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EStateAtomTypeMatcher.java

/* $RCSfile: $
 * $Author: egonw $
 * $Date: 2006-05-04 19:29:58 +0000 (Thu, 04 May 2006) $
 * $Revision: 6171 $
 *
 * Copyright (C) 2006-2007  Todd Martin (Environmental Protection Agency)
 *
 * 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 org.openscience.cdk.CDKConstants;
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;
import org.openscience.cdk.ringsearch.AllRingsFinder;

/**
 * Determines the EState atom types.
 * 
 * @author     Todd Martin
 * @cdk.module standard
 */
00041 public class EStateAtomTypeMatcher  implements IAtomTypeMatcher {

00043       public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom) {
            IAtomType atomType = null;
            
            try {
                  String fragment = "";
                  
                  AllRingsFinder arf = new AllRingsFinder();
                  IRingSet rs = arf.findAllRings(atomContainer);
                  
                  int NumSingleBonds2 = 0;
                  int NumDoubleBonds2 = 0;
                  int NumTripleBonds2 = 0;
                  int NumAromaticBonds2 = 0;
                  int NumAromaticBondsTotal2 = 0;
                  
                  String element = atom.getSymbol();
                  
                  java.util.List 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 (atom.getFlag(CDKConstants.ISAROMATIC)
                                    && attached
                                                     .getFlag(CDKConstants.ISAROMATIC)) {
                              
                              boolean SameRing = inSameAromaticRing(atomContainer, atom,
                                          attached, rs);
                              
                              if (SameRing) {
                                    NumAromaticBonds2++;
                                    if (element.equals("N")) {
                                          if (b.getOrder() == 1)
                                                NumAromaticBondsTotal2++;
                                          if (b.getOrder() == 2)
                                                NumAromaticBondsTotal2 = NumAromaticBondsTotal2 + 2;
                                    }
                              } else {
                                    if (b.getOrder() == 1)
                                          NumSingleBonds2++;
                                    if (b.getOrder() == 2)
                                          NumDoubleBonds2++;
                                    if (b.getOrder() == 3)
                                          NumTripleBonds2++;
                              }
                              
                        } else {
                              
                              if (b.getOrder() == 1)
                                    NumSingleBonds2++;
                              if (b.getOrder() == 2)
                                    NumDoubleBonds2++;
                              if (b.getOrder() == 3)
                                    NumTripleBonds2++;
                        }
                  }
                  
                  // 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";
                  }
                  
                  fragment += "*";// flag it as unassigned fragment
                  
                  // for now set #H = 0 TODO- add routine to figure out #Hs for
                  // possible valence states
                  atom.setHydrogenCount(0);

                  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;
      }

      public static boolean inSameAromaticRing(IAtomContainer m, IAtom atom1,
                  IAtom atom2, IRingSet rs) {
            
            for (int i = 0; i <= rs.getAtomContainerCount() - 1; i++) {
                  IRing r = (IRing) rs.getAtomContainer(i);
                  
                  if (!r.getFlag(CDKConstants.ISAROMATIC))
                        continue;
                  
                  // ArrayList al=new ArrayList();
                  
                  boolean HaveOne = false;
                  boolean HaveTwo = false;
                  
                  for (int j = 0; j <= r.getAtomCount() - 1; j++) {
                        if (m.getAtomNumber(r.getAtom(j)) == m.getAtomNumber(atom1))
                              HaveOne = true;
                        if (m.getAtomNumber(r.getAtom(j)) == m.getAtomNumber(atom2))
                              HaveTwo = true;
                  }
                  
                  if (HaveOne && HaveTwo) {
                        return true;
                  }
                  
            } // end ring for loop
            
            return false;
      }
      
      
}

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