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import java.util.List;
import java.util.Arrays;
import java.util.*;
import java.io.*;
import java.awt.*;
import java.awt.image.*;
import java.awt.geom.*;
import javax.imageio.*;
import org.openscience.cdk.*;
import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.layout.*;
import org.openscience.cdk.renderer.*;
import org.openscience.cdk.renderer.font.*;
import org.openscience.cdk.renderer.generators.*;
import org.openscience.cdk.renderer.visitor.*;
import org.openscience.cdk.templates.*;
import org.openscience.cdk.smiles.*;
import org.openscience.cdk.smiles.smarts.*;
import org.openscience.cdk.graph.*;
import org.openscience.cdk.geometry.*;
public class Display{
int size;
Rectangle drawArea;
IMolecule molecule = new Molecule();
IMoleculeSet moleculeSet;
IMolecule[] coordinated_mols;
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
AtomContainer matches = new AtomContainer();
Vector<Integer> idlist = new Vector<Integer>();
List generators = new ArrayList();
Renderer renderer;
BufferedImage image;
Graphics2D g2;
ByteArrayOutputStream out = new ByteArrayOutputStream();
public Display (String smiles, int s) {
size = s;
// generators make the image elements
generators.add(new BasicSceneGenerator());
generators.add(new BasicBondGenerator());
generators.add(new RingGenerator());
generators.add(new BasicAtomGenerator());
renderer = new Renderer(generators, new AWTFontManager());
try { molecule = sp.parseSmiles(smiles); }
catch (Exception ex) { ex.printStackTrace(); }
moleculeSet = ConnectivityChecker.partitionIntoMolecules(molecule);
coordinated_mols = new IMolecule[moleculeSet.getMoleculeCount()];
drawArea = new Rectangle(size, size);
image = new BufferedImage(size, size , BufferedImage.TYPE_INT_RGB);
g2 = (Graphics2D)image.getGraphics();
g2.setColor(Color.yellow);
g2.fillRect(0, 0, size, size);
}
public byte[] image() {
try {
Rectangle2D last = new Rectangle(0,0);
for (int i = 0; i < moleculeSet.getMoleculeCount(); i++) {
IAtomContainer mol = moleculeSet.getMolecule(i);
sdg.setMolecule((IMolecule) mol);
sdg.generateCoordinates();
mol = sdg.getMolecule();
GeometryTools.translateAllPositive(mol);
// get size of previous mol and shift
last = GeometryTools.shiftContainer(mol, GeometryTools.getRectangle2D(mol), last,2);
coordinated_mols[i] = (IMolecule) mol;
}
moleculeSet.setMolecules(coordinated_mols);
renderer.paintMoleculeSet(moleculeSet, new AWTDrawVisitor(g2), drawArea, true);
//matchSmarts("NN",Color.green);
ImageIO.write(image, "png", out);
} catch (Exception ex) {
ex.printStackTrace();
}
return out.toByteArray();
}
// public Image match(String smiles, String smarts) {
// }
private void matchSmarts(String smarts, Color color) {
try {
// map smarts
SMARTSQueryTool querytool = new SMARTSQueryTool(smarts);
boolean status = querytool.matches(molecule);
if (status) {
List<List<java.lang.Integer>> mappings = querytool.getMatchingAtoms();
int nmatch = querytool.countMatches();
for (int i = 0; i < nmatch; i++) {
List atomIndices = (List) mappings.get(i);
for (int n = 0; n < atomIndices.size(); n++) {
Integer atomID = (Integer) atomIndices.get(n);
idlist.add(atomID);
}
}
}
// get a unique list of bond ID's and add them to an AtomContainer
HashSet<Integer> hs = new HashSet<Integer>(idlist);
for (Integer h : hs) {
IAtom a = molecule.getAtom(h);
List bond_list = molecule.getConnectedBondsList(a);
for (int i = 0; i < bond_list.size(); i++) {
IBond b = (IBond) bond_list.get(i);
Integer connectedNr = molecule.getAtomNumber(b.getConnectedAtom(a));
//if (hs.contains(connectedNr)) renderer.getRenderer2DModel().getColorHash().put(b, color);
}
}
} catch (Exception exc) {
exc.printStackTrace();
}
}
}
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