johnmay

public class Main {
  public static void main(String[] args) throws CDKException, IOException {

    String smi = "C1[C@H]([C@@H](OC2=CC(=CC(=C21)O)O)*)O |$;;;;;;;;;;;;_AP1$|";
    SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
    IAtomContainer mol = smipar.parseSmiles(smi);

    // atom indexes to highlight
    int[] idxs = new int[]{3,4,5,9};
    boolean outgoing = true;

johnmay

  private static IAtomContainer getChains(IAtomContainer mol) {
    IAtomContainer result = mol.getBuilder().newInstance(IAtomContainer.class);
    for (IAtom atom : mol.atoms())
      atom.setFlag(CDKConstants.VISITED, false);
    for (IBond bond : mol.bonds()) {
      if (!bond.isInRing()) {
        IAtom beg = bond.getAtom(0);
        IAtom end = bond.getAtom(1);
        if (!beg.getFlag(CDKConstants.VISITED)) {
          result.addAtom(beg);

johnmay

String             smi    = "[CH3:9][CH:8]([CH3:10])[c:7]1[cH:11][cH:12][cH:13][cH:14][cH:15]1.[CH2:3]([CH2:4][C:5](=[O:6])Cl)[CH2:2][Cl:1]>[Al+3].[Cl-].[Cl-].[Cl-].C(Cl)Cl>[CH3:9][CH:8]([CH3:10])[c:7]1[cH:11][cH:12][c:13]([cH:14][cH:15]1)[C:5](=[O:6])[CH2:4][CH2:3][CH2:2][Cl:1] |f:2.3.4.5| Friedel-Crafts acylation [3.10.1]";

IChemObjectBuilder bldr   = SilentChemObjectBuilder.getInstance();

SmilesParser       smipar = new SmilesParser(bldr);
IReaction          rxn    = smipar.parseReactionSmiles(smi);

new DepictionGenerator().withAtomMapHighlight(new Color[]{new Color(0xAAC0FF),
                                                          new Color(0x8BFFB9)})
                        .withOuterGlowHighlight()

johnmay

MDLV2000Reader mdlr = ...;
IAtomContainer mol;
while ((mol = mdlr.read(new AtomContainer(0,0,0,0)) != null) {
  // do something with mol
}

johnmay

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

Pattern ptrn = SmartsPattern.create("O=[C,N]aa[N,O;!H0]", null);

try (Reader         frdr = new FileReader(fname);
     BufferedReader brdr = new BufferedReader(frdr)) {
    
    String line;
    

johnmay

new DepictionGenerator().withSize(256, 256)
                        .depict(mol)
                        .writeTo("molecule.png");

johnmay

StructureDiagramGenerator sdg = new StructureDiagramGenerator();
sdg.setMolecule(mol, false);
sdg.generateCoordinates();

AtomContainerRenderer renderer =
        new AtomContainerRenderer(Arrays.asList(new BasicSceneGenerator(),
                                                new BasicBondGenerator(),
                                                new ExtendedAtomGenerator()),
                                  new AWTFontManager());
BufferedImage img = new BufferedImage(256, 256, BufferedImage.TYPE_4BYTE_ABGR);

johnmay

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

final String fname = "/data/nci_aug00.smi";

SMARTSQueryTool sqt = new SMARTSQueryTool("O=[C,N]aa[N,O;!H0]");

int num_hits = 0;
try (BufferedReader brdr = new BufferedReader(new FileReader(fname))) {
    String line;

johnmay

import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.isomorphism.Pattern;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.smiles.SmilesGenerator;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.smiles.smarts.SmartsPattern;

johnmay

ICountFingerprint fp;

int numBins = fp.numOfPopulatedbins();
for (int i = 0; i < numBins; i++) {
  int hash = fp.getHash(i);
  int freq = fp.getCount(i);
}