/* $Revision: 5855 $ $Author: egonw $ $Date: 2006-03-29 10:27:08 +0200 (Wed, 29 Mar 2006) $
*
* Copyright (C) 2005-2007 Egon Willighagen <egonw@users.sf.net>
*
* 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, version 2.1.
*
* 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.atomtype;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
import org.openscience.cdk.tools.manipulator.BondManipulator;
/**
* AtomTypeMatcher that finds an AtomType by matching the Atom's element symbol.
* This atom type matcher takes into account formal charge and number of
* implicit hydrogens, and requires bond orders to be given.
*
* <p>This class uses the <b>cdk/config/data/structgen_atomtypes.xml</b>
* list. If there is not an atom type defined for the tested atom, then null
* is returned.
*
* @author egonw
* @cdk.created 2006-09-22
* @cdk.module structgen
* @cdk.githash
*/
public class StructGenMatcher implements IAtomTypeMatcher {
private static AtomTypeFactory factory = null;
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(StructGenMatcher.class);
/**
* Constructor for the StructGenMatcher object.
*/
public StructGenMatcher() {
}
@TestMethod("testFindMatchingAtomType_IAtomContainer")
public IAtomType[] findMatchingAtomType(IAtomContainer atomContainer) throws CDKException {
IAtomType[] types = new IAtomType[atomContainer.getAtomCount()];
int typeCounter = 0;
for (IAtom atom : atomContainer.atoms()) {
types[typeCounter] = findMatchingAtomType(atomContainer, atom);
typeCounter++;
}
return types;
}
/**
* Finds the AtomType matching the Atom's element symbol, formal charge and
* hybridization state.
*
* @param atomContainer AtomContainer
* @param atom the target atom
* @exception CDKException Exception thrown if something goes wrong
* @return the matching AtomType
*/
public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom) throws CDKException {
if (factory == null) {
try {
factory = AtomTypeFactory.getInstance("org/openscience/cdk/config/data/structgen_atomtypes.xml",
atom.getBuilder());
} catch (Exception ex1) {
logger.error(ex1.getMessage());
logger.debug(ex1);
throw new CDKException("Could not instantiate the AtomType list!", ex1);
}
}
double bondOrderSum = atomContainer.getBondOrderSum(atom);
IBond.Order maxBondOrder = atomContainer.getMaximumBondOrder(atom);
int charge = atom.getFormalCharge();
int hcount = atom.getHydrogenCount() == null ? 0 : atom.getHydrogenCount();
IAtomType[] types = factory.getAtomTypes(atom.getSymbol());
for (IAtomType type : types) {
logger.debug(" ... matching atom ", atom, " vs ", type);
if (bondOrderSum - charge + hcount == type.getBondOrderSum() &&
!BondManipulator.isHigherOrder(maxBondOrder, type.getMaxBondOrder())) {
return type;
}
}
logger.debug(" No Match");
return null;
}
}