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import java.util.List;
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.renderer.selection.*;
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 Structure{
int size;
List generators = new ArrayList();
IMolecule molecule = new Molecule();
IMoleculeSet moleculeSet;
IMolecule[] coordinated_mols;
StructureDiagramGenerator sdg = new StructureDiagramGenerator();
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
Renderer renderer;
BufferedImage image;
Rectangle drawArea;
Graphics2D g2;
LogicalSelection selection = new LogicalSelection(LogicalSelection.Type.ALL);
MoleculeSet selectionMoleculeSet = new MoleculeSet();
ChemModel selectionChemModel = new ChemModel();
ByteArrayOutputStream out = new ByteArrayOutputStream();
public Structure (String smiles, int imageSize) {
size = imageSize;
// generators make the image elements
generators.add(new BasicSceneGenerator());
generators.add(new RingGenerator());
generators.add(new BasicBondGenerator());
generators.add(new BasicAtomGenerator());
generators.add(new SelectBondGenerator());
generators.add(new SelectAtomGenerator());
renderer = new Renderer(generators, new AWTFontManager());
renderer.getRenderer2DModel().set( SelectBondGenerator.SelectionBondColor.class,Color.RED);
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.WHITE);
g2.fillRect(0, 0, size, size);
layout();
}
public byte[] show() {
try {
// create a fake ChemModel to make the LogicalSelection happy
selectionChemModel.setMoleculeSet(selectionMoleculeSet);
selection.select(selectionChemModel);
renderer.getRenderer2DModel().setSelection(selection);
renderer.paintMoleculeSet(moleculeSet, new AWTDrawVisitor(g2), drawArea, true);
ImageIO.write(image, "png", out);
}
catch (Exception ex) { ex.printStackTrace(); }
return out.toByteArray();
}
private void layout() {
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 to the right
last = GeometryTools.shiftContainer(mol, GeometryTools.getRectangle2D(mol), last,2);
coordinated_mols[i] = (IMolecule) mol;
}
moleculeSet.setMolecules(coordinated_mols);
}
catch (Exception ex) { ex.printStackTrace(); }
}
public void match_activating(String[] smarts) {
for (int i = 0; i < smarts.length; i++) {
match(smarts[i]);
}
}
public void match_deactivating(String[] smarts) {
renderer.getRenderer2DModel().set( SelectBondGenerator.SelectionBondColor.class,Color.GREEN);
for (int i = 0; i < smarts.length; i++) {
match(smarts[i]);
}
}
public void match(String smarts) {
try {
SMARTSQueryTool querytool = new SMARTSQueryTool(smarts);
// iterate over molecule set
for (int i = 0; i < moleculeSet.getMoleculeCount(); i++) {
IAtomContainer mol = moleculeSet.getMolecule(i);
ChemModel fragment = new ChemModel();
// match smarts
boolean status = querytool.matches(mol);
if (status) {
List matches = querytool.getUniqueMatchingAtoms();
//System.out.print("Matches: ");
//System.out.println(matches);
// iterate over all matches
for (int j = 0; j < matches.size(); j++) {
IAtomContainer selectionContainer = new AtomContainer();
List atomIndices = (List) matches.get(j);
// itrate over all atoms
for (int k = 0; k < atomIndices.size(); k++) {
IAtom a1 = mol.getAtom( (Integer) atomIndices.get(k));
if (!selectionContainer.contains(a1)) { selectionContainer.addAtom(a1); }
// find bonds
for (int l = k + 1; l < atomIndices.size(); l++) {
IAtom a2 = mol.getAtom( (Integer) atomIndices.get(l));
IBond bond = mol.getBond(a1,a2);
if (bond != null) { selectionContainer.addBond(bond); }
}
}
// create a fake MoleculeSet to make the LogicalSelection happy
selectionMoleculeSet.addMolecule(new Molecule(selectionContainer));
}
}
}
}
catch (Exception exc) { exc.printStackTrace(); }
}
}
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