From d381360584e3cde2a66a2a478c674266253b86f1 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Tue, 27 Jul 2010 11:06:20 +0200
Subject: moved to java dir in application root

---
 java/Structure.java | 158 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 158 insertions(+)
 create mode 100644 java/Structure.java

diff --git a/java/Structure.java b/java/Structure.java
new file mode 100644
index 0000000..d1ac188
--- /dev/null
+++ b/java/Structure.java
@@ -0,0 +1,158 @@
+import java.util.List;
+import java.util.HashMap;
+import java.util.Map;
+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());
+  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 {
+      renderer.getRenderer2DModel().set( RendererModel.ColorHash.class, coloredMatches );
+      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, 5);
+        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],Color.RED);
+    }
+  }
+
+  public void match_deactivating(String[] smarts) {
+    for (int i = 0; i < smarts.length; i++) {
+      match(smarts[i],Color.GREEN);
+    }
+  }
+
+  public void match(String smarts) { match(smarts, Color.BLUE); }
+
+  public void match(String smarts, Color color) {
+
+    IAtom a1 = new Atom();
+    IAtom a2 = new Atom();
+    IBond bond = new Bond();
+
+    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++) {
+            List atomIndices = (List) matches.get(j);
+            // itrate over all atoms
+            for (int k = 0; k < atomIndices.size(); k++) {
+              a1 = mol.getAtom( (Integer) atomIndices.get(k));
+              // find bonds
+              for (int l = k + 1; l < atomIndices.size(); l++) {
+                a2 = mol.getAtom( (Integer) atomIndices.get(l));
+                bond = mol.getBond(a1,a2);
+                if (bond != null) { coloredMatches.put((IChemObject) bond , color); }
+              }
+            }
+          }
+        }
+      }
+
+    }
+    catch (Exception exc) { exc.printStackTrace(); }
+
+  }
+
+}
-- 
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