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/* $Revision: 8067 $ $Author: egonw $ $Date: 2007-03-09 14:59:01 +0100 (Fri, 09 Mar 2007) $
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* Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project
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* Contact: cdk-devel@lists.sourceforge.net
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public License
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* as published by the Free Software Foundation; either version 2.1
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* of the License, or (at your option) any later version.
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* All I ask is that proper credit is given for my work, which includes
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* - but is not limited to - adding the above copyright notice to the beginning
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* of your source code files, and to any copyright notice that you may distribute
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* with programs based on this work.
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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* You should have received a copy of the GNU Lesser General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
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package org.openscience.cdk.tools;
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import java.util.Collections;
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import java.util.Comparator;
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import java.util.List;
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import java.util.ArrayList;
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import org.openscience.cdk.CDKConstants;
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import org.openscience.cdk.ChemObject;
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import org.openscience.cdk.Molecule;
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import org.openscience.cdk.config.IsotopeFactory;
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import org.openscience.cdk.exception.CDKException;
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import org.openscience.cdk.graph.invariant.CanonicalLabeler;
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import org.openscience.cdk.interfaces.IAtom;
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import org.openscience.cdk.interfaces.IAtomContainer;
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import org.openscience.cdk.interfaces.IIsotope;
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import org.openscience.cdk.interfaces.IRing;
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import org.openscience.cdk.interfaces.IRingSet;
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import org.openscience.cdk.ringsearch.SSSRFinder;
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* Generates HOSE codes {@cdk.cite BRE78}.
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* IMPORTANT: Your molecule must contain implicit or explicit hydrogens
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* for this method to work properly
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* @cdk.keyword HOSE code, spherical atom search
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* @cdk.created 2002-05-10
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public class HOSECodeGenerator implements java.io.Serializable
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private LoggingTool logger;
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private static final long serialVersionUID = -4353471818831864513L;
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* Container for the nodes in a sphere.
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protected List sphereNodes = null;
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protected List sphereNodesWithAtoms = null;
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* Container for the node in the next sphere Assembled in a recursive method
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* and then passed to the next recursion to become "sphereNodes"
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protected List nextSphereNodes = null;
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* Counter for the sphere in which we currently work
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protected int sphere = 0;
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* How many spheres are we supposed inspect.
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protected int maxSphere = 0;
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* Here we store the spheres that we assemble, in order to parse them into a
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protected List[] spheres = null;
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protected List[] spheresWithAtoms = null;
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* The HOSECode string that we assemble
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protected StringBuffer HOSECode = null;
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* The molecular structure on which we work
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protected IAtomContainer atomContainer;
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* Delimiters used to separate spheres in the output string. Bremser uses the
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* sequence"(//)" for the first four spheres.
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protected String[] sphereDelimiters =
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"(", "/", "/", ")", "/", "/", "/", "/", "/", "/", "/", "/"
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* The bond symbols used for bond orders "single", "double", "triple" and
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protected String bondSymbols[] =
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"", "", "=", "%", "*"
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protected String centerCode = null;
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public TreeNode rootNode = null;
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boolean debug = false;
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private IAtomContainer acold=null;
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private IRingSet soar=null;
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* The rank order for the given element symbols
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static final String[] rankedSymbols =
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"C", "O", "N", "S", "P", "Si", "B", "F", "Cl", "Br", ";", "I", "#", "&", ","
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* The ranking values to be used for the symbols above
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static final int[] symbolRankings =
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9000, 8900, 8800, 8700,
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8600, 8500, 8400, 8300, 8200, 8100, 8000, 7900, 1200, 1100, 1000
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* The bond rankings to be used for the four bond order possibilities
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static final int[] bondRankings =
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0, 0, 200000, 300000, 100000
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* Constructor for the HOSECodeGenerator
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public HOSECodeGenerator()
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logger = new LoggingTool(this);
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sphereNodes = new ArrayList();
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sphereNodesWithAtoms = new ArrayList();
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nextSphereNodes = new ArrayList();
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HOSECode = new StringBuffer();
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* This method is intended to be used to get the atoms around an atom in spheres. It is not used in this class, but is provided for other classes to use.
