EStateAtomTypeMatcher.java

/* $RCSfile: $
 * $Author$
 * $Date$
 * $Revision$
 *
 * Copyright (C) 2006-2007  Todd Martin (Environmental Protection Agency) <Martin.Todd@epamail.epa.gov>
 *
 * 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.
 *
 * 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 java.util.List;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
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.interfaces.IRing;
import org.openscience.cdk.interfaces.IRingSet;

/**
 * Determines the EState atom types.
 *
 * @author Todd Martin
 * @author nick
 * @cdk.module standard
 * @cdk.githash
 * @cdk.keyword atom type, E-state
 */
@TestClass("org.openscience.cdk.atomtype.EStateAtomTypeMatcherTest")
public class EStateAtomTypeMatcher  implements IAtomTypeMatcher {

	IRingSet ringSet = null;

	public void setRingSet(IRingSet rs)
	{
		ringSet = rs;
	}

	@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;
  }

    @TestMethod("testSP3Atoms,testNaCl,testNaphthalene,testSP2Atoms,testSPAtoms,testBenzeneFromSmiles")
    public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
	{

		IAtomType atomType = null;
		try {
			String fragment = "";
			int NumHAtoms = 0;
			int NumSingleBonds2 = 0;
			int NumDoubleBonds2 = 0;
			int NumTripleBonds2 = 0;
			int NumAromaticBonds2 = 0;
			int NumAromaticBondsTotal2 = 0;

			String element = atom.getSymbol();

			List<IAtom> attachedAtoms = atomContainer.getConnectedAtomsList(atom);

			for (int j = 0; j <= attachedAtoms.size() - 1; j++) {
				IAtom attached = (IAtom)attachedAtoms.get(j);
				IBond b = atomContainer.getBond(atom, attached);
				if(attached.getSymbol().equals("H"))
					NumHAtoms++;

				if (atom.getFlag(CDKConstants.ISAROMATIC)
						&& attached.getFlag(CDKConstants.ISAROMATIC)) {

					boolean SameRing = inSameAromaticRing(atomContainer, atom,
							attached, ringSet);

					if (SameRing) {
						NumAromaticBonds2++;
						if (element.equals("N")) {
							if (b.getOrder() == IBond.Order.SINGLE)
								NumAromaticBondsTotal2++;
							if (b.getOrder() == IBond.Order.DOUBLE)
								NumAromaticBondsTotal2 = NumAromaticBondsTotal2 + 2;
						}
					} else {
						if (b.getOrder() == IBond.Order.SINGLE)
							NumSingleBonds2++;
						if (b.getOrder() == IBond.Order.DOUBLE)
							NumDoubleBonds2++;
						if (b.getOrder() == IBond.Order.TRIPLE)
							NumTripleBonds2++;
					}

				} else {

					if (b.getOrder() == IBond.Order.SINGLE)
						NumSingleBonds2++;
					if (b.getOrder() == IBond.Order.DOUBLE)
						NumDoubleBonds2++;
					if (b.getOrder() == IBond.Order.TRIPLE)
						NumTripleBonds2++;
				}
			}
			NumSingleBonds2 = NumSingleBonds2 - NumHAtoms;

			// assign frag here
			fragment = "S";

			for (int j = 0; j <= NumTripleBonds2 - 1; j++) {
				fragment += "t";
			}

			for (int j = 0; j <= NumDoubleBonds2 - 1; j++) {
				fragment += "d";
			}

			for (int j = 0; j <= NumSingleBonds2 - 1; j++) {
				fragment += "s";
			}

			for (int j = 0; j <= NumAromaticBonds2 - 1; j++) {
				fragment += "a";
			}

			fragment += element;

			if (atom.getFormalCharge() == 1) {
				fragment += "p";
			} else if (atom.getFormalCharge() == -1) {
				fragment += "m";
			}

			if (NumHAtoms == 1)
				fragment += "H";
			else
				if (NumHAtoms > 1)
					fragment += ("H" + NumHAtoms);

			atomType = atom.getBuilder().newAtomType(fragment, atom.getSymbol());
			atomType.setFormalCharge(atom.getFormalCharge());
			if (atom.getFlag(CDKConstants.ISAROMATIC))
				atomType.setFlag(CDKConstants.ISAROMATIC, true);

		} catch (Exception e) {
			e.printStackTrace();
		}

		return atomType;
	}

    @TestMethod("testAromaticAtoms")
    public static boolean inSameAromaticRing(IAtomContainer m, IAtom atom1,
			IAtom atom2, IRingSet rs)
	{
		if (rs == null) 
			return false;
		for (int i = 0; i <= rs.getAtomContainerCount() - 1; i++)
		{
			IRing r = (IRing) rs.getAtomContainer(i);
			if (r.contains(atom1) && r.contains(atom2))
			{
				if (isAromaticRing(r))
					return(true);
			}
		}
		return false;
	}

    @TestMethod("testAromaticAtoms")
	static boolean  isAromaticRing(IRing ring)
	{
		for (int i = 0; i < ring.getAtomCount(); i++)
			if(!ring.getAtom(i).getFlag(CDKConstants.ISAROMATIC))
				return(false);

		return(true);
	}

}