diff options
author | Christoph Helma <helma@in-silico.ch> | 2010-07-22 18:20:05 +0200 |
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committer | Christoph Helma <helma@in-silico.ch> | 2010-07-22 18:20:05 +0200 |
commit | eecee560ffd6afccde7b0c383b42b67a9d18993c (patch) | |
tree | f8b9c59f6efb5fc51cdbd29c4b5f75c70d372756 /public | |
parent | 040d6022a42c9e5fab97a42cded77fd20d3def3f (diff) |
matching of fragemnt sets implemented
Diffstat (limited to 'public')
-rw-r--r-- | public/java/Structure.java | 154 |
1 files changed, 154 insertions, 0 deletions
diff --git a/public/java/Structure.java b/public/java/Structure.java new file mode 100644 index 0000000..e1b2fa6 --- /dev/null +++ b/public/java/Structure.java @@ -0,0 +1,154 @@ +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; + Rectangle drawArea; + IMolecule molecule = new Molecule(); + IMoleculeSet moleculeSet; + IMolecule[] coordinated_mols; + StructureDiagramGenerator sdg = new StructureDiagramGenerator(); + SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); + Vector<Integer> idlist = new Vector<Integer>(); + List generators = new ArrayList(); + Renderer renderer; + BufferedImage image; + Graphics2D g2; + MoleculeSet highBSet = new MoleculeSet(); + ChemModel chemModel = new ChemModel(); + LogicalSelection selection = new LogicalSelection(LogicalSelection.Type.ALL); + ByteArrayOutputStream out = new ByteArrayOutputStream(); + + public Structure (String smiles, int s) { + + size = s; + // generators make the image elements + generators.add(new BasicSceneGenerator()); + generators.add(new RingGenerator()); + generators.add(new BasicBondGenerator()); + generators.add(new BasicAtomGenerator()); + //generators.add(new AtomNumberGenerator()); + generators.add(new SelectBondGenerator()); + generators.add(new SelectAtomGenerator()); + 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.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 + 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) { + Color color = Color.RED; + for (int i = 0; i < smarts.length; i++) { + match(smarts[i], color); + } + } + + public void match_deactivating(String[] smarts) { + Color color = Color.GREEN; + for (int i = 0; i < smarts.length; i++) { + match(smarts[i], color); + } + } + + public void match(String smarts, Color color) { + 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); + for (int j = 0; j < matches.size(); j++) { + IAtomContainer highB = new AtomContainer(); + List atomIndices = (List) matches.get(j); + for (int k = 0; k < atomIndices.size(); k++) { + IAtom a1 = mol.getAtom( (Integer) atomIndices.get(k)); + if (!highB.contains(a1)) { highB.addAtom(a1); } + 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) { highB.addBond(bond); } + } + } + highBSet.addMolecule(new Molecule(highB)); + } + } + } + + chemModel.setMoleculeSet(highBSet); + selection.select(chemModel); + renderer.getRenderer2DModel().setSelection(selection); + renderer.getRenderer2DModel().set( SelectBondGenerator.SelectionBondColor.class,color); + + } catch (Exception exc) { + exc.printStackTrace(); + } + + } + +} |