gilleain

void plot_line(GraphPoint[] line, int m, int c) {
  Point next = new Point(0, c);

  while (next.x < line.length) {
      line[next.x] = new GraphPoint(next, graphpoint.crosshair);
      next.x += 1;
      next.y += m;
  }
}

gilleain

public class AtomTests {
	
	public final static IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance(); 

	@Test
	public void one_four_cyclohexadiene() throws InvalidSmilesException {
		String acpString = "C0C1C2C3C4C5 0:1(2),0:5(1),1:2(1),2:3(1),3:4(2),4:5(1)";
		IAtomContainer cyclohexadiene = AtomContainerPrinter.fromString(acpString, builder);
		AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
		PermutationGroup aut = refiner.getAutomorphismGroup(cyclohexadiene);

gilleain

import java.util.ArrayList;
import java.util.List;

public class Atom {
    
    public Atom(String element) {
        this.element = element;
    }
    
    public String element;

gilleain

import org.openscience.cdk.Molecule;
import org.openscience.cdk.io.CDKSourceCodeWriter;
import org.openscience.cdk.io.MDLReader;
import org.eclipse.jgit.api.*;
import org.eclipse.jgit.lib.*;
import org.eclipse.jgit.storage.file.*;

element = bsh.args[0];
FileRepositoryBuilder builder = new FileRepositoryBuilder();
Repository repository = builder.readEnvironment().findGitDir().build();

gilleain

for e in Ag Au
do
echo "Checking out $e"
git checkout $e
git reset --soft HEAD~1
java -cp ~/jgit/org.eclipse.jgit-1.0.0.201106090707-r.jar bsh.Interpreter patcher.bsh $e
git add src/
git commit -m "$e final"
git checkout master
done

gilleain

package customgenerator;

import java.awt.Color;
import java.util.ArrayList;
import java.util.List;

import javax.vecmath.Point2d;
import javax.vecmath.Vector2d;

import org.openscience.cdk.geometry.GeometryTools;

gilleain

package customgenerator;

import java.awt.Color;
import java.util.ArrayList;
import java.util.List;

import javax.vecmath.Point2d;
import javax.vecmath.Vector2d;

import org.openscience.cdk.geometry.GeometryTools;

gilleain

 public void drawMolecule(IMolecule molecule, String name) throws Exception {
        
        // layout the molecule
        StructureDiagramGenerator sdg = new StructureDiagramGenerator();
        sdg.setMolecule(molecule, false);
        sdg.generateCoordinates();
        
        // make generators
        List<IGenerator<IAtomContainer>> generators = new ArrayList<IGenerator<IAtomContainer>>();
        generators.add(new BasicSceneGenerator());

gilleain

From 5a86e14eef2b516dab2c4e369376d76bb6dfdd7b Mon Sep 17 00:00:00 2001
From: maclean <gilleain.torrance@gmail.com>
Date: Wed, 30 Mar 2011 07:59:03 +0100
Subject: [PATCH] Use IAtomContainer instead of AtomContainer in AtomContainerSet

---
 src/main/org/openscience/cdk/AtomContainerSet.java |    6 +++---
 1 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/main/org/openscience/cdk/AtomContainerSet.java b/src/main/org/openscience/cdk/AtomContainerSet.java

gilleain

Caused by: java.lang.NullPointerException
     [java] 	at net.sf.cdk.tools.MakeJavafilesFiles.readBlackList(MakeJavafilesFiles.java:79)
     [java] 	at net.sf.cdk.tools.MakeJavafilesFiles.<init>(MakeJavafilesFiles.java:66)
     [java] 	at net.sf.cdk.tools.MakeJavafilesFiles.main(MakeJavafilesFiles.java:241)
     [java] 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
     [java] 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
     [java] 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
     [java] 	at java.lang.reflect.Method.invoke(Method.java:597)
     [java] 	at org.apache.tools.ant.taskdefs.ExecuteJava.run(ExecuteJava.java:217)
     [java] 	at org.apache.tools.ant.taskdefs.ExecuteJava.execute(ExecuteJava.java:152)