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[Cdk-commits] SF.net SVN: cdk: [11474] cdk/trunk
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From: <eg...@us...> - 2008-07-01 07:55:29
|
Revision: 11474
http://cdk.svn.sourceforge.net/cdk/?rev=11474&view=rev
Author: egonw
Date: 2008-07-01 00:55:15 -0700 (Tue, 01 Jul 2008)
Log Message:
-----------
Removed the deterministics structure generator; it never functioned properly
Modified Paths:
--------------
cdk/trunk/META-INF/MANIFEST.MF
cdk/trunk/src/test/org/openscience/cdk/modulesuites/MstructgenTests.java
Removed Paths:
-------------
cdk/trunk/src/main/org/openscience/cdk/structgen/deterministic/EquivalentClassesDeterministicGenerator.java
cdk/trunk/src/main/org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.java
cdk/trunk/src/main/org/openscience/cdk/structgen/deterministic/Graph.java
cdk/trunk/src/test/org/openscience/cdk/structgen/deterministic/EquivalentClassesDeterministicGeneratorTest.java
cdk/trunk/src/test/org/openscience/cdk/structgen/deterministic/GENMDeterministicGeneratorTest.java
cdk/trunk/src/test/org/openscience/cdk/structgen/deterministic/structuregenerator.html
Modified: cdk/trunk/META-INF/MANIFEST.MF
===================================================================
--- cdk/trunk/META-INF/MANIFEST.MF 2008-06-30 18:45:26 UTC (rev 11473)
+++ cdk/trunk/META-INF/MANIFEST.MF 2008-07-01 07:55:15 UTC (rev 11474)
@@ -101,7 +101,6 @@
org.openscience.cdk.smiles.smarts.parser,
org.openscience.cdk.smiles.smarts.parser.visitor,
org.openscience.cdk.structgen,
- org.openscience.cdk.structgen.deterministic,
org.openscience.cdk.structgen.stochastic,
org.openscience.cdk.structgen.stochastic.operator,
org.openscience.cdk.templates,
Deleted: cdk/trunk/src/main/org/openscience/cdk/structgen/deterministic/EquivalentClassesDeterministicGenerator.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/structgen/deterministic/EquivalentClassesDeterministicGenerator.java 2008-06-30 18:45:26 UTC (rev 11473)
+++ cdk/trunk/src/main/org/openscience/cdk/structgen/deterministic/EquivalentClassesDeterministicGenerator.java 2008-07-01 07:55:15 UTC (rev 11474)
@@ -1,79 +0,0 @@
-/* $Revision$ $Author$ $Date$
- *
- * Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project
- *
- * Contact: cdk...@li...
- *
- * 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.structgen.deterministic;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.openscience.cdk.interfaces.IAtom;
-import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.tools.LoggingTool;
-
-/**
- * An implementation of Faulons equivalent classes deterministic generator.
- *
- * @author steinbeck
- * @cdk.created 2000-10-02
- * @cdk.module structgen
- * @cdk.svnrev $Revision$
- */
-public class EquivalentClassesDeterministicGenerator {
-
- LoggingTool logger = new LoggingTool(EquivalentClassesDeterministicGenerator.class);
-
- /* The initial, unbonded AtomContainer
- * From this we construct a number of AtomContainers that contain the
- * initial heavy atoms with assigned hydrogen counts.
- */
- IAtomContainer baseAtomContainer = null;
- List graphs = null;
-
- public EquivalentClassesDeterministicGenerator()
- {
- Graph graph = new Graph();
- graphs = new ArrayList();
- graphs.add(graph);
- }
-
- public void setAtomContainer(IAtomContainer ac) {
- baseAtomContainer = ac;
- initGraph();
- logger.debug("Number of classes after initialization: ", ((Graph)graphs.get(0)).size());
- }
-
- private void initGraph()
- {
- IAtomContainer ac = null;
- IAtom atom = null;
- Graph graph = (Graph)graphs.get(0);
- for (int f = 0; f < baseAtomContainer.getAtomCount(); f++)
- {
- ac = baseAtomContainer.getBuilder().newAtomContainer();
- atom = baseAtomContainer.getAtom(f);
- ac.addAtom(atom);
- ac.setProperty("class", new Integer(atom.getHydrogenCount()));
- graph.add(ac);
- }
- graph.partition();
- logger.debug("Number of initial distinct classes: ", graph.getNumberOfClasses());
- }
-
-}
Deleted: cdk/trunk/src/main/org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.java 2008-06-30 18:45:26 UTC (rev 11473)
+++ cdk/trunk/src/main/org/openscience/cdk/structgen/deterministic/GENMDeterministicGenerator.java 2008-07-01 07:55:15 UTC (rev 11474)
@@ -1,2932 +0,0 @@
-/* $Revision$ $Author$ $Date$
- *
- * Copyright (C) 2004-2007 Junfeng Hao
- *
- * Contact: cdk...@li...
- *
- * 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.structgen.deterministic;
-
-import java.io.FileWriter;
-import java.io.PrintWriter;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.openscience.cdk.formula.MolecularFormulaManipulator;
-import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IBond;
-import org.openscience.cdk.interfaces.IChemObjectBuilder;
-import org.openscience.cdk.interfaces.IMolecularFormula;
-import org.openscience.cdk.interfaces.IMolecule;
-import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
-import org.openscience.cdk.structgen.IStructureGenerationListener;
-import org.openscience.cdk.tools.LoggingTool;
-
-
-/**
- * An adapted implementation of the Molodtsov structure generator.
- * Changes to the original idea include issues of
- * normalization and strong canonicity criteria
- *
- * <pre>
- * gdg = new GENMDeterministicGenerator(formula,"");
- * gdg.addListener(this);
- * gdg.setStructuresAtATime(500);
- * gdg.generate();
- * </pre>
- *
- * <p>Please note that the number of isomers generated by this generator can quickly
- * become quite large and their storage in memory will take some space.
- * In order to handle to large amount of potential data, the generator hands you the
- * structures in small packets. You register with the generator as a
- * StructureGeneratorListener. In the respective stateChanged() method which you
- * must implement, you can do with the latest list of generated structures
- * whatever you want. Please not that the generatore deletes things internally
- * after handing over the list. Make sure to remove reference to structure in
- * which you are not interested anymore, to the garbage collector can clean them up.
- *
- * <p>If no StructureGeneratorListener is registered, the generator will not store
- * the molecular structures, and only count them. The total number of constitutional
- * isomers can be calculated with:
- * <pre>
- * gdg = new GENMDeterministicGenerator(formula,"");
- * gdg.generate();
- * int isomerCount = gdg.getNumberOfStructure();
- * </pre>
- *
- * <p>Details are found in the following papers
- * {@cdk.cite Molodtsov94, Molchanova96, Hu94, Hu94b, Hu99}.
- *
- * @author Junfeng Hao
- * @author Christoph Steinbeck
- * @cdk.created 2004-02-16
- * @cdk.module structgen
- * @cdk.svnrev $Revision$
- * @cdk.bug 1678346
- * @cdk.bug 1743861
- * @cdk.bug 1744463
- */
-public class GENMDeterministicGenerator {
-
- private LoggingTool logger;
-
- private int numberOfSetFragment;
- private int numberOfStructures;
- private IAtomContainer atomContainer;
- private int[] molecularFormula;
- private int[] numberOfBasicUnit;
- private int[] numberOfBasicFragment;
- private List basicFragment;
- private List structures;
- private PrintWriter structureout;
- private long returnedStructureCount = 500;
- private static double LOST=0.000000000001;
- private List listeners = null;
- boolean hasMoreStructures = false;
- int structuresAtATime = 500;
-
- private IChemObjectBuilder builder = null;
-
- /**
- * Constructor for the GENMDeterministicGenerator.
- * Allows for setting the molecular formula for which the
- * isomers are to be generated as well as for setting an output path
- * for a file with generated structures.
- *
- * @param mf molecular formula string
- * @param path Path to the file used for writing structures. Leave blank if current directory should be used.
- * If set to null then no structure file is written.
- */
- public GENMDeterministicGenerator(String mf, String path) throws Exception
- {
- logger = new LoggingTool(GENMDeterministicGenerator.class);
- builder = NoNotificationChemObjectBuilder.getInstance();
-
- numberOfSetFragment=0;
- numberOfStructures=0;
- logger.debug(mf);
- molecularFormula=new int[12];
- numberOfBasicUnit=new int[23];
- numberOfBasicFragment=new int[34];
- basicFragment=new ArrayList();
- structures=new ArrayList();
- listeners = new ArrayList();
-
- if (path != null) structureout=new PrintWriter(new FileWriter(path+"structuredata.txt"),true);
- else structureout = null;
-
- initializeParameters();
- analyseMolecularFormula(MolecularFormulaManipulator.getMolecularFormula(mf, builder));
-
- }
-
- /**
- * Central method of this Generator. Call
- *
- * @throws Exception
- */
- public void generate() throws Exception
- {
- numberOfStructures = 0;
- generateBasicUnits();
- logger.debug("numberofstructure is=", numberOfStructures);
- fireChange();
-
- }
-
-
- public void setBasicUnits(List basicUnits)
- {
- if(basicUnits!=null)getBasicUnit(basicUnits);
- else
- logger.error("input false");
- }
-
- /**
- * Get basic units from input information.
