johnmay

// compute labelling (others are available)
final long[] labels = Canon.label(m, GraphUtil.toAdjList(m));

IAtom[] atoms = AtomContainerManipulator.getAtomArray(m);
IBond[] bonds = AtomContainerManipulator.getBondArray(m);
 
// atoms don't know their index
for (int i = 0; i < labels.length; i++)
  atoms[i].setProperty("rank", labels);
  

johnmay

public class Main {
    public static void main(String[] args) throws Exception {
        while(System.out.getClass()
                        .getMethod("println", String.class)
                        .invoke(System.out, "Hello world!") != null) {
        }
    }
}

johnmay

// imports can be inlined but excluded for readability
// import javax.script.SimpleScriptContext;
// import java.io.PrintWriter;

public class Main {
    public static void main(String[] args) {
        new SimpleScriptContext() {{
            new PrintWriter(writer) {{
                println("Hello World!");
                flush();

johnmay

Map<AtomPair,IBond> bondMap = new HashMap<>();

for (IBond bond : container.bonds())
    bondMap.put(new AtomPair(bond.getAtom(0), bond.getAtom(1)), 
                bond);
                
class AtomPair { 
    IAtom a, b;
    AtomPair(IAtom a, IAtom b) {
        this.a = a, this.b = b;

johnmay

IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
SmilesParser smipar = new SmilesParser(bldr);
SmilesGenerator smigen = SmilesGenerator.unique();

System.out.println(smigen.create(smipar.parseSmiles("c1cc2c(cc1)cccc2")));
System.out.println(smigen.create(smipar.parseSmiles("C1=CC2=C(C=C1)C=CC=C2")));
System.out.println(smigen.create(smipar.parseSmiles("C=1C=C2C(=CC=1)C=CC=C2")));
System.out.println(smigen.create(smipar.parseSmiles("C1=CC=2C(C=C1)=CC=CC=2")));

johnmay

static IAtomContainer mykekule(IAtomContainer org) throws Exception {
        
    final IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
    final SmilesParser smipar = new SmilesParser(bldr);
    final SmilesGenerator smigen = SmilesGenerator.unique();

    final int n = org.getAtomCount();
    int[] ordering = new int[n];
        
    // generate a kekule assignment via SMILES and store the output order (a permutation of

johnmay

IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
SmilesParser smipar = new SmilesParser(bldr);
SmilesGenerator smigen = SmilesGenerator.generic();

System.out.println(smigen.create(mykekule(smipar.parseSmiles("c1cc2c(cc1)cccc2"))));
System.out.println(smigen.create(mykekule(smipar.parseSmiles("C1=CC2=C(C=C1)C=CC=C2"))));
System.out.println(smigen.create(mykekule(smipar.parseSmiles("C=1C=C2C(=CC=1)C=CC=C2"))));
System.out.println(smigen.create(mykekule(smipar.parseSmiles("C1=CC=2C(C=C1)=CC=CC=2"))));

johnmay

BufferedReader     brdr   = ...;

// create once and reuse
IChemObjectBuilder bldr   = SilentChemObjectBuilder.getInstance();
Aromaticity        arom   = new Aromaticity(ElectronDonation.daylight(),
                                            Cycles.or(Cycles.all(), Cycles.all(6)));

// SMILES, implicit h already present
SmilesParser smipar = new SmilesParser(bldr);
String line;

johnmay

if (GeometryTools.has2DCoordinates(container)) {
    renderer.paint(container, new AWTDrawVisitor(g2), bounds, true);
} else {
    // can log or invoke g2.drawString() to display "no coordinates"
}

johnmay

static int aromStatus(IAtomContainer mol) {
    int res = 0;
    for (IAtom atom : mol.atoms()) {
        if (atom.getImplicitHydrogenCount() == null && atom.getFlag(CDKConstants.ISAROMATIC)) {
            // N and P are ambiguous
            if (atom.getAtomicNumber() == 7 || atom.getAtomicNumber() == 15)
                res = 2;
            else if (res < 2)
                res = 1;
        }