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AtomContainerManipulator.java

/* $RCSfile$
 * $Author: egonw $ 
 * $Date: 2007-08-28 11:31:14 +0200 (Tue, 28 Aug 2007) $
 * $Revision: 8739 $
 * 
 * Copyright (C) 2003-2007  The Chemistry Development Kit (CDK) project
 * 
 * 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.tools.manipulator;

import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.*;

import java.util.*;

/**
 * Class with convenience methods that provide methods to manipulate
 * AtomContainer's. For example:
 * <pre>
 * AtomContainerManipulator.replaceAtomByAtom(container, atom1, atom2);
 * </pre>
 * will replace the Atom in the AtomContainer, but in all the ElectronContainer's
 * it participates too.
 *
 * @cdk.module standard
 *
 * @author  Egon Willighagen
 * @cdk.created 2003-08-07
 */
00049 public class AtomContainerManipulator {
      
      /**
       * Returna an atom in an atomcontainer identified by id
       * 
       * @param ac The AtomContainer to search in
       * @param id The id to search for
       * @return An atom having id id
       * @throws CDKException There is no such atom
       */
00059       public static IAtom getAtomById(IAtomContainer ac, String id) throws CDKException{
            for(int i=0;i<ac.getAtomCount();i++){
                  if(ac.getAtom(i).getID()!=null && ac.getAtom(i).getID().equals(id))
                        return ac.getAtom(i);
            }
            throw new CDKException("no suc atom");
      }

    public static boolean replaceAtomByAtom(IAtomContainer container, IAtom atom, IAtom newAtom) {
        if (!container.contains(atom)) {
            // it should complain
          return false;
        } else {
            container.setAtom(container.getAtomNumber(atom), newAtom);
            Iterator eContainers = container.electronContainers();
            while (eContainers.hasNext()){
                  IElectronContainer eContainer = (IElectronContainer)eContainers.next();
                if (eContainer instanceof IBond) {
                    IBond bond = (IBond)eContainer;
                    if (bond.contains(atom)) {
                        for (int j=0; j<bond.getAtomCount(); j++) {
                            if (atom.equals(bond.getAtom(j))) {
                                bond.setAtom(newAtom, j);
                            }
                        }
                    }
                } else if (eContainer instanceof ILonePair) {
                    ILonePair lonePair = (ILonePair)eContainer;
                    if (atom.equals(lonePair.getAtom())) {
                        lonePair.setAtom(newAtom);
                    }
                }
            }
            return true;
        }
    }


    /**
     * @return The summed charges of all atoms in this AtomContainer.
     */
00100     public static double getTotalCharge(IAtomContainer atomContainer) {
        double charge = 0.0;
        for (int i = 0; i < atomContainer.getAtomCount(); i++) {
            charge += atomContainer.getAtom(i).getCharge();
        }
        return charge;
    }

    /**
     * @return The summed formal charges of all atoms in this AtomContainer.
     */
00111     public static int getTotalFormalCharge(IAtomContainer atomContainer) {
        int chargeP = getTotalNegativeFormalCharge(atomContainer);
        int chargeN = getTotalPositiveFormalCharge(atomContainer);
        int totalCharge = chargeP + chargeN;
        
        return totalCharge;
    }
    /**
     * @return The summed negative formal charges of all atoms in this AtomContainer. 
     */
00121     public static int getTotalNegativeFormalCharge(IAtomContainer atomContainer) {
        int charge = 0;
        for (int i = 0; i < atomContainer.getAtomCount(); i++) {
            double chargeI = atomContainer.getAtom(i).getFormalCharge();
            if(chargeI < 0)
                  charge += chargeI;
        }
        return charge;
    }
    /**
     * @return The summed positive formal charges of all atoms in this AtomContainer. 
     */
00133     public static int getTotalPositiveFormalCharge(IAtomContainer atomContainer) {
        int charge = 0;
        for (int i = 0; i < atomContainer.getAtomCount(); i++) {
            double chargeI = atomContainer.getAtom(i).getFormalCharge();
            if(chargeI > 0)
                  charge += chargeI;
        }
        return charge;
    }

    /**
     * @return The summed implicit hydrogens of all atoms in this AtomContainer.
     */
00146     public static int getTotalHydrogenCount(IAtomContainer atomContainer) {
        int hCount = 0;
        for (int i = 0; i < atomContainer.getAtomCount(); i++) {
            hCount += atomContainer.getAtom(i).getHydrogenCount();
        }
        return hCount;
    }

