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import java.util.List;
import java.util.HashMap;
import java.util.Map;
import java.util.*;
import java.lang.Math;
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());
List<IChemObject> matchingBonds = new ArrayList<IChemObject>();
List<IChemObject> activatingBonds = new ArrayList<IChemObject>();
List<IChemObject> deactivatingBonds = new ArrayList<IChemObject>();
Map<IChemObject,Color> coloredMatches = new HashMap<IChemObject,Color>();
Renderer renderer;
BufferedImage image;
Rectangle drawArea;
Graphics2D g2;
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());
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.WHITE);
g2.fillRect(0, 0, size, size);
layout();
}
public byte[] show() {
try {
// set colors
for (int i = 0; i < matchingBonds.size(); i++) {
float red = 0;
float green = 0;
IChemObject bond = (IChemObject) matchingBonds.get(i);
if (activatingBonds.contains(bond)) { red = 1; };
if (deactivatingBonds.contains(bond)) { green = 1; };
coloredMatches.put((IChemObject) bond , new Color(red,green,0));
}
renderer.getRenderer2DModel().set( RendererModel.ColorHash.class, coloredMatches );
// render and write
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);
// reverse iteration to show small molecules at the right side
for (int i = moleculeSet.getMoleculeCount()-1; i >= 0 ; i--) {
IAtomContainer mol = moleculeSet.getMolecule(i);
sdg.setMolecule((IMolecule) mol);
sdg.generateCoordinates();
mol = sdg.getMolecule();
// get size of previous mol and shift to the right
// gives nasty results for single atom molecules, but works otherwise
// last = GeometryTools.shiftContainer(mol, GeometryTools.getRectangle2D(mol), last, 0);
// fix suggested by http://sourceforge.net/mailarchive/forum.php?thread_name=AANLkTikJQSjFkNCmO2gb0jw5PQxZRoFSTbruOa2DMCmZ%40mail.gmail.com&forum_name=cdk-jchempaint
// shifts single atoms to the right, but does not adjust the layout of larger structures
Rectangle2D bb = GeometryTools.getRectangle2D(mol);
Rectangle2D minBB = new Rectangle2D.Double(bb.getX(), bb.getY(), Math.max(bb.getWidth(), 15), bb.getHeight());
last = GeometryTools.shiftContainer(mol, minBB, last, 0);
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],true);
}
}
public void match_deactivating(String[] smarts) {
for (int i = 0; i < smarts.length; i++) {
match(smarts[i],false);
}
}
public void match(String smarts) { match(smarts, true); }
public void match(String smarts, Boolean active) {
try {
int count;
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();
// iterate over all matches
for (int j = 0; j < matches.size(); j++) {
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));
// find bonds
for (int l = k + 1; l < atomIndices.size(); l++) {
IAtom a2 = mol.getAtom( (Integer) atomIndices.get(l));
IChemObject bond = (IChemObject) mol.getBond(a1,a2);
if (bond != null) {
// collect all/active/inactive bonds
if (!matchingBonds.contains(bond)) { matchingBonds.add(bond); }
if (active) {
if (!activatingBonds.contains(bond)) { activatingBonds.add(bond); }
} else {
if (!deactivatingBonds.contains(bond)) { deactivatingBonds.add(bond); }
}
}
}
}
}
}
}
}
catch (Exception exc) { exc.printStackTrace(); }
}
}
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