- *
- * @param basicUnits vector contains basic units which stored as string
- */
- public void getBasicUnit(List basicUnits)
- {
- int i;
- for(i=0;i<basicUnits.size();i++)
- {
- String s=(String)basicUnits.get(i);
- if(s.equals("Si"))numberOfBasicUnit[1]+=1;
- else if(s.equals("P"))numberOfBasicUnit[2]+=1;
- else if(s.equals("S"))numberOfBasicUnit[3]+=1;
- else if(s.equals("N"))numberOfBasicUnit[4]+=1;
- else if(s.equals("O"))numberOfBasicUnit[5]+=1;
- else if(s.equals("C"))numberOfBasicUnit[6]+=1;
- else if(s.equals("SiH3"))numberOfBasicUnit[7]+=1;
- else if(s.equals("SiH2"))numberOfBasicUnit[8]+=1;
- else if(s.equals("SiH"))numberOfBasicUnit[9]+=1;
- else if(s.equals("PH2"))numberOfBasicUnit[10]+=1;
- else if(s.equals("PH"))numberOfBasicUnit[11]+=1;
- else if(s.equals("SH"))numberOfBasicUnit[12]+=1;
- else if(s.equals("NH2"))numberOfBasicUnit[13]+=1;
- else if(s.equals("NH"))numberOfBasicUnit[14]+=1;
- else if(s.equals("OH"))numberOfBasicUnit[15]+=1;
- else if(s.equals("CH3"))numberOfBasicUnit[16]+=1;
- else if(s.equals("CH2"))numberOfBasicUnit[17]+=1;
- else if(s.equals("CH"))numberOfBasicUnit[18]+=1;
- else
- logger.error("input error");
- }
- }
-
-
- /**
- * Initialize the basic fragment. For the definition, please see the BasicFragment class.
- */
- public void initializeParameters() throws java.lang.Exception
- {
-
- basicFragment.add(new BasicFragment(1,4,1,0,1,">C<","C"));
- basicFragment.add(new BasicFragment(2,3,102,0,2,">C=","C"));
- basicFragment.add(new BasicFragment(3,2,2,0,3,"=C=","C"));
- basicFragment.add(new BasicFragment(4,2,103,0,4,"-C#","C"));
- basicFragment.add(new BasicFragment(5,3,1,1,5,">CH-","C"));
- basicFragment.add(new BasicFragment(6,2,102,1,6,"=CH-","C"));
- basicFragment.add(new BasicFragment(7,1,3,1,6,"CH#","C"));
- basicFragment.add(new BasicFragment(8,3,1,0,8,">N-","N"));
- basicFragment.add(new BasicFragment(9,2,102,0,9,"=N-","N"));
- basicFragment.add(new BasicFragment(10,1,3,0,10,"N#","N"));
- basicFragment.add(new BasicFragment(11,2,1,2,11,"-CH2-","C"));
- basicFragment.add(new BasicFragment(12,1,2,2,12,"CH2=","C"));
-
- basicFragment.add(new BasicFragment(13,2,1,1,13,"-NH-","N"));
- basicFragment.add(new BasicFragment(14,1,2,1,14,"NH=","N"));
- basicFragment.add(new BasicFragment(15,2,1,0,15,"-O-","O"));
- basicFragment.add(new BasicFragment(16,1,2,0,16,"O=","O"));
- basicFragment.add(new BasicFragment(17,2,1,0,17,"-S-","S"));
- basicFragment.add(new BasicFragment(18,1,2,0,18,"S=","S"));
- basicFragment.add(new BasicFragment(19,1,1,3,19,"CH3-","C"));
- basicFragment.add(new BasicFragment(20,1,1,2,20,"NH2-","N"));
- basicFragment.add(new BasicFragment(21,1,1,1,21,"OH-","O"));
- basicFragment.add(new BasicFragment(22,1,1,1,22,"-SH","S"));
- basicFragment.add(new BasicFragment(23,3,1,0,23,">P-","P"));
- basicFragment.add(new BasicFragment(24,2,1,1,24,"-PH-","P"));
- basicFragment.add(new BasicFragment(25,1,1,2,25,"PH2-","P"));
- basicFragment.add(new BasicFragment(26,4,1,0,26,">Si<","Si"));
- basicFragment.add(new BasicFragment(27,3,1,1,26,">SiH-","Si"));
- basicFragment.add(new BasicFragment(28,2,1,2,28,"-SiH2-","Si"));
- basicFragment.add(new BasicFragment(29,1,1,3,29,"SiH3-","Si"));
- basicFragment.add(new BasicFragment(30,1,1,0,30,"F-","F"));
- basicFragment.add(new BasicFragment(31,1,1,0,31,"Cl-","Cl"));
- basicFragment.add(new BasicFragment(32,1,1,0,32,"Br-","Br"));
- basicFragment.add(new BasicFragment(33,1,1,0,33,"I-","I"));
-
- /*for decompose the complex fragment*/
-
- basicFragment.add(new BasicFragment(42,2,1,0,2,">C","C"));
- basicFragment.add(new BasicFragment(43,1,2,0,2,"C=","C"));
-
-
- basicFragment.add(new BasicFragment(44,1,1,0,4,"C-","C"));
- basicFragment.add(new BasicFragment(45,1,3,0,4,"C#","C"));
-
-
- basicFragment.add(new BasicFragment(46,1,1,1,6,"CH-","C"));
- basicFragment.add(new BasicFragment(47,1,2,1,6,"CH=","C"));
-
-
- basicFragment.add(new BasicFragment(50,1,1,0,9,"N-","N"));
- basicFragment.add(new BasicFragment(51,1,2,0,9,"N=","N"));
- //Maybe add later
- return;
- }
-
- /**
- * Analyse molecular formula to verify it is valid.
- *
- * @param mfa MFAnalyser object to operate the molecular formula
- */
- public void analyseMolecularFormula(IMolecularFormula formula) throws java.lang.Exception
- {
- molecularFormula[1]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("C"));
- molecularFormula[2]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("H"));
- molecularFormula[3]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("O"));
- molecularFormula[4]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("N"));
- molecularFormula[5]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("S"));
- molecularFormula[6]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("P"));
- molecularFormula[7]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("Si"));
- molecularFormula[8]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("F"));
- molecularFormula[9]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("Cl"));
- molecularFormula[10]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("Br"));
- molecularFormula[11]= MolecularFormulaManipulator.getElementCount(formula, builder.newElement("I"));
-
- molecularFormula[0]=2*molecularFormula[1]+molecularFormula[4]+molecularFormula[6]+
- 2*molecularFormula[7]+2-molecularFormula[2]-molecularFormula[8]-molecularFormula[9]-
- molecularFormula[10]-molecularFormula[11];
- if(molecularFormula[0]<0)
- {
- logger.debug("Input molecular formula error!");
- }
-
- // for(i=1;i<=11;i++)
- // logger.debug("molecularFormula["+i+"]="+molecularFormula[i]);
-
-
- return;
- }
-
- /**
- * The first step: generate sets of basic units by backtracking algorithm.