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* It also creates the HOSE code in HOSECode as a side-effect
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*@param ac The AtomContainer with the molecular skeleton in which the root atom resides.
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*@param root The root atom for which to produce the spheres.
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*@param noOfSpheres The number of spheres to look at.
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*@paramm ringsize Shall the center code have the ring size in it? Only use if you want to have the hose code later, else say false.
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*@return An array of Vectors. The vector at i-1 contains the atoms at sphere i as TreeNodes.
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public List[] getSpheres(Molecule ac, IAtom root, int noOfSpheres, boolean ringsize) throws org.openscience.cdk.exception.CDKException
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this.atomContainer = ac;
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maxSphere = noOfSpheres;
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spheres = new List[noOfSpheres + 1];
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spheresWithAtoms = new List[noOfSpheres + 1];
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for (int i = 0; i < ac.getAtomCount(); i++)
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ac.getAtom(i).setFlag(CDKConstants.VISITED, false);
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root.setFlag(CDKConstants.VISITED, true);
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rootNode = new TreeNode(root.getSymbol(), null, root, (double)0, atomContainer.getConnectedBondsCount(root), 0);
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* All we need to observe is how the ranking of substituents
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* in the subsequent spheres of the root nodes influences the
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* ranking of the first sphere, sinces the order of a node in a sphere
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* depends on the order the preceding node in its branch
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HOSECode = new StringBuffer();
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createCenterCode(root,ac,ringsize);
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breadthFirstSearch(root, false);
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fillUpSphereDelimiters();
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logger.debug("HOSECodeGenerator -> HOSECode: " + HOSECode.toString());
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return spheresWithAtoms;
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* Produces a HOSE code for Atom 'root' in the AtomContainer 'ac'. The HOSE
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* code is produced for the number of spheres given by noOfSpheres
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* IMPORTANT: if you want aromaticity to be included in the code, you need
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* to run the AtomContainer ac to the HueckelAromaticityDetector prior to
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* using getHOSECode(). This method only gives proper results if the molecule is
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* fully saturated (if not, the order of the HOSE code might depend on atoms in higher spheres).
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* This method is known to fail for protons sometimes.
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* IMPORTANT: Your molecule must contain implicit or explicit hydrogens
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* for this method to work properly
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*@param ac The AtomContainer with the molecular skeleton in which the root atom resides
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*@param root The root atom for which to produce the HOSE code
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*@param noOfSpheres The number of spheres to look at
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*@return The HOSECode value
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*@exception org.openscience.cdk.exception.CDKException Thrown if something is wrong
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public String getHOSECode(IAtomContainer ac, IAtom root, int noOfSpheres) throws org.openscience.cdk.exception.CDKException
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return getHOSECode(ac,root,noOfSpheres, false);
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* Produces a HOSE code for Atom 'root' in the AtomContainer 'ac'. The HOSE
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* code is produced for the number of spheres given by noOfSpheres
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* IMPORTANT: if you want aromaticity to be included in the code, you need
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* to run the AtomContainer ac to the HueckelAromaticityDetector prior to
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* using getHOSECode(). This method only gives proper results if the molecule is
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* fully saturated (if not, the order of the HOSE code might depend on atoms in higher spheres).
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* This method is known to fail for protons sometimes.
