johnmay

final SmilesParser       smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
final DepictionGenerator dg     = new DepictionGenerator().withMolTitle();
dg.depict(Arrays.asList(smipar.parseSmiles("[H]N1C([H])=C([H])C([H])=C1([H]) expl H (C4H5N)"),
                        smipar.parseSmiles("N1C=CC=C1 impl H (C4H5N)"),
                        smipar.parseSmiles("[N]1C([H])=C([H])C([H])=C([H])1 expl H rad (C4H4N)"),
                        smipar.parseSmiles("[N]1C=CC=C1 impl H rad (C4H4N)"),
                        smipar.parseSmiles("N1[C]=C([H])C([H])=C([H])1 expl H rad (C4H4N)"),
                        smipar.parseSmiles("N1[C]=CC=C1 impl H rad (C4H4N)")),
          3, 2)
  .writeTo("~/hdisplay.png");

johnmay

// Pattern interface should be used for matching rather than SMARTSQueryTool,
// more efficient and easier to use.
Pattern carboxy = SmartsPattern.compile("[Ov2X2H1+0]-[Cv4X3]=[Ov2X1H0]", bldr);

// Mappings object has several utils, we need basics only here 
for (int[] mapping : caboxy.matchAll(mol).uniqueAtoms()) {
  IAtom hydroxy = mol.getAtom(mapping[0]); 
  hydroxy.setImplicitHydrogenCount(0);
  hydroxy.setFormalCharge(-1);
}

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;
        }

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

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

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.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

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

// 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

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) {
        }
    }
}