- */
- public void generateBasicUnits() throws java.lang.Exception
- {
- int[] maxNumberOfBasicUnit=new int[23];
- int i,j,k;
- int iter1,iter2,iter3,iter4;
- int numberSi,numberP,numberS,numberN,numberNH; // numberSiH,numberSH,numberPH
- int numberO,numberOH,numberCH,numberH;
- int basicUnit;
-
- /* Generate the maximum number of basic units based on molecular formula. The corresponding
- basic units is Si,P,S,N,O,C,SiH3,SiH2,SiH,PH2,PH,SH,NH2,NH,OH,CH3,CH2,CH,F,Cl,Br,I. We could
- get the basic units directly for F,Cl,Br,I as they do not contain hydrogen atoms.*/
- maxNumberOfBasicUnit[1]=molecularFormula[7];//Si
- maxNumberOfBasicUnit[2]=molecularFormula[6];//P
- maxNumberOfBasicUnit[3]=molecularFormula[5];//S
- maxNumberOfBasicUnit[4]=molecularFormula[4];//N
- maxNumberOfBasicUnit[5]=molecularFormula[3];//O
- maxNumberOfBasicUnit[6]=molecularFormula[1];//C
- maxNumberOfBasicUnit[7]=molecularFormula[7];//SiH3
- maxNumberOfBasicUnit[8]=molecularFormula[7];//SiH2
- maxNumberOfBasicUnit[9]=molecularFormula[7];//SiH
- maxNumberOfBasicUnit[10]=molecularFormula[6];//PH2
- maxNumberOfBasicUnit[11]=molecularFormula[6];//PH
- maxNumberOfBasicUnit[12]=molecularFormula[5];//SH
- maxNumberOfBasicUnit[13]=molecularFormula[4];//NH2
- maxNumberOfBasicUnit[14]=molecularFormula[4];//NH
- maxNumberOfBasicUnit[15]=molecularFormula[3];//OH
- maxNumberOfBasicUnit[16]=molecularFormula[1];//CH3
- maxNumberOfBasicUnit[17]=molecularFormula[1];//CH2
- maxNumberOfBasicUnit[18]=molecularFormula[1];//CH
-
- /* for CH3, CH2 the number of H should be consider at the same time*/
- i=molecularFormula[2];
- j=i/3;
- k=i/2;
- if(maxNumberOfBasicUnit[16]>j)maxNumberOfBasicUnit[16]=j;
- if(maxNumberOfBasicUnit[17]>k)maxNumberOfBasicUnit[17]=k;
-
- /* initialization */
- for(i=1;i<=22;i++)numberOfBasicUnit[i]=0;
- numberSi=0;
- //numberSiH=0;
- numberP=0;
- //numberPH=0;
- numberS=0;
- //numberSH=0;
- numberN=0;
- numberNH=0;
- numberO=0;
- numberOH=0;
- numberCH=0;
- numberH=0;
- basicUnit=0;
-
- /* to distribute the hydrogen into heavy atoms. It is easily to see that only the basic
- units which contain hydrogens need to be considered. Therefore */
- iter1=6;
- iter2=18;
- do
- {
- iter1++;
- while(iter1<iter2)
- {
- numberOfBasicUnit[iter1]=0;
- switch(iter1-1)
- {
- case 9:
- numberSi=numberOfBasicUnit[7]+numberOfBasicUnit[8]+numberOfBasicUnit[9];
- //numberSiH=numberSi+2*numberOfBasicUnit[7]+numberOfBasicUnit[8];
- break;
- case 11:
- numberP=numberOfBasicUnit[10]+numberOfBasicUnit[11];
- //numberPH=numberSiH+numberP+numberOfBasicUnit[10];
- break;
- case 12:
- numberS=numberOfBasicUnit[12];
- //numberSH=numberPH+numberS;
- break;
- case 14:
- numberN=numberOfBasicUnit[13]+numberOfBasicUnit[14];
- numberNH=numberS+numberN+numberOfBasicUnit[13];
- break;
- case 15:
- numberO=numberOfBasicUnit[15];
- numberOH=numberNH+numberO;
- break;
- }
- iter1++;
- }
-
- do
- {
- /* begin from CH*/
- numberCH=numberOH+3*numberOfBasicUnit[16]+2*numberOfBasicUnit[17];
- numberH=molecularFormula[2]-numberCH;//left number of hydrogen atoms
- if(numberH>maxNumberOfBasicUnit[18])break;
- if(numberH<0)break;
- numberOfBasicUnit[18]=numberH;
-
- /* for Si */
- numberOfBasicUnit[1]=molecularFormula[7]-numberSi;
- if(numberOfBasicUnit[1]>maxNumberOfBasicUnit[1])break;
- if(numberOfBasicUnit[1]<0)break;
-
- /* for P */
- numberOfBasicUnit[2]=molecularFormula[6]-numberP;
- if(numberOfBasicUnit[2]>maxNumberOfBasicUnit[2])break;
- if(numberOfBasicUnit[2]<0)break;
-
- /* for S */
- numberOfBasicUnit[3]=molecularFormula[5]-numberS;
- if(numberOfBasicUnit[3]>maxNumberOfBasicUnit[3])break;
- if(numberOfBasicUnit[3]<0)break;
-
- /* for N */
- numberOfBasicUnit[4]=molecularFormula[4]-numberN;
- if(numberOfBasicUnit[4]>maxNumberOfBasicUnit[4])break;
- if(numberOfBasicUnit[4]<0)break;
-
- /* for O */
- numberOfBasicUnit[5]=molecularFormula[3]-numberO;
- if(numberOfBasicUnit[5]>maxNumberOfBasicUnit[5])break;
- if(numberOfBasicUnit[5]<0)break;
-
- /* for C */
- numberOfBasicUnit[6]=molecularFormula[1]-numberOfBasicUnit[16]-numberOfBasicUnit[17]-numberOfBasicUnit[18];
- if(numberOfBasicUnit[6]>maxNumberOfBasicUnit[6])break;
- if(numberOfBasicUnit[6]<0)break;
-
-
- basicUnit+=1;
- numberOfBasicUnit[0]=basicUnit;
- /* for F,Cl,Br,I */
- for(i=19;i<=22;i++)
- if(molecularFormula[i-11]!=0)numberOfBasicUnit[i]=molecularFormula[i-11];
- if (logger.isDebugEnabled()) {
- for(i=0;i<=22;i++) {
- if(numberOfBasicUnit[i]!=0) {
- logger.debug("numberOfBasicUnit["+i+"]="+numberOfBasicUnit[i]);
- logger.debug("numberOfBasicUnit["+i+"]="+numberOfBasicUnit[i]);
- }
- }
- }
-
- /* If all the following judgement are satisfactory, it should be one set of basic unit.Output them*/
- generateBasicFragments();
- }while(false);
-
- /* exit from the distribution hydrogen, backtracking*/
- do
- {
- iter1-=1;
- if(iter1==6)return;
- if(numberOfBasicUnit[iter1]>=maxNumberOfBasicUnit[iter1])continue;
-
- do
- {
- numberOfBasicUnit[iter1]+=1;
- if(iter1==7)//SiH3
- {
- iter3=numberOfBasicUnit[7];
- if(iter3>molecularFormula[7])break;
- }
- else if(iter1==8)//SiH2
- {
- iter3=numberOfBasicUnit[7]+numberOfBasicUnit[8];
- if(iter3>molecularFormula[7])break;
- }
- else if(iter1==9)//SiH2
- {
- iter3=numberOfBasicUnit[7]+numberOfBasicUnit[8]+numberOfBasicUnit[9];
- if(iter3>molecularFormula[7])break;
- }
- else if(iter1==10)//PH2
- {
- iter3=numberOfBasicUnit[10];
- if(iter3>molecularFormula[6])break;
- }
- else if(iter1==11)//PH
- {
- iter3=numberOfBasicUnit[10]+numberOfBasicUnit[11];
- if(iter3>molecularFormula[6])break;
- }
- else if(iter1==13)//NH2
- {
- iter3=numberOfBasicUnit[13];
- if(iter3>molecularFormula[4])break;
- }
- else if(iter1==14)//NH
- {
- iter3=numberOfBasicUnit[13]+numberOfBasicUnit[14];
- if(iter3>molecularFormula[4])break;
- }
- else if(iter1==16)//CH3
- {
- iter3=numberOfBasicUnit[16];
- if(iter3>molecularFormula[1])break;
- iter4=numberOH+3*numberOfBasicUnit[16];
- if(iter4>molecularFormula[2])break;
- i=molecularFormula[2]-iter4;
- j=molecularFormula[1]-iter3;
- k=2*j;
- if(i>k)continue;
- else break;
- }
- else if(iter1==17)//CH2
- {
- iter3=numberOfBasicUnit[16]+numberOfBasicUnit[17];
- if(iter3>molecularFormula[1])break;
- iter4=numberOH+3*numberOfBasicUnit[16]+2*numberOfBasicUnit[17];
- if(iter4>molecularFormula[2])break;
- i=molecularFormula[2]-iter4;
- j=molecularFormula[1]-iter3;
- if(i>j)continue;
- else break;
- }
- else
- {
- break;
- }
- break;
- }while(true);
- break;
- }while(true);
-
- }while(iter1>6);
- return;
- }
-
-
- /**
- * Second step: generate basic fragments, the generating rules from basic
- * units are as follows.
