gilleain

<?xml version="1.0" encoding="UTF-8"?>
<project name="Test" default="cdk-ant">
	<target name="cdk-ant" description="build cdk">
		<echo>"Building CDK"</echo>
		<subant target="dist-all" buildpath="../cdk">
		</subant>
	</target>
</project>

gilleain

Apache Ant(TM) version 1.8.2 compiled on February 28 2011
Buildfile: /Users/maclean/development/projects/SMSD/build-smsd.xml
Adding reference: ant.PropertyHelper
Detected Java version: 1.6 in: /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
Detected OS: Mac OS X
Adding reference: ant.ComponentHelper
Setting ro project property: ant.file -> /Users/maclean/development/projects/SMSD/build-smsd.xml
Setting ro project property: ant.file.type -> file
Adding reference: ant.projectHelper
Adding reference: ant.parsing.context

gilleain

<het/TBD> <prop/hasAtom> <atom/TBD> .
<atom/TBD> <prop/hasH2Sig> "[B]([H][H][H][P]([O][O][O]))" .
<atom/TBD> <prop/hasAtomSymbol> "B1A" .
<atom/TBD> <prop/hasH2Sig> "[P]([B]([H][H][H])[O]([C])[O]([H])[O]([P]))" .
<atom/TBD> <prop/hasAtomSymbol> "PA" .
<atom/TBD> <prop/hasAtomID> "TBD" .

gilleain

<rdf:RDF
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:j.0="http://cpt/p/" > 
  <rdf:Description rdf:about="http://cpt/r/">
    <j.0:HET rdf:resource="http://cpt/r/TBE"/>
    <j.0:HET rdf:resource="http://cpt/r/TBD"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://cpt/r/TBD">
    <j.0:hasHeight2Sig>[B]([H][H][H][P]([O][O][O]))</j.0:hasHeight2Sig>
    <j.0:hasAtomSymbol>B1A</j.0:hasAtomSymbol>

gilleain

 public static IAtomContainer extractSubstructure(
            IAtomContainer atomContainer, int... atomIndices) throws CloneNotSupportedException {
        IAtomContainer substructure = (IAtomContainer) atomContainer.clone();
        int numberOfAtoms = substructure.getAtomCount();
        IAtom[] atoms = new IAtom[numberOfAtoms];
        for (int atomIndex = 0; atomIndex < numberOfAtoms; atomIndex++) {
            atoms[atomIndex] = substructure.getAtom(atomIndex);
        }
        
        Arrays.sort(atomIndices);

gilleain

IMoleculeSet molSet = makeMolSet();
Vector2d axis = new Vector2d(1.25, .5);
axis.normalize();
LinearMoleculeSetLayout layout = new LinearMoleculeSetLayout(new StandardMoleculeLayout(), 3, axis);

gilleain

/**
 * Layout an object.
 * 
 * @author maclean
 *
 * @param <T>
 */
public interface ILayout<T> {
    
    public enum AxisOrientation { X, Y };

gilleain

AxisOrientation orientationA = AxisOrientation.Y;
AxisOrientation orientationB = AxisOrientation.X;
ILayout<IReaction> layout = new LinearReactionLayout(
                               new LinearMoleculeSetLayout(
                                  new StandardMoleculeLayout(), orientationA),
                               new LinearMoleculeSetLayout(
                                  new StandardMoleculeLayout(), orientationA),
                               2, orientationB);

gilleain

public class TechnicallyJava {

public Map<Integer, Integer> zip(int[] a, int[] b) {
        assert a.length == b.length;
        Map<Integer, Integer> map = new HashMap<Integer, Integer>();
        for (int i = 0; i < a.length; i++) {
            map.put(a[i], b[i]);
        }
        return map;
    }

gilleain

 public class ArcDrawer extends AWTDrawVisitor  {
        
        private Graphics2D g2;
        
        public ArcDrawer(Graphics2D g) {
            super(g);
            this.g2 = g;
        }

        @Override