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*@param ac The AtomContainer with the molecular skeleton in which the root atom resides
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*@param root The root atom for which to produce the HOSE code
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*@param noOfSpheres The number of spheres to look at
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*@param ringsize The size of the ring(s) it is in is included in center atom code
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*@return The HOSECode value
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*@exception org.openscience.cdk.exception.CDKException Thrown if something is wrong
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public String getHOSECode(IAtomContainer ac, IAtom root, int noOfSpheres, boolean ringsize) throws org.openscience.cdk.exception.CDKException
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CanonicalLabeler canLabler = new CanonicalLabeler();
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canLabler.canonLabel(ac);
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this.atomContainer = ac;
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maxSphere = noOfSpheres;
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spheres = new List[noOfSpheres + 1];
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for (int i = 0; i < ac.getAtomCount(); i++)
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ac.getAtom(i).setFlag(CDKConstants.VISITED, false);
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root.setFlag(CDKConstants.VISITED, true);
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rootNode = new TreeNode(root.getSymbol(), null, root, (double)0, atomContainer.getConnectedBondsCount(root), 0);
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* All we need to observe is how the ranking of substituents
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* in the subsequent spheres of the root nodes influences the
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* ranking of the first sphere, sinces the order of a node in a sphere
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* depends on the order the preceding node in its branch
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HOSECode = new StringBuffer();
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createCenterCode(root, ac, ringsize);
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breadthFirstSearch(root,true);
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fillUpSphereDelimiters();
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logger.debug("HOSECodeGenerator -> HOSECode: ", HOSECode);
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return HOSECode.toString();
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private void createCenterCode(IAtom root, IAtomContainer ac, boolean ringsize)
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int partnerCount = 0;
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partnerCount = atomContainer.getConnectedBondsCount(root) + root.getHydrogenCount();
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centerCode = root.getSymbol() + "-" + partnerCount + createChargeCode(root)+(ringsize ? getRingcode(root, ac) : "" )+";";
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private String getRingcode(IAtom root, IAtomContainer ac){
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soar=new SSSRFinder(ac).findSSSR();
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boolean[] bool=new boolean[1000];
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StringBuffer sb=new StringBuffer();
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for(int i=0;i<soar.getRings(root).getAtomContainerCount();i++){
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if(((IRing)soar.getRings(root).getAtomContainer(i)).getAtomCount()<bool.length)
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bool[((IRing)soar.getRings(root).getAtomContainer(i)).getAtomCount()]=true;
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for(int i=0;i<bool.length;i++){
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if(sb.toString().equals(""))
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return "-"+sb.toString();
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private String createChargeCode(IAtom atom){
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StringBuffer tempCode=new StringBuffer();
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if (atom != null && atom.getFormalCharge()!=0){
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if(Math.abs(atom.getFormalCharge())==1){
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if(atom.getFormalCharge()<0)
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tempCode.append("-");
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tempCode.append("+");
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tempCode.append("'");
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if(atom.getFormalCharge()>0)
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tempCode.append("+");
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tempCode.append(atom.getFormalCharge()+"'");
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* Prepares for a breadth first search within the AtomContainer. The actual
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* recursion is done in nextSphere()
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*@param root The atom at which we start the search
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*@exception org.openscience.cdk.exception.CDKException If something goes wrong.
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private void breadthFirstSearch(IAtom root,boolean addTreeNode) throws org.openscience.cdk.exception.CDKException
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TreeNode tempNode = null;
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java.util.List conAtoms = atomContainer.getConnectedAtomsList(root);
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org.openscience.cdk.interfaces.IBond bond = null;
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sphereNodesWithAtoms.clear();
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for (int i = 0; i < conAtoms.size(); i++){
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atom = (IAtom)conAtoms.get(i);
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if(atom.getSymbol().equals("H"))
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bond = atomContainer.getBond(root, atom);
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* In the first sphere the atoms are labled with
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* their own atom atom as source
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if (bond.getFlag(CDKConstants.ISAROMATIC))
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tempNode = new TreeNode(atom.getSymbol(), new TreeNode(root.getSymbol(), null, root, (double) 0, 0, (long) 0), atom, 4, atomContainer.getConnectedBondsCount(atom), 0);
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tempNode = new TreeNode(atom.getSymbol(), new TreeNode(root.getSymbol(), null, root, (double) 0, 0, (long) 0), atom, bond.getOrder(), atomContainer.getConnectedBondsCount(atom), 0);
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sphereNodes.add(tempNode);