- * For carbon:
- * <ul>
- * <li>>C<, >C=,=C=,-C#(triple bond), 1~4
- * <li>CH: >CH-,=CH-,CH#, 5~7
- * <li>CH2: -CH2-,CH2=, 11~12
- * <li>CH3: CH3-,19
- * </ul>
- *
- * For nitrogen:
- * <ul>
- * <li>>N-,-N=,N#,8~10
- * <li>NH: -NH-, NH= ,13~14
- * <li>NH2: NH2-,20
- * </ul>
- *
- * For oxygen:
- * <ul>
- * <li>-O-,O=, 15~16
- * <li>OH: -OH, 21
- * </ul>
- *
- * For sulfur:
- * <ul>
- * <li>-S-,S=, 17~18
- * <li>SH, -SH,22
- * </ul>
- *
- * For phosphorus:
- * <ul>
- * <li>>P-, 23
- * <li>PH: -PH-,24
- * <li>PH2: -PH2,25
- * </ul>
- *
- * For silicon:
- * <ul>
- * <li>>Si< 26
- * <li>SiH: >SiH- 27
- * <li>SiH2: -SiH2- 28
- * <li>SiH3: SiH3- 29
- * </ul>
- *
- * For others:
- * <ul>
- * <li>F- 30
- * <li>Cl- 31
- * <li>Br- 32
- * <li>I- 33
- * </ul>
- * It could be easily add the new fragments, such as valence, variable
- * valence, such as N,P,also, fragments contains charges.
- * It is a combinatorial algorithm, as in n1*n2*n3.
- */
- public void generateBasicFragments() throws java.lang.Exception
- {
- int i,k;
- int iter1;
- boolean flag;
- int[] maxNumberOfBasicFragment=new int[34];
- /*initialization for the variables*/
- if (logger.isDebugEnabled()) for(i=0;i<=22;i++) if(numberOfBasicUnit[i]!=0)logger.debug("numberOfBasicUnit["+i+"]=", numberOfBasicUnit[i]);
- for(i=1;i<34;i++)numberOfBasicFragment[i]=0;
-
- /* maximum number of basic fragments*/
- maxNumberOfBasicFragment[1]=numberOfBasicUnit[6];//>C<
- maxNumberOfBasicFragment[2]=numberOfBasicUnit[6];//>C=
- maxNumberOfBasicFragment[3]=numberOfBasicUnit[6];//=C=
- maxNumberOfBasicFragment[4]=numberOfBasicUnit[6];//-C#
-
- maxNumberOfBasicFragment[5]=numberOfBasicUnit[18];//>CH-
- maxNumberOfBasicFragment[6]=numberOfBasicUnit[18];//=CH-
- maxNumberOfBasicFragment[7]=numberOfBasicUnit[18];//CH#
-
- maxNumberOfBasicFragment[8]=numberOfBasicUnit[4];//>N-
- maxNumberOfBasicFragment[9]=numberOfBasicUnit[4];//-N=
- maxNumberOfBasicFragment[10]=numberOfBasicUnit[4];//N#
-
- maxNumberOfBasicFragment[11]=numberOfBasicUnit[17];//-CH2-
- maxNumberOfBasicFragment[12]=numberOfBasicUnit[17];//CH2=
-
- maxNumberOfBasicFragment[13]=numberOfBasicUnit[14];//-NH-
- maxNumberOfBasicFragment[14]=numberOfBasicUnit[14];//NH=
-
- maxNumberOfBasicFragment[15]=numberOfBasicUnit[5];//-O-
- maxNumberOfBasicFragment[16]=numberOfBasicUnit[5];//O=
-
- maxNumberOfBasicFragment[17]=numberOfBasicUnit[3];//-S-
- maxNumberOfBasicFragment[18]=numberOfBasicUnit[3];//S=
-
- numberOfBasicFragment[19]=numberOfBasicUnit[16];
- numberOfBasicFragment[20]=numberOfBasicUnit[13];
- numberOfBasicFragment[21]=numberOfBasicUnit[15];
- numberOfBasicFragment[22]=numberOfBasicUnit[12];
- numberOfBasicFragment[23]=numberOfBasicUnit[2];
- numberOfBasicFragment[24]=numberOfBasicUnit[11];
- numberOfBasicFragment[25]=numberOfBasicUnit[10];
- numberOfBasicFragment[26]=numberOfBasicUnit[1];
- numberOfBasicFragment[27]=numberOfBasicUnit[9];
- numberOfBasicFragment[28]=numberOfBasicUnit[8];
- numberOfBasicFragment[29]=numberOfBasicUnit[7];
- numberOfBasicFragment[30]=numberOfBasicUnit[19];
- numberOfBasicFragment[31]=numberOfBasicUnit[20];
- numberOfBasicFragment[32]=numberOfBasicUnit[21];
- numberOfBasicFragment[33]=numberOfBasicUnit[22];
-
- iter1=17;
- //iter2=0;
- while(iter1>0)
- {
- iter1+=1;
-
- while(iter1<18)
- {
- numberOfBasicFragment[iter1]=0;
- iter1+=1;
- }
-
- do
- {
- numberOfBasicFragment[18]=numberOfBasicUnit[3]-numberOfBasicFragment[17];
- if(numberOfBasicFragment[18]<0)break;
- numberOfBasicFragment[16]=numberOfBasicUnit[5]-numberOfBasicFragment[15];
- if(numberOfBasicFragment[16]<0)break;
- numberOfBasicFragment[14]=numberOfBasicUnit[14]-numberOfBasicFragment[13];
- if(numberOfBasicFragment[14]<0)break;
- numberOfBasicFragment[12]=numberOfBasicUnit[17]-numberOfBasicFragment[11];
- if(numberOfBasicFragment[12]<0)break;
- numberOfBasicFragment[10]=numberOfBasicUnit[4]-numberOfBasicFragment[8]-numberOfBasicFragment[9];
- if(numberOfBasicFragment[10]<0)break;
-
- numberOfBasicFragment[7]=numberOfBasicUnit[18]-numberOfBasicFragment[5]-numberOfBasicFragment[6];
- if(numberOfBasicFragment[7]<0)break;
- numberOfBasicFragment[4]=numberOfBasicUnit[6]-numberOfBasicFragment[1]-numberOfBasicFragment[2]-numberOfBasicFragment[3];
- if(numberOfBasicFragment[4]<0)break;
-
- flag=testBasicFragment();
- if(flag)
- {
- numberOfSetFragment+=1;
- logger.debug("Fragment Set ", numberOfSetFragment);
- if (logger.isDebugEnabled()) {
- for(i=1;i<34;i++) {
- if(numberOfBasicFragment[i]!=0)logger.debug(((BasicFragment)(basicFragment.get(i-1))).getBasicFragment()+" "+numberOfBasicFragment[i]);
- }
- }
- generateIsomers();
- }
-
- }while(false);
-
- do
- {
- iter1=iter1-1;
- if(iter1==0)return;
-
- if(numberOfBasicFragment[iter1]>=maxNumberOfBasicFragment[iter1])continue;
- numberOfBasicFragment[iter1]=numberOfBasicFragment[iter1]+1;
-
- if(iter1==2)
- {
- k=numberOfBasicFragment[1]+numberOfBasicFragment[2];
- if(k>numberOfBasicUnit[6])continue;
- else break;
- }
- else if(iter1==3)
- {
- k=numberOfBasicFragment[1]+numberOfBasicFragment[2]+numberOfBasicFragment[3];
- if(k>numberOfBasicUnit[6])continue;
- else break;
- }
- else if(iter1==4)
- {
- k=numberOfBasicFragment[1]+numberOfBasicFragment[2]+numberOfBasicFragment[3]+numberOfBasicFragment[4];
- if(k>numberOfBasicUnit[6])continue;
- else break;
- }
- else if(iter1==6)
- {
- k=numberOfBasicFragment[5]+numberOfBasicFragment[6];
- if(k>numberOfBasicUnit[18])continue;
- else break;
- }
- else if(iter1==7)
- {
- k=numberOfBasicFragment[5]+numberOfBasicFragment[6]+numberOfBasicFragment[7];
- if(k>numberOfBasicUnit[18])continue;
- else break;
- }
-
- else if(iter1==9)
- {
- k=numberOfBasicFragment[8]+numberOfBasicFragment[9];
- if(k>numberOfBasicUnit[4])continue;
- else break;
- }
- else if(iter1==10)
- {
- k=numberOfBasicFragment[8]+numberOfBasicFragment[9]+numberOfBasicFragment[10];
- if(k>numberOfBasicUnit[4])continue;
- else break;
- }
- else if(iter1==12)
- {
- k=numberOfBasicFragment[11]+numberOfBasicFragment[12];
- if(k>numberOfBasicUnit[17])continue;
- else break;
- }
- else if(iter1==14)
- {
- k=numberOfBasicFragment[13]+numberOfBasicFragment[14];
- if(k>numberOfBasicUnit[14])continue;
- else break;
- }
- else if(iter1==16)
- {
- k=numberOfBasicFragment[15]+numberOfBasicFragment[16];
- if(k>numberOfBasicUnit[5])continue;
- else break;
- }
- else if(iter1==18)
- {
- k=numberOfBasicFragment[17]+numberOfBasicFragment[18];
- if(k>numberOfBasicUnit[3])continue;
- else break;
- }
- break;
- }while(true);
- }
- }
-
-
-
- /**
- * Test for the set of basic fragment.
