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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")
00049 public class EStateAtomTypeMatcher  implements IAtomTypeMatcher {

      IRingSet ringSet = null;

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

      @TestMethod("testFindMatchingAtomType_IAtomContainer")
00059   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")
00070     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);
      }

}

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