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sphereNodesWithAtoms.add(atom);
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// rootNode.childs.addElement(tempNode);
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atom.setFlag(CDKConstants.VISITED, true);
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} catch (Exception exc)
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throw new CDKException("Error in HOSECodeGenerator->breadthFirstSearch.", exc);
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Collections.sort(sphereNodes,new TreeNodeComparator());
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nextSphere(sphereNodes);
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* The actual recursion method for our breadth first search Each node in
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* sphereNodes is inspected for its decendants which are then stored in
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* nextSphereNodes, which again is passed to the next recursion level of
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*@param sphereNodes The sphereNodes to be inspected
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*@exception org.openscience.cdk.exception.CDKException If something goes wrong
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private void nextSphere(List sphereNodes) throws org.openscience.cdk.exception.CDKException
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spheres[sphere] = sphereNodes;
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if(spheresWithAtoms!=null)
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spheresWithAtoms[sphere] = sphereNodesWithAtoms;
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* From here we start assembling the next sphere
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java.util.List conAtoms = null;
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TreeNode treeNode = null;
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nextSphereNodes = new ArrayList();
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org.openscience.cdk.interfaces.IBond bond = null;
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for (int i = 0; i < sphereNodes.size(); i++)
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treeNode = (TreeNode) sphereNodes.get(i);
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if (!("&;#:,".indexOf(treeNode.symbol) >= 0))
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node = treeNode.atom;
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if(node.getSymbol().equals("H"))
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conAtoms = atomContainer.getConnectedAtomsList(node);
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if (conAtoms.size() == 1){
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nextSphereNodes.add(new TreeNode(",", treeNode, null, 0, 0, treeNode.score));
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for (int j = 0; j < conAtoms.size(); j++)
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toNode = (IAtom)conAtoms.get(j);
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if (toNode != treeNode.source.atom)
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bond = atomContainer.getBond(node, toNode);
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if (bond.getFlag(CDKConstants.ISAROMATIC))
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nextSphereNodes.add(new TreeNode(toNode.getSymbol(), treeNode, toNode, 4, atomContainer.getConnectedBondsCount(toNode), treeNode.score));
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nextSphereNodes.add(new TreeNode(toNode.getSymbol(), treeNode, toNode, bond.getOrder(), atomContainer.getConnectedBondsCount(toNode), treeNode.score));
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Collections.sort(nextSphereNodes,new TreeNodeComparator());
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if (sphere < maxSphere)
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nextSphere(nextSphereNodes);
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public String makeBremserCompliant(String code)
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int sepIndex = code.indexOf(";");
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code = code.substring(sepIndex + 1, code.length());
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* After recursivly having established the spheres and assigning each node an
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* appropriate score, we now generate the complete HOSE code.
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*@exception org.openscience.cdk.exception.CDKException Thrown if something goes wrong
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private void createCode() throws org.openscience.cdk.exception.CDKException
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List sphereNodes = null;
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for (int f = 0; f < atomContainer.getAtomCount(); f++)
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atomContainer.getAtom(f).setFlag(CDKConstants.VISITED, false);
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for (int f = 0; f < maxSphere; f++)
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sphereNodes = spheres[maxSphere - f];
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for (int g = 0; g < sphereNodes.size(); g++)
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tn = (TreeNode) sphereNodes.get(g);
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if (tn.source != null)
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tn.source.ranking += tn.degree;
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for (int f = 0; f < maxSphere; f++)
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sphereNodes = spheres[f];
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calculateNodeScores(sphereNodes);
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sortNodesByScore(sphereNodes);
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for (int f = 0; f < maxSphere; f++)
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sphereNodes = spheres[f];
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for (int g = 0; g < sphereNodes.size() ; g++)
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tn = (TreeNode) sphereNodes.get(g);
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tn.score += tn.ranking;
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sortNodesByScore(sphereNodes);
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for (int f = 0; f < maxSphere; f++)
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sphereNodes = spheres[f];
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for (int g = 0; g < sphereNodes.size() ; g++)
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tn = (TreeNode) sphereNodes.get(g);
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String localscore=tn.score+"";
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while(localscore.length()<6){
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localscore="0"+localscore;
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tn.stringscore=tn.source.stringscore+""+localscore;
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sortNodesByScore(sphereNodes);
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HOSECode.append(centerCode);