- */
- public boolean testBasicFragment()
- {
- int i,j;
- int numberOfFragment,numberOfOneFreeValence,numberOfTwoFreeValence;
- int numberOfThreeFreeValence,numberOfFourFreeValence;
- int numberOfSideDoubleBond,numberOfMiddleDoubleBond;
- int totalFreeValence,totalDoubleBond,totalTripleBond;
- int numberOfSideTripleBond,numberOfMiddleTripleBond;
- //boolean flag=true;
-
- /* initialization the variable*/
- numberOfFragment=0;
- numberOfOneFreeValence=0;
- numberOfTwoFreeValence=0;
- numberOfThreeFreeValence=0;
- numberOfFourFreeValence=0;
- numberOfSideDoubleBond=0;
- numberOfMiddleDoubleBond=0;
- numberOfSideTripleBond=0;
- numberOfMiddleTripleBond=0;
- totalTripleBond=0;
- totalFreeValence=0;
-
- for(i=1;i<34;i++)
- {
- numberOfFragment+=numberOfBasicFragment[i];
- j=((BasicFragment)(basicFragment.get(i-1))).getNumberOfFreeValence();
- switch(j)
- {
- case 1: numberOfOneFreeValence+=numberOfBasicFragment[i];break;
- case 2: numberOfTwoFreeValence+=numberOfBasicFragment[i];break;
- case 3: numberOfThreeFreeValence+=numberOfBasicFragment[i];break;
- case 4: numberOfFourFreeValence+=numberOfBasicFragment[i];break;
- }
-
- }
- /* 1. total free valence test*/
- totalFreeValence=numberOfOneFreeValence+numberOfTwoFreeValence*2+numberOfThreeFreeValence*3+numberOfFourFreeValence*4;
- if((totalFreeValence%2)!=0)return false;
-
- totalFreeValence/=2;
- if(numberOfFragment>(totalFreeValence+1))return false;
-
- /*2. double bond test: */
- numberOfSideDoubleBond=numberOfBasicFragment[12]+numberOfBasicFragment[14]+numberOfBasicFragment[16]+numberOfBasicFragment[18];
- numberOfMiddleDoubleBond=numberOfBasicFragment[2]+numberOfBasicFragment[6]+numberOfBasicFragment[9];
- if(numberOfBasicFragment[3]==0)
- {
- if(numberOfSideDoubleBond>numberOfMiddleDoubleBond && numberOfMiddleDoubleBond>0)return false;
- totalDoubleBond=numberOfSideDoubleBond+numberOfMiddleDoubleBond;
- if((totalDoubleBond%2)!=0)return false;
- if((numberOfMiddleDoubleBond==0)&& (numberOfSideDoubleBond==2)&&(numberOfFragment>2))return false;
- }
- if(numberOfBasicFragment[3]>0)
- {
- if((numberOfMiddleDoubleBond==0)&&(numberOfBasicFragment[3]<(numberOfFragment-2)))return false;
- if((numberOfMiddleDoubleBond+numberOfSideDoubleBond==0)&&(numberOfBasicFragment[3]<numberOfFragment))return false;
- }
-
- /*triple bond test*/
-
- numberOfSideTripleBond=numberOfBasicFragment[7]+numberOfBasicFragment[10];
- numberOfMiddleTripleBond=numberOfBasicFragment[4];
- totalTripleBond=numberOfSideTripleBond+numberOfMiddleTripleBond;
-
- if((totalTripleBond%2)!=0)return false;
- if(numberOfMiddleTripleBond==0 && numberOfSideTripleBond!=0)return false;
- return true;
- }
-
- List setOfBasicFragment = new ArrayList();
- IntArray storedSymbolOfStructure = new IntArray();
-
- /**
- * The thrid step: generate all the possible consititional isomers.
- */
- public void generateIsomers()
- {
- int i,j,rows;
- int step,firstUnfilledRow;//equivalentClass;
- int[] totalNumberOfTheSet=new int[1];
- int totalNumberOfAtomAndBond=0;
- totalNumberOfTheSet[0]=0;
-
- boolean flag,nextWCF,isForced,isPossibleFilling;
- int[][] adjacencyMatrix;
- int[][] previousMatrix;
- int[] rowMatrix;
- //int[] setOfStability;
- //int[] category;
- int[] bondAttribute;
- int[] parentID;
- // reinitialize
- storedSymbolOfStructure.clear();
- setOfBasicFragment.clear();
- IAtomContainer atomContainer=null;
-
- /*1. prepare the vector of basic fragment and atomContainer
- * atomContainer put the bond formed, while set of basic fragment
- * put the source basic fragment.
- */
-
-
- for(i=1;i<34;i++)
- if(numberOfBasicFragment[i]!=0)
- {
- for(j=1;j<=numberOfBasicFragment[i];j++)
- totalNumberOfAtomAndBond+=((BasicFragment)(basicFragment.get(i-1))).getNumberOfFreeValence();
-
- }
- totalNumberOfAtomAndBond/=2;
-
-
- for(i=1;i<34;i++)
- if(numberOfBasicFragment[i]!=0)
- {
- for(j=1;j<=numberOfBasicFragment[i];j++)
- {
- totalNumberOfAtomAndBond+=1;
- }
-
- // consider the complex fragment
- switch(i)
- {
- case 2:
- for(j=1;j<=numberOfBasicFragment[i];j++)
- {
- setOfBasicFragment.add((BasicFragment)(basicFragment.get(33)));
- setOfBasicFragment.add((BasicFragment)(basicFragment.get(34)));
- }
-
- break;
- case 4:
- for(j=1;j<=numberOfBasicFragment[i];j++)
- {
- setOfBasicFragment.add((BasicFragment)(basicFragment.get(35)));
- setOfBasicFragment.add((BasicFragment)(basicFragment.get(36)));
- }
- break;
- case 6:
- for(j=1;j<=numberOfBasicFragment[i];j++)
- {
- setOfBasicFragment.add((BasicFragment)(basicFragment.get(37)));
- setOfBasicFragment.add((BasicFragment)(basicFragment.get(38)));
- }
- break;
- case 9:
- for(j=1;j<=numberOfBasicFragment[i];j++)
- {
- setOfBasicFragment.add((BasicFragment)(basicFragment.get(39)));
- setOfBasicFragment.add((BasicFragment)(basicFragment.get(40)));
- }
- break;
- default:
- for(j=1;j<=numberOfBasicFragment[i];j++)
- setOfBasicFragment.add((BasicFragment)(basicFragment.get(i-1)));
- break;
- }
-
- }
-
- //order the fragments
- atomContainer= builder.newAtomContainer();
-
- parentID=new int[setOfBasicFragment.size()];
-
- /* sort the fragment set according to the free valence*/
- setOfBasicFragment=getOrderOfBasicFragmentSet(setOfBasicFragment,parentID);
-
- rows=setOfBasicFragment.size();
- adjacencyMatrix=new int[rows][rows];
- previousMatrix=new int[rows][rows];
- rowMatrix=new int[rows];
- //setOfStability=new int[rows];
- bondAttribute=new int[rows];
-
- for(i=0;i<rows;i++)
- {
- bondAttribute[i]=((BasicFragment)(setOfBasicFragment.get(i))).getAttribute();
- }
-
- for(i=0;i<setOfBasicFragment.size();i++)
- {
- atomContainer.addAtom(
- builder.newAtom(((BasicFragment)(setOfBasicFragment.get(i))).getHeavyAtomSymbol())
- );
- }
-
- //IAtom[] atom=atomContainer.getAtoms();
-
- for(i=0;i<atomContainer.getAtomCount();i++)
- {
- atomContainer.getAtom(i).setHydrogenCount(((BasicFragment)(setOfBasicFragment.get(i))).getNumberOfHydrogen());
- }
-
- //2. initialize the matrix
- initializeMatrix(setOfBasicFragment,bondAttribute,adjacencyMatrix,previousMatrix);
- // Initial equivalent
- //equivalentClass=getEquivalentClass(setOfBasicFragment,setOfStability);
- //3. begin, see the flowchart
- step=0;
-
- //Maximum WCF(M)
- isPossibleFilling=getMaximumWCF(setOfBasicFragment,0,rowMatrix,adjacencyMatrix,previousMatrix,parentID);
- if(!isPossibleFilling)return;
- while(step<(rows-1))
- {
- // Force filling the left lines
- step+=1;
- firstUnfilledRow=forceFilling(step,setOfBasicFragment,adjacencyMatrix,previousMatrix);
- do
- {
- // Check admissibility
- flag=checkAdmissibility(step,setOfBasicFragment,adjacencyMatrix);
- if(!flag)break;
-
- // constraint checker
- flag=checkConstraint(firstUnfilledRow,setOfBasicFragment,adjacencyMatrix,atomContainer);
- if(!flag)break;
- }while(false);
-
- if(flag)
- {
- if(firstUnfilledRow<rows)
- {
- step=firstUnfilledRow;
- isPossibleFilling=getMaximumWCF(setOfBasicFragment,step,rowMatrix,adjacencyMatrix,previousMatrix,parentID);
- if(!isPossibleFilling)return;
- continue;
- }
- else
- {
- getFinalStructure(setOfBasicFragment,adjacencyMatrix,storedSymbolOfStructure,totalNumberOfTheSet,totalNumberOfAtomAndBond);
- step-=1;
- }
- }
- else step-=1;
-
- // judge whether the line is forcefilling or not
- isForced=isForceFilling(step,previousMatrix,adjacencyMatrix);
- while(isForced)
- {
- step-=1;
- isForced=isForceFilling(step,previousMatrix,adjacencyMatrix);
- }
-
- //get rowMatrix
- for(i=0;i<rowMatrix.length;i++)rowMatrix[i]=adjacencyMatrix[step][i];
- // backtracking: restore the matrix to previous step
- restoreMatrix(step,bondAttribute,previousMatrix,adjacencyMatrix);
- nextWCF=getNextWCF(setOfBasicFragment,step,rowMatrix,adjacencyMatrix,previousMatrix,parentID);
-
- while(!nextWCF)
- {
- step-=1;
- if(step<0)return;
- else
- {
- isForced=isForceFilling(step,previousMatrix,adjacencyMatrix);
- while(isForced)
- {
- step-=1;
- isForced=isForceFilling(step,previousMatrix,adjacencyMatrix);
- }
- for(i=0;i<rowMatrix.length;i++)
- {
- rowMatrix[i]=adjacencyMatrix[step][i];
- }
- restoreMatrix(step,bondAttribute,previousMatrix,adjacencyMatrix);
- nextWCF=getNextWCF(setOfBasicFragment,step,rowMatrix,adjacencyMatrix,previousMatrix,parentID);
- if(nextWCF)break;
- }
- }
- }
- return;
- }
-
- /**
- * Initialized the adjacency matrix.
