1 files changed, 0 insertions, 164 deletions
diff --git a/public/java/Structure.java b/public/java/Structure.java
deleted file mode 100644
index c46ea05..0000000
--- a/public/java/Structure.java
+++ /dev/null
@@ -1,164 +0,0 @@
-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(); }
-
-  }
-
-}