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for (int f = 0; f < maxSphere; f++)
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sphereNodes = spheres[f];
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String s = getSphereCode(sphereNodes);
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* Generates the string code for a given sphere
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*@param sphereNodes A vector of TreeNodes for which a string code is to be generated
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*@return The SphereCode value
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*@exception org.openscience.cdk.exception.CDKException Thrown if something goes wrong
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private String getSphereCode(List sphereNodes) throws org.openscience.cdk.exception.CDKException
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if (sphereNodes == null || sphereNodes.size() < 1)
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return sphereDelimiters[sphere - 1];
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TreeNode treeNode = null;
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StringBuffer code = new StringBuffer();
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* append the tree node code to the HOSECode in
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* their now determined order, using commas to
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* separate nodes from different branches
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IAtom branch = ((TreeNode) (((TreeNode) sphereNodes.get(0)).source)).atom;
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StringBuffer tempCode = null;
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for (int i = 0; i < sphereNodes.size(); i++)
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treeNode = (TreeNode) sphereNodes.get(i);
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tempCode = new StringBuffer();
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if (!treeNode.source.stopper && treeNode.source.atom != branch)
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branch = treeNode.source.atom;
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if (!treeNode.source.stopper && treeNode.source.atom == branch)
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if (treeNode.bondType <= 4)
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tempCode.append(bondSymbols[(int) treeNode.bondType]);
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throw new CDKException("Unknown bond type");
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if (treeNode.atom != null && !treeNode.atom.getFlag(CDKConstants.VISITED))
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tempCode.append(getElementSymbol(treeNode.symbol));
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else if (treeNode.atom != null && treeNode.atom.getFlag(CDKConstants.VISITED))
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tempCode.append("&");
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treeNode.stopper = true;
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code.append(tempCode+createChargeCode(treeNode.atom));
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treeNode.hSymbol = tempCode.toString();
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if (treeNode.atom != null) treeNode.atom.setFlag(CDKConstants.VISITED, true);
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if (treeNode.source.stopper) treeNode.stopper = true;
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code.append(sphereDelimiters[sphere - 1]);
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return code.toString();
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* Gets the element rank for a given element symbol as given in Bremser's
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*@param symbol The element symbol for which the rank is to be determined
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*@return The element rank
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private double getElementRank(String symbol)
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for (int f = 0; f < rankedSymbols.length; f++)
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if (rankedSymbols[f].equals(symbol))
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return symbolRankings[f];
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IIsotope isotope = IsotopeFactory.getInstance(new ChemObject().getBuilder()).getMajorIsotope(symbol);
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return ((double) 800000 - isotope.getMassNumber());
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} catch (Exception exception) {
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System.err.println("Could not find major isotope for this element!!! : " + symbol);
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System.err.println("Because of this error: " + exception.getMessage());
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return (double)800000;
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* Returns the Bremser-compatible symbols for a given element. Silicon, for
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* example, is actually "Q". :-)
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*@param sym The element symbol to be converted
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*@return The converted symbol
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private String getElementSymbol(String sym)
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if (sym.equals("Si"))
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if (sym.equals("Cl"))
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if (sym.equals("Br"))
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* Determines the ranking score for each node, allowing for a sorting of nodes
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*@param sphereNodes The nodes for which the score is to be calculated.
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*@exception org.openscience.cdk.exception.CDKException Thrown if something goes wrong.
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private void calculateNodeScores(List sphereNodes) throws org.openscience.cdk.exception.CDKException
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TreeNode treeNode = null;
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for (int i = 0; i < sphereNodes.size(); i++)
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treeNode = (TreeNode) sphereNodes.get(i);
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treeNode.score += getElementRank(treeNode.symbol);
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if (treeNode.bondType <= 4)
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treeNode.score += bondRankings[(int) treeNode.bondType];
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throw new CDKException("Unknown bond type encountered in HOSECodeGenerator");
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* Sorts the nodes (atoms) in the sphereNode vector according to their score
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* This is used for the essential ranking of nodes in HOSE code sphere
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*@param sphereNodes A vector with sphere nodes to be sorted.