- *
- * @param setOfBasicFragment set of basic fragment
- * @param bondAttribute to distinguish the bond
- * @param adjacency adjacency matrix
- * @param previousMatrix tracing the change of adjacency matrix
- */
- public void initializeMatrix(List setOfBasicFragment, int[] bondAttribute,int[][] adjacency,int[][] previousMatrix)
- {
- int i,j,row,sum;
- row=setOfBasicFragment.size();
-
- int[] valenceOfFragment=new int[row];
-
-
- for(i=0;i<adjacency.length;i++)
- for(j=0;j<adjacency.length;j++)
- adjacency[i][j]=-1;
- for(i=0;i<adjacency.length;i++)
- {
- adjacency[i][i]=0;
- valenceOfFragment[i]=0;
- }
-
-
- /* if there are two basic fragments which is 1 free valence, appraently it is impossible to
- * be bonded between these two fragments.
- */
- sum=0;
- if(row>2)
- {
- for(i=0;i<row;i++)
- {
- if(((BasicFragment)(setOfBasicFragment.get(i))).getNumberOfFreeValence()==1
- && ((BasicFragment)(setOfBasicFragment.get(i))).getID()<=33)valenceOfFragment[i]=1;
- sum+=valenceOfFragment[i];
- }
- if(sum>1)
- for(i=0;i<row-1;i++)
- for(j=i+1;j<row;j++)
- {
- if(valenceOfFragment[i]==1 &&valenceOfFragment[j]==1)
- {
- adjacency[i][j]=0;
- adjacency[j][i]=0;
- }
- }
- }
- // The following loop is to give the zero element for bond unmatch. 28-11-2003
- for(i=0;i<row-1;i++)
- for(j=i;j<row;j++)
- if(bondAttribute[i]!=bondAttribute[j])
- {
- adjacency[i][j]=0;
- adjacency[j][i]=0;
- }
- for(i=0;i<adjacency.length;i++)
- {
- for(j=0;j<adjacency.length;j++)
- {
- previousMatrix[i][j]=adjacency[i][j];
- }
- }
- return;
- }
-
-
- /**
- * Restore the adjacency matrix to previous step.
- *
- * @param step the line is filling
- * @param freeValence array for free valence of each node left
- * @param sourceMatrix the reference matrix
- * @param destMatrix the matrix need to backtrack
- */
- public void restoreMatrix(int step,int[] freeValence,int[][] sourceMatrix,int[][] destMatrix)
- {
- int i,j;
- for(i=step;i<sourceMatrix.length;i++)
- {
- if(sourceMatrix[i][i]>step)
- {
- destMatrix[i][i]=0;sourceMatrix[i][i]=0;
- }
-
- for(j=0;j<sourceMatrix.length;j++)
- {
- if(sourceMatrix[i][j]>step)
- {
- if(i!=j)
- {
- destMatrix[i][j]=-1;sourceMatrix[i][j]=-1;
- }
- }
- }
- }
- return;
- }
-
- /**
- * Maximum weakly canonical filling of line M.
- *
- * @param setOfBasicFragment set of basic fragment
- * @param step the line is filling
- * @param rowMatrix the row which contains the filling line
- * @param adjacency adjacency matrix
- * @param previousMatrix matrix is used for tracing the change of adjacency matrix.
- * @param parentID mainly used for unsaturated part
- */
- public boolean getMaximumWCF(List setOfBasicFragment,int step,int[] rowMatrix, int[][] adjacency,int[][] previousMatrix,int[] parentID)
- {
- int i,iter,bondOrder,size;
- int totalBond,existBond,leftBond;
- int[] setOfStability;
- setOfStability=new int[rowMatrix.length];
-
- /*Get the row matrix*/
- size=setOfBasicFragment.size();
- iter=0;
- for(i=0;i<adjacency.length;i++)
- {
- rowMatrix[i]=adjacency[step][i];
- if(rowMatrix[i]==-1)iter+=1;
- }
- getSetOfStability(setOfBasicFragment,step,rowMatrix,adjacency,setOfStability,parentID);
- existBond=0;
- for(i=0;i<adjacency.length;i++)if(rowMatrix[i]>0)existBond+=rowMatrix[i];
- totalBond=((BasicFragment)(setOfBasicFragment.get(step))).getNumberOfFreeValence();
- bondOrder=((BasicFragment)(setOfBasicFragment.get(step))).getAttribute();
- leftBond=totalBond-existBond;
- if(leftBond>iter)return false;
-
- /* maximum this line*/
- iter=leftBond;
- for(i=1;i<rowMatrix.length;i++)
- {
- if(setOfStability[i]!=0)
- {
- if(iter>0){rowMatrix[i]=bondOrder;iter-=1;}
- else rowMatrix[i]=0;
- }
- }
- /* A(i,j)=A(j,i)*/
- for(i=0;i<adjacency.length;i++)
- {
- adjacency[step][i]=rowMatrix[i];
- if(previousMatrix[step][i]==-1)previousMatrix[step][i]=step+1;
-
- adjacency[i][step]=rowMatrix[i];
- if(previousMatrix[i][step]==-1)previousMatrix[i][step]=step+1;
- }
-
- //for unsaturated part
- int decomposedNumber=0;
- int number1=0;
- int number2=0;
- if(parentID[step]==-1)return true;
- else
- {
-
- for(i=0;i<size;i++)
- if(parentID[i]!=-1)decomposedNumber+=1;
- for(i=0;i<adjacency.length;i++)
- if(rowMatrix[i]>0 && parentID[i]!=-1)
- {
-
- number1=parentID[step];
- number2=parentID[i];
- if((adjacency[step][i]>0 || adjacency[i][step]>0) && adjacency[number1][number2]==-1)
- {
- adjacency[number1][number2]=0;
- adjacency[number2][number1]=0;
- if(previousMatrix[number1][number2]==-1)
- previousMatrix[number1][number2]=step+1;
- if(previousMatrix[number2][number1]==-1)
- previousMatrix[number2][number1]=step+1;
- }
- }
- }
- return true;
- }
-
-
- /**
- * Get the partition for the left fragment at every step.
