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[Cdk-commits] SF.net SVN: cdk:[15371] detgen/trunk
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From: <sh...@us...> - 2010-02-04 18:18:01
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Revision: 15371
http://cdk.svn.sourceforge.net/cdk/?rev=15371&view=rev
Author: shk3
Date: 2010-02-04 18:17:54 +0000 (Thu, 04 Feb 2010)
Log Message:
-----------
generation can now start from fragments
Modified Paths:
--------------
detgen/trunk/lib/cdk-extra.jar
detgen/trunk/src/org/openscience/cdk/structgen/deterministic/DeterministcGeneratorTest.java
detgen/trunk/src/org/openscience/cdk/structgen/deterministic/DeterministicGenerator.java
detgen/trunk/src/org/openscience/cdk/structgen/deterministic/Fragment.java
Modified: detgen/trunk/lib/cdk-extra.jar
===================================================================
(Binary files differ)
Modified: detgen/trunk/src/org/openscience/cdk/structgen/deterministic/DeterministcGeneratorTest.java
===================================================================
--- detgen/trunk/src/org/openscience/cdk/structgen/deterministic/DeterministcGeneratorTest.java 2010-02-04 10:31:33 UTC (rev 15370)
+++ detgen/trunk/src/org/openscience/cdk/structgen/deterministic/DeterministcGeneratorTest.java 2010-02-04 18:17:54 UTC (rev 15371)
@@ -2,14 +2,18 @@
import java.io.IOException;
import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
import java.util.Scanner;
import org.junit.Assert;
import org.junit.Test;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.iterator.IteratingMDLReader;
+import org.openscience.cdk.templates.MoleculeFactory;
public class DeterministcGeneratorTest {
@@ -31,10 +35,48 @@
}
+ @Test public void testWithStartFragments() throws CloneNotSupportedException, CDKException, IOException, ClassNotFoundException {
+ DeterministicGenerator dg = new DeterministicGenerator(true);
+ List<IMolecule> input = new ArrayList<IMolecule>();
+ IMolecule benzene = MoleculeFactory.makeBenzene();
+ benzene.getAtom(1).setHydrogenCount(0);
+ benzene.getAtom(1).setHydrogenCount(1);
+ benzene.getAtom(1).setHydrogenCount(2);
+ benzene.getAtom(1).setHydrogenCount(3);
+ benzene.getAtom(1).setHydrogenCount(4);
+ benzene.getAtom(0).setHydrogenCount(5);
+ input.add(benzene);
+ IMolecule secondFragment = MoleculeFactory.makeCyclopentane();
+ secondFragment.getAtom(0).setSymbol("N");
+ secondFragment.getAtom(1).setSymbol("O");
+ secondFragment.getAtom(2).setHydrogenCount(1);
+ secondFragment.getAtom(3).setHydrogenCount(2);
+ secondFragment.getAtom(0).setHydrogenCount(0);
+ secondFragment.getAtom(1).setHydrogenCount(0);
+ secondFragment.getAtom(4).setHydrogenCount(0);
+ secondFragment.getBond(secondFragment.getAtom(0),secondFragment.getAtom(4)).setOrder(IBond.Order.DOUBLE);
+ input.add(secondFragment);
+ IMolecule mol = DefaultChemObjectBuilder.getInstance().newMolecule();
+ mol.addAtom(DefaultChemObjectBuilder.getInstance().newAtom("C"));
+ input.add(mol);
+ mol = DefaultChemObjectBuilder.getInstance().newMolecule();
+ mol.addAtom(DefaultChemObjectBuilder.getInstance().newAtom("C"));
+ input.add(mol);
+ mol = DefaultChemObjectBuilder.getInstance().newMolecule();
+ mol.addAtom(DefaultChemObjectBuilder.getInstance().newAtom("O"));
+ input.add(mol);
+ mol = DefaultChemObjectBuilder.getInstance().newMolecule();
+ mol.addAtom(DefaultChemObjectBuilder.getInstance().newAtom("N"));
+ input.add(mol);
+ FragmentList result = dg.generateIsomers(input);
+ //TODO: insert real value
+ Assert.assertEquals(15, result.size());
+ }
+
public static void main(String[] args) throws CloneNotSupportedException, CDKException, IOException, ClassNotFoundException{