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private void sortNodesByScore(List sphereNodes)
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if (sphereNodes.size() == 0) return;
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* Now we sort by score
668
for (int i = 0; i < sphereNodes.size() - 1; i++)
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if (((TreeNode) sphereNodes.get(i + 1)).stringscore.compareTo(((TreeNode) sphereNodes.get(i)).stringscore)>0)
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obj = sphereNodes.get(i + 1);
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sphereNodes.remove(i + 1);
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sphereNodes.add(i, obj);
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/* Having sorted a sphere, we lable the nodes with their sort order */
680
TreeNode temp = null;
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for (int i = 0; i < sphereNodes.size(); i++)
683
temp = ((TreeNode) sphereNodes.get(i));
684
temp.sortOrder = sphereNodes.size() - i;
689
* If we use less than four sphere, this fills up the code with the missing
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* delimiters such that we are compatible with Bremser's HOSE code table.
692
private void fillUpSphereDelimiters()
694
logger.debug("Sphere: " + sphere);
695
for (int f = sphere; f < 4; f++)
697
HOSECode.append(sphereDelimiters[f]);
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class TreeNodeComparator implements Comparator {
704
*The compare method, compares by canonical label of atoms
706
* @param obj1 The first TreeNode
707
* @param obj2 The second TreeNode
710
public int compare(Object obj1, Object obj2) {
711
if(obj1==null || obj2==null || ((TreeNode) obj1).getAtom()==null || ((TreeNode) obj2).getAtom()==null)
713
Long label1 = (Long)((TreeNode) obj1).getAtom().getProperty("CanonicalLable");
714
Long label2 = (Long)((TreeNode) obj2).getAtom().getProperty("CanonicalLable");
715
if(label1==null || label2==null)
717
if (label1.intValue() < label2.intValue()) {
720
if (label1.intValue() > label2.intValue()) {
728
* Helper class for storing the properties of a node in our breadth first
732
* @cdk.created 2002-11-16
745
String hSymbol = null;
746
boolean stopper = false;
747
String stringscore="";
750
* Constructor for the TreeNode object
752
*@param symbol The Element symbol of the node
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*@param source The preceding node for this node
754
*@param atom The cdk atom object belonging to this node
755
*@param bondType The bond type by which this node was connect to its
757
*@param score The score used to rank this node within its sphere.
758
*@param degree Description of the Parameter
760
TreeNode(String symbol, TreeNode source, IAtom atom, double bondType, int degree, long score)
762
this.symbol = symbol;
763
this.source = source;
765
this.degree = degree;
767
this.bondType = bondType;
770
childs = new ArrayList();
773
public IAtom getAtom(){
779
* A TreeNode is equal to another TreeNode if it
780
* stands for the same atom object
782
*@param o The object tht we compare this TreeNode to
783
*@return True, if the this TreeNode's atom object equals the one of the other TreeNode
785
public boolean equals(Object o)
789
if (this.atom == ((TreeNode) o).atom)
796
/* we do nothing here because anything
797
that could seriously happen here is the we
798
got something which is not a TreeNode and then got
799
a class cast exception. Thus we can just wait until the
800
end of the method returns a "false" */
805
public String toString()
810
s += (atomContainer.getAtomNumber(atom) + 1);
813
s += "; r=" + ranking;
814
s += "; d = " + degree;
818
return exc.toString();
825
public List getNodesInSphere(int sphereNumber){
826
sphereNodes = spheres[sphereNumber-1];
827
List atoms=new ArrayList();
828
for (int g = 0; g < sphereNodes.size() ; g++) {
829
atoms.add(((TreeNode) sphereNodes.get(g)).atom);
added
removed
src/org/openscience/cdk/tools/HOSECodeGenerator.java