- *
- * @param setOfBasicFragment set of basic fragment
- * @param step the line is filling
- * @param rowMatrix the row which contains the filling line
- * @param adjacency adjacency matrix
- * @param setOfStability the previous equivalent partition
- * @param parentID mainly used for unsaturated part
- */
- public void getSetOfStability(List setOfBasicFragment,int step,int[] rowMatrix, int[][] adjacency,int[] setOfStability,int[] parentID)
- {
- int i,j,count,line;
- int temp,size;
- size=rowMatrix.length;
- //boolean[] isAdded=new boolean[size];
- int[] category=new int[size+1];
- int[] equivalentClass=new int[size];
-
- line=0;
- for(i=0;i<adjacency.length;i++)setOfStability[i]=0;
- if(step==0)
- {
- for(i=1;i<setOfBasicFragment.size();i++)
- {
- if(rowMatrix[i]==-1)
- {
- setOfStability[i]=((BasicFragment)(setOfBasicFragment.get(i))).getID();
- }
- }
-
- }
- else
- {
- for(i=step+1;i<setOfBasicFragment.size();i++)
- {
- if(rowMatrix[i]==-1)
- {
- setOfStability[i]=((BasicFragment)(setOfBasicFragment.get(i))).getID();
- }
- }
-
- /* judge temporatory equivalent at this line. */
- for(i=step+1;i<setOfStability.length-1;i++)
- for(j=i+1;j<setOfStability.length;j++)
- {
- if(rowMatrix[i]==-1 && rowMatrix[j]==-1 && setOfStability[i]==setOfStability[j])
- {
- for(line=0;line<step;line++)
- {
- if(adjacency[line][i]==adjacency[line][j])continue;
- else break;
- }
- if(line<step)setOfStability[j]+=100;//
- }
- }
- }
-
- temp=0;
- for(i=0;i<parentID.length;i++)
- {
- if(parentID[i]!=-1)temp+=1;
- }
- if(temp>4)
- {
- int[] fragmentID=new int[setOfBasicFragment.size()];
- for(i=0;i<setOfBasicFragment.size();i++)
- fragmentID[i]=((BasicFragment)(setOfBasicFragment.get(i))).getID();
- for(i=step+1;i<setOfBasicFragment.size()-1;i++)
- for(j=i+1;j<setOfBasicFragment.size();j++)
- {
- int temp1=parentID[i];
- int temp2=parentID[j];
- if(rowMatrix[i]==-1 && rowMatrix[j]==-1)
- {
- if(fragmentID[i]>33 && fragmentID[j]>33
- && rowMatrix[temp1]!=-1 && rowMatrix[temp2]!=-1
- && setOfStability[i]==setOfStability[j])
- setOfStability[j]+=100;
- }
- }
- }
- /* get the category for this line*/
- count=1;
- for(i=step+1;i<setOfStability.length;i++)if(rowMatrix[i]==-1){line=i;break;}
- category[1]=setOfStability[line];
- for(i=step+1;i<setOfStability.length;i++)
- {
- if(setOfStability[i]!=0)
- {
- for(j=1;j<=count;j++)
- {
- if(rowMatrix[i]==-1)
- {
- temp=setOfStability[i]-category[j];
- if(temp==0)break;
- }
- else continue;
- }
- if(j>count)
- {
- count+=1;
- category[count]=setOfStability[i];
- }
- }
- }
- for(i=1;i<setOfStability.length;i++)
- for(j=1;j<=count;j++)
- {
- if(rowMatrix[i]==-1)
- {
- temp=setOfStability[i]-category[j];
- if(temp==0)equivalentClass[i]=j;
- }
- }
- equivalentClass[0]=count;
-
- for(i=0;i<setOfStability.length;i++)
- {
- setOfStability[i]=equivalentClass[i];
- }
- }
-
- /**
- * Force filling the left matrix at every step.
- *
- * @param step the line is filling
- * @param setOfBasicFragment vector contains the set of basic fragment.
- * @param adjacencyMatrix adjacency matrix of the given basic fragment.
- * @param previousMatrix matrix is used for tracing the change of adjacency matrix.
- * @return the first line which is unfilled
- */
- public int forceFilling(int step,List setOfBasicFragment,int[][] adjacencyMatrix,int[][] previousMatrix)
- {
- /* 1. Minimal forcing. The sum of filled elements of each unfilled row i->J(B)
- * is equal to the valence of the corresponding vertex.
- * 2. Maximal forcing. The sum of all maximal multiplicity of edges of the Vi-th vertex, i->J(B)
- * is equal to the valence of the vertex.
- */
- int i,j,iter,sum,bondOrder;
- int filledValence,unfilledValence,changedLine;
-
- do
- {
- changedLine=0;
- for(i=step;i<adjacencyMatrix.length;i++)
- {
- sum=0;
- unfilledValence=0;
- if(previousMatrix[i][i]>0)continue;
- for(j=0;j<adjacencyMatrix.length;j++)
- {
- if(adjacencyMatrix[i][j]>0)sum+=1;
- else if(adjacencyMatrix[i][j]==-1)unfilledValence+=1;
- }
-
- if(previousMatrix[i][i]==0 && unfilledValence==0)
- {
- previousMatrix[i][i]=step;
- }
- if(sum==((BasicFragment)(setOfBasicFragment.get(i))).getNumberOfFreeValence() && unfilledValence>0)
- {
- //Satisfy the minimal forcing, fill this line
- for(iter=0;iter<adjacencyMatrix.length;iter++)
- {
- if(adjacencyMatrix[i][iter]==-1)
- {
- adjacencyMatrix[i][iter]=0;
- previousMatrix[i][iter]=step;
- adjacencyMatrix[iter][i]=0;
- previousMatrix[iter][i]=step;
- }
-
- }
- previousMatrix[i][i]=step;
- changedLine+=1;
- }
- }
-
- /* maximal forcing. */
- for(i=step;i<adjacencyMatrix.length;i++)
- {
- sum=0;
- filledValence=0;
- if(previousMatrix[i][i]>0)continue;
- for(j=0;j<adjacencyMatrix.length;j++)
- {
-
- if(adjacencyMatrix[i][j]==-1)sum+=1;
- else if(adjacencyMatrix[i][j]>0)filledValence+=1;
- }
- if(previousMatrix[i][i]==0 && sum==0)
- {
- previousMatrix[i][i]=step;
- }
- if(sum==(((BasicFragment)(setOfBasicFragment.get(i))).getNumberOfFreeValence()-filledValence) && sum>0)
- {
- bondOrder=((BasicFragment)(setOfBasicFragment.get(i))).getAttribute();
- //Satisfy the maximal forcing, fill this line
- for(iter=0;iter<adjacencyMatrix.length;iter++)
- {
- if(adjacencyMatrix[i][iter]==-1)
- {
- adjacencyMatrix[i][iter]=bondOrder;
- previousMatrix[i][iter]=step;
- adjacencyMatrix[iter][i]=bondOrder;
- previousMatrix[iter][i]=step;
- }
-
- }
- previousMatrix[i][i]=step;
- changedLine+=1;
- }
- }
- }while(changedLine>0);
-
- /* find the first unfilled line*/
- for(i=step;i<adjacencyMatrix.length;i++)
- for(j=0;j<adjacencyMatrix.length;j++)if(adjacencyMatrix[i][j]==-1)return i;
- return adjacencyMatrix.length;
- }
-
-
- /**
- * Check admissibility of the matrix.
- * Details see Sergey G. Molodtsov, Computer-Aided Generation of Molecular Graphs,
- * Match, 30(213),1994
- *
- * @param step the line is filling.
- * @param setOfBasicFragment set of basic fragment
- * @param adjacencyMatrix adjacency matrix
- * @return a boolean value whether this line could pass adissibility or not
- */
- public boolean checkAdmissibility(int step,List setOfBasicFragment,int[][] adjacencyMatrix)
- {
- for(int i=step;i<adjacencyMatrix.length;i++)
- {
- int sum=0;
- int unfilledValence=0;
- {
- for(int j=0;j<adjacencyMatrix.length;j++)
- {
- if(adjacencyMatrix[i][j]>0)sum+=1;
- if(adjacencyMatrix[i][j]==-1)unfilledValence+=1;
- }
- if(sum>((BasicFragment)(setOfBasicFragment.get(i))).getNumberOfFreeValence()){return false;}
- if(unfilledValence<(((BasicFragment)(setOfBasicFragment.get(i))).getNumberOfFreeValence()-sum) && unfilledValence>=0)
- {
- return false;
- }
- }
-
- }
- return true;
- }
-
-
- /**
- * Check constraint of the matrix. Currently, there is only connectivity test.
- * Later, there might be other tests.
- *
- * @param step the line is filling.