long start = System.currentTimeMillis();
DeterministicGenerator dg = new DeterministicGenerator(true);
- FragmentList result = dg.generateIsomers("C4O1H4");
+ FragmentList result = dg.generateIsomers("C2O1H1");
long end = System.currentTimeMillis();
System.out.println("Results "+result.size()+", time "+(end-start)/1000+" s, hit Enter to finish!");
Scanner sc = new Scanner(System.in);
Modified: detgen/trunk/src/org/openscience/cdk/structgen/deterministic/DeterministicGenerator.java
===================================================================
--- detgen/trunk/src/org/openscience/cdk/structgen/deterministic/DeterministicGenerator.java 2010-02-04 10:31:33 UTC (rev 15370)
+++ detgen/trunk/src/org/openscience/cdk/structgen/deterministic/DeterministicGenerator.java 2010-02-04 18:17:54 UTC (rev 15371)
@@ -22,6 +22,7 @@
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IIsotope;
import org.openscience.cdk.interfaces.IMolecularFormula;
+import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator;
public class DeterministicGenerator {
@@ -187,4 +188,35 @@
level--;
alreadyExploredGenerations.add(input);
}
+
+
+ public FragmentList generateIsomers(List<IMolecule> fragments) throws CloneNotSupportedException, CDKException, IOException, ClassNotFoundException {
+ DefaultMutableTreeNode rootNode = null;
+ if(debug){
+ JFrame frame = new JFrame("Deterministic Generator");
+ frame.setLayout(new GridLayout(1, 0));
+ rootNode = new DefaultMutableTreeNode("Root Node");
+ treeModel = new DefaultTreeModel(rootNode);
+ tree = new JTree(treeModel);
+ tree.setEditable(true);
+ tree.getSelectionModel().setSelectionMode
+ (TreeSelectionModel.SINGLE_TREE_SELECTION);
+ tree.setShowsRootHandles(true);
+
+ JScrollPane treepane = new JScrollPane(tree);
+ frame.add(treepane);
+ frame.setSize(500,500);
+ frame.setPreferredSize(new Dimension(500,500));
+ frame.setMinimumSize(new Dimension(500,500));
+ frame.pack();
+ frame.setVisible(true);
+ }
+ FragmentList solutions=new FragmentList();
+ Map<Fragment, Integer> input=new HashMap<Fragment, Integer>();
+ for(int i=0;i<fragments.size();i++){
+ input.put(new Fragment(fragments.get(i)),1);
+ }
+ makeNextGeneration(input, solutions, rootNode);
+ return solutions;
+ }
}
Modified: detgen/trunk/src/org/openscience/cdk/structgen/deterministic/Fragment.java
===================================================================
--- detgen/trunk/src/org/openscience/cdk/structgen/deterministic/Fragment.java 2010-02-04 10:31:33 UTC (rev 15370)
+++ detgen/trunk/src/org/openscience/cdk/structgen/deterministic/Fragment.java 2010-02-04 18:17:54 UTC (rev 15371)
@@ -86,13 +86,17 @@
}
attachmentPoints = new HashMap<String,Map<IAtom,Integer>>();
for(int i=0;i<this.getAtomCount();i++){
- if(this.getAtom(i).getSymbol().equals("C") || this.getAtom(i).getSymbol().equals("H") || this.getAtom(i).getSymbol().equals("O")){
+ if(this.getAtom(i).getSymbol().equals("C") || this.getAtom(i).getSymbol().equals("H") || this.getAtom(i).getSymbol().equals("O") || this.getAtom(i).getSymbol().equals("N")){
int sum = (int) this.getBondOrderSum(this.getAtom(i));
int desired = 1;
if(this.getAtom(i).getSymbol().equals("C"))
desired = 4;
if(this.getAtom(i).getSymbol().equals("O"))
desired=2;
+ if(this.getAtom(i).getSymbol().equals("N"))
+ desired=3;
+ if(this.getAtom(i).getHydrogenCount()!=null)
+ desired -= this.getAtom(i).getHydrogenCount();
for(int k=sum;k<desired;k++){
if(attachmentPoints.get(morganNumbers[i])==null){
Map<IAtom, Integer> map = new HashMap<IAtom, Integer>();
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