    /**
     * @return The number of explicit hydrogens on the given IAtom.
     */
00157     public static int countExplicitHydrogens(IAtomContainer atomContainer, IAtom atom) {
      int hCount = 0;
        Iterator connectedAtoms = atomContainer.getConnectedAtomsList(atom).iterator(); 
        while (connectedAtoms.hasNext()) {
            IAtom connectedAtom = (IAtom)connectedAtoms.next();
            if (connectedAtom.getSymbol().equals("H"))
                  hCount++;
        }
        return hCount;
    }
    /**
     * @return The summed implicit + explicit hydrogens of the given IAtom.
     */
00170       public static int countHydrogens(IAtomContainer atomContainer, IAtom atom) {
        int hCount = atom.getHydrogenCount();
        hCount += countExplicitHydrogens(atomContainer, atom);
        return hCount;
      }

    public static List getAllIDs(IAtomContainer mol) {
      List idList = new ArrayList();
        if (mol != null) {
            if (mol.getID() != null) idList.add(mol.getID());
            java.util.Iterator atoms = mol.atoms();
            while (atoms.hasNext()) {
                IAtom atom = (IAtom)atoms.next();
                if (atom.getID() != null) idList.add(atom.getID());
            }

            Iterator bonds = mol.bonds();
            while (bonds.hasNext()) {
                IBond bond = (IBond) bonds.next();                            
                if (bond.getID() != null) idList.add(bond.getID());
            }
        }
        return idList;
    }


    /**
     * Produces an AtomContainer without explicit Hs but with H count from one with Hs.
     * The new molecule is a deep copy.
     *
     * @param atomContainer The AtomContainer from which to remove the hydrogens
     * @return              The molecule without Hs.
     * @cdk.keyword         hydrogen, removal
     */
00204     public static IAtomContainer removeHydrogens(IAtomContainer atomContainer)
    {
        Map map = new HashMap();        // maps original atoms to clones.
        List remove = new ArrayList();  // lists removed Hs.

        // Clone atoms except those to be removed.
        IMolecule mol = atomContainer.getBuilder().newMolecule();
        int count = atomContainer.getAtomCount();
        for (int i = 0;
                i < count;
                i++)
        {
            // Clone/remove this atom?
            IAtom atom = atomContainer.getAtom(i);
            if (!atom.getSymbol().equals("H"))
            {
                IAtom clonedAtom = null;
                        try {
                              clonedAtom = (IAtom) atom.clone();
                        } catch (CloneNotSupportedException e) {
                              // TODO Auto-generated catch block
                              e.printStackTrace();
                        }
                clonedAtom.setHydrogenCount(0);
                mol.addAtom(clonedAtom);
                map.put(atom, clonedAtom);
            }
            else
            {
                remove.add(atom);   // maintain list of removed H.
            }
        }

        // Clone bonds except those involving removed atoms.
        count = atomContainer.getBondCount();
        for (int i = 0;
                i < count;
                i++)
        {
            // Check bond.
            final IBond bond = atomContainer.getBond(i);
            boolean removedBond = false;
            final int length = bond.getAtomCount();
            for (int k = 0;
                    k < length;
                    k++)
            {
                if (remove.contains(bond.getAtom(k)))
                {
                    removedBond = true;
                    break;
                }
            }

            // Clone/remove this bond?
            if (!removedBond)
                // if (!remove.contains(atoms[0]) && !remove.contains(atoms[1]))
            {
                IBond clone = null;
                        try {
                              clone = (IBond) atomContainer.getBond(i).clone();
                        } catch (CloneNotSupportedException e) {
                              // TODO Auto-generated catch block
                              e.printStackTrace();
                        }
                clone.setAtoms(new IAtom[]{(IAtom) map.get(bond.getAtom(0)), (IAtom) map.get(bond.getAtom(1))});
                mol.addBond(clone);
            }
        }

        // Recompute hydrogen counts of neighbours of removed Hydrogens.
        for (Iterator i = remove.iterator();
                i.hasNext();)
        {
            // Process neighbours.
            for (Iterator n = atomContainer.getConnectedAtomsList((IAtom) i.next()).iterator();
                    n.hasNext();)
            {
                final IAtom neighb = (IAtom) map.get(n.next());
                neighb.setHydrogenCount(neighb.getHydrogenCount() + 1);
            }
        }
        mol.setProperties(atomContainer.getProperties());
        mol.setFlags(atomContainer.getFlags());

        return (mol);
    }
    
    /**
     * Sets a property on all <code>Atom</code>s in the given container.
     */
00295     public static void setAtomProperties(IAtomContainer container, Object propKey, Object propVal) {
        if (container != null) {
            java.util.Iterator atoms = container.atoms();
            while (atoms.hasNext()) {
                IAtom atom = (IAtom)atoms.next();
                atom.setProperty(propKey, propVal);
            }
        }
    }