- * @param setOfBasicFragment set of basic fragment
- * @param adjacencyMatrix adjacency matrix
- * @param ac atomContainer of the node set, not used now
- * @return a boolean value whether this adjacency matrix pass the constraint check or not
- */
- public boolean checkConstraint(int step,List setOfBasicFragment,int[][] adjacencyMatrix, IAtomContainer ac)
- {
- int i,j,partialSum,totalSum,decomposedNumber;
- //boolean isConnectivity;
- boolean[] isVisited=new boolean[adjacencyMatrix.length];
- int[] isDecomposed=new int[adjacencyMatrix.length];
- int[] parentID=new int[adjacencyMatrix.length];
- for(i=0;i<adjacencyMatrix.length;i++)
- {
- isVisited[i]=false;
- isDecomposed[i]=0;
- parentID[i]=0;
- }
- /* check connectivity first. This time, it is substructure or structure*/
- if(step==1)return true;
- else if(step==adjacencyMatrix.length)
- {
- decomposedNumber=0;
- for(i=0;i<adjacencyMatrix.length;i++)
- {
- if(((BasicFragment)(setOfBasicFragment.get(i))).getID()>33)
- {
- isDecomposed[i]=((BasicFragment)(setOfBasicFragment.get(i))).getID();
- parentID[i]=((BasicFragment)(setOfBasicFragment.get(i))).getParentID();
- decomposedNumber+=1;
- }
- }
- if(decomposedNumber>0)
- {
- for(i=0;i<adjacencyMatrix.length-1;i++)
- for(j=i+1;j<adjacencyMatrix.length;j++)
- if(isDecomposed[i]!=isDecomposed[j] && parentID[i]==parentID[j] &&
- i!=j && adjacencyMatrix[i][i]==0 && adjacencyMatrix[j][j]==0)
- {
- adjacencyMatrix[i][j]=10;
- adjacencyMatrix[j][i]=10;
- adjacencyMatrix[i][i]=10;
- adjacencyMatrix[j][j]=10;
- }
- }
-
- DFSM(adjacencyMatrix,0,isVisited);
- if(decomposedNumber>0)
- {
- for(i=0;i<adjacencyMatrix.length;i++)
- for(j=0;j<adjacencyMatrix.length;j++)
- if(adjacencyMatrix[i][j]==10)adjacencyMatrix[i][j]=0;
- }
- for(i=0;i<adjacencyMatrix.length;i++)if(!isVisited[i])return false;
- return true;
- // }
-
- }
- else
- {
- decomposedNumber=0;
- for(i=0;i<adjacencyMatrix.length;i++)
- {
- if(((BasicFragment)(setOfBasicFragment.get(i))).getID()>33)
- {
- isDecomposed[i]=((BasicFragment)(setOfBasicFragment.get(i))).getID();
- parentID[i]=((BasicFragment)(setOfBasicFragment.get(i))).getParentID();
- decomposedNumber+=1;
- }
- }
- if(decomposedNumber>0)
- {
- for(i=0;i<adjacencyMatrix.length-1;i++)
- for(j=i;j<adjacencyMatrix.length;j++)
- if(isDecomposed[i]!=isDecomposed[j] && parentID[i]==parentID[j] &&
- i!=j && adjacencyMatrix[i][i]==0 && adjacencyMatrix[j][j]==0)
- {
- adjacencyMatrix[i][j]=10;
- adjacencyMatrix[j][i]=10;
- adjacencyMatrix[i][i]=10;
- adjacencyMatrix[j][j]=10;
- }
- }
- DFSM(adjacencyMatrix,0,isVisited);
- if(decomposedNumber>0)
- {
- for(i=0;i<adjacencyMatrix.length;i++)
- for(j=0;j<adjacencyMatrix.length;j++)
- if(adjacencyMatrix[i][j]==10)adjacencyMatrix[i][j]=0;
- }
-
- partialSum=0;
- totalSum=0;
- for(i=0;i<step;i++)
- {
- if(isVisited[i])partialSum+=1;
- }
- for(i=0;i<adjacencyMatrix.length;i++)
- {
- if(isVisited[i])totalSum+=1;
- }
- if(partialSum==step && partialSum==totalSum)return false;
- else if(totalSum==adjacencyMatrix.length)return true;
- else return true;
- }
- }
-
- /**
- * Get the next WCF (weakly canonical complement).
- * Details see Sergey G. Molodtsov, Computer-Aided Generation of Molecular Graphs,
- * Match, 30(213),1994
- *
- * @param setOfBasicFragment set of basic fragment
- * @param step the step of the generation
- * @param rowMatrix the row which contains the filling line
- * @param adjacencyMatrix adjacency matrix
- * @param previousMatrix matrix to trace the change of adjacency matrix
- * @param parentID array mainly used for complex bond
- * @return a boolean value whether there is next WCF or not
- *
- */
- public boolean getNextWCF(List setOfBasicFragment,int step,int[] rowMatrix,int[][] adjacencyMatrix,int[][] previousMatrix,int[] parentID)
- {
- int i,j,iter,existBond,leftBond,totalBond,changedCategory,sum; // changedFilledValue,nextNonZeroElement
- int bondOrder;
- int[] setOfStability;
- int[] previousLine;
- int[] category;
- int[] previousFilledValue;
- int[] currentFilledValue;
-
- setOfStability=new int[rowMatrix.length];
- previousLine=new int[rowMatrix.length];
- category=new int[rowMatrix.length];
- previousFilledValue=new int[rowMatrix.length];
- currentFilledValue=new int[rowMatrix.length];
- for(i=step;i<rowMatrix.length;i++)
- {
- previousLine[i]=rowMatrix[i];
- }
-
- iter=0;
- for(i=0;i<rowMatrix.length;i++)
- {
- rowMatrix[i]=adjacencyMatrix[step][i];
- if(rowMatrix[i]==-1)iter+=1;
- }
- getSetOfStability(setOfBasicFragment,step,rowMatrix,adjacencyMatrix,setOfStability,parentID);
-
- existBond=0;
- for(i=0;i<adjacencyMatrix.length;i++)if(rowMatrix[i]>0)existBond+=1;
- totalBond=((BasicFragment)(setOfBasicFragment.get(step))).getNumberOfFreeValence();
- bondOrder=((BasicFragment)(setOfBasicFragment.get(step))).getAttribute();
- leftBond=totalBond-existBond;
- iter=1;
- while(iter<=setOfStability[0])
- {
- for(i=1;i<rowMatrix.length;i++)
- {
- if(setOfStability[i]==iter)category[iter]+=1;
- if(setOfStability[i]==iter)
- if(previousLine[i]>0)previousFilledValue[iter]+=1;
- }
- iter+=1;
- }
- category[0]=setOfStability[0];
- changedCategory=0;
- for(i=category[0];i>=1;i--)if(previousFilledValue[i]!=0){changedCategory=i;break;}
-
- /* judge mininal WCF*/
- if(changedCategory==category[0])
- {
- if(previousFilledValue[category[0]]< category[changedCategory] && previousFilledValue[category[0]]==leftBond)
- return false;
- else if(previousFilledValue[category[0]]==category[changedCategory])
- {
- sum=0;
- for(i=category[0];i>=1;i--)
- {
- sum+=previousFilledValue[i];
- if(previousFilledValue[i]==category[i] && sum<leftBond)continue;
- if(sum==leftBond)return false;
- break;//non-termination
- }
- }
- }
-
- /*get next WCF*/
- if(changedCategory!=category[0])
- {
- for(i=1;i<=category[0];i++)
- {
- if(i<changedCategory)currentFilledValue[i]=previousFilledValue[i];
- else if(i==changedCategory)currentFilledValue[i]=previousFilledValue[i]-1;
- else if(i==(changedCategory+1))currentFilledValue[i]=1;
- }
- }
- else if(changedCategory==category[0] && (previousFilledValue[changedCategory]<category[changedCategory]||previousFilledValue[changedCategory-1]==0))
- {
- while(previousFilledValue[changedCategory-1]==0)changedCategory-=1;
- sum=0;
- for(i=1;i<(changedCategory-1);i++)
- {
- currentFilledValue[i]=previousFilledValue[i];
- sum+=currentFilledValue[i];
- }
-
- currentFilledValue[changedCategory-1]=previousFilledValue[changedCategory-1]-1;
- sum+=currentFilledValue[changedCategory-1];
- iter=changedCategory;
- while(leftBond>sum)
- {
- currentFilledValue[iter]=leftBond-sum;
- if(currentFilledValue[iter]>category[iter] && iter<category[0])
- {
- currentFilledValue[iter]=category[iter];
- sum+=currentFilledValue[iter];
- iter+=1;
- continue;
- }
- else break;
- }
- }
- else if(changedCategory==category[0]&& previousFilledValue[changedCategory]==category[changedCategory] &&
- previousFil...
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