}
private List<String> parseValues(XmlPullParser parser, String endTag, String fieldTag) throws Exception {
List<String> values = new ArrayList<String>();
while (parser.next() != XmlPullParser.END_DOCUMENT) {
if (parser.getEventType() == XmlPullParser.END_TAG) {
if (endTag.equals(parser.getName())) {
// done parsing the values
break;
}
} else if (parser.getEventType() == XmlPullParser.START_TAG) {
if (fieldTag.equals(parser.getName())) {
String value = parser.nextText();
values.add(value);
}
}
}
return values;
}
}