      /**
       *  A method to remove ElectronContainerListeners. 
       *  ElectronContainerListeners are used to detect changes 
       *  in ElectronContainers (like bonds) and to notifiy
       *  registered Listeners in the event of a change.
       *  If an object looses interest in such changes, it should 
       *  unregister with this AtomContainer in order to improve 
       *  performance of this class.
       */
00314       public static void unregisterElectronContainerListeners(IAtomContainer container)
      {
            for (int f = 0; f < container.getElectronContainerCount(); f++)
            {
                  container.getElectronContainer(f).removeListener(container);      
            }
      }

      /**
       *  A method to remove AtomListeners. 
       *  AtomListeners are used to detect changes 
       *  in Atom objects within this AtomContainer and to notifiy
       *  registered Listeners in the event of a change.
       *  If an object looses interest in such changes, it should 
       *  unregister with this AtomContainer in order to improve 
       *  performance of this class.
       */
00331       public static void unregisterAtomListeners(IAtomContainer container)
      {
            for (int f = 0; f < container.getAtomCount(); f++)
            {
                  container.getAtom(f).removeListener(container); 
            }
      }

      /**
       * Compares this AtomContainer with another given AtomContainer and returns
       * the Intersection between them. <p>
       * 
       * <b>Important Note</b> : This is not the maximum common substructure.
       *
       * @param  container1 an AtomContainer object
       * @param  container2 an AtomContainer object
       * @return            An AtomContainer containing the intersection between
       *                    container1 and container2
       */
00350       public static IAtomContainer getIntersection(
            IAtomContainer container1, IAtomContainer container2)
      {
            IAtomContainer intersection = container1.getBuilder().newAtomContainer();

            for (int i = 0; i < container1.getAtomCount(); i++)
            {
                  if (container2.contains(container1.getAtom(i)))
                  {
                        intersection.addAtom(container1.getAtom(i));
                  }
            }
            for (int i = 0; i < container1.getElectronContainerCount(); i++)
            {
                  if (container2.contains(container1.getElectronContainer(i)))
                  {
                        intersection.addElectronContainer(container1.getElectronContainer(i));
                  }
            }
            return intersection;
      }
      
      /**
       * Constructs an array of Atom objects from an AtomContainer.
       * @param  container The original AtomContainer.
       * @return The array of Atom objects.
       */
00377       public static IAtom[] getAtomArray(IAtomContainer container) {
            IAtom[] ret = new IAtom[container.getAtomCount()];
            for (int i = 0; i < ret.length; ++i) ret[i] = container.getAtom(i);
            return ret;
      }
      
      /**
       * Constructs an array of Atom objects from a List of Atom objects.
       * @param  container The original List.
       * @return The array of Atom objects.
       */
00388       public static IAtom[] getAtomArray(java.util.List list) {
            IAtom[] ret = new IAtom[list.size()];
            for (int i = 0; i < ret.length; ++i) ret[i] = (IAtom)list.get(i);
            return ret;
      }
      
      /**
       * Constructs an array of Bond objects from an AtomContainer.
       * @param  container The original AtomContainer.
       * @return The array of Bond objects.
       */
00399       public static IBond[] getBondArray(IAtomContainer container) {
            IBond[] ret = new IBond[container.getBondCount()];
            for (int i = 0; i < ret.length; ++i) ret[i] = container.getBond(i);
            return ret;
      }
      
      /**
       * Constructs an array of Atom objects from a List of Atom objects.
       * @param  container The original List.
       * @return The array of Atom objects.
       */
00410       public static IBond[] getBondArray(java.util.List list) {
            IBond[] ret = new IBond[list.size()];
            for (int i = 0; i < ret.length; ++i) ret[i] = (IBond)list.get(i);
            return ret;
      }
      
      /**
       * Constructs an array of Bond objects from an AtomContainer.
       * @param  container The original AtomContainer.
       * @return The array of Bond objects.
       */
00421       public static IElectronContainer[] getElectronContainerArray(IAtomContainer container) {
            IElectronContainer[] ret = new IElectronContainer[container.getElectronContainerCount()];
            for (int i = 0; i < ret.length; ++i) ret[i] = container.getElectronContainer(i);
            return ret;
      }
      
      /**
       * Constructs an array of Atom objects from a List of Atom objects.
       * @param  container The original List.
       * @return The array of Atom objects.
       */
00432       public static IElectronContainer[] getElectronContainerArray(java.util.List list) {
            IElectronContainer[] ret = new IElectronContainer[list.size()];
            for (int i = 0; i < ret.length; ++i) ret[i] = (IElectronContainer)list.get(i);
            return ret;
      }
      
}


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