initial cdk structure visualizer added

2 files changed, 144 insertions, 3 deletions

diff --git a/application.rb b/application.rb
index 6a7e4c6..cc0279b 100644
--- a/application.rb
+++ b/application.rb
@@ -1,9 +1,25 @@
+# Java environment
+ENV["JAVA_HOME"] = "/usr/lib/jvm/java-6-sun" unless ENV["JAVA_HOME"]
+java_dir = File.join File.expand_path(File.dirname(__FILE__)),"public/java"
+cdk = File.join java_dir, "cdk-1.3.5.jar"
+jchempaint = File.join java_dir, "cdk-jchempaint-15.jar"
+ENV["CLASSPATH"] = "#{ENV["CLASSPATH"]}:#{java_dir}:#{cdk}:#{jchempaint}"
+
 require 'rubygems'
+require 'rjb'
 gem "opentox-ruby-api-wrapper", "= 1.5.7"
 require 'opentox-ruby-api-wrapper'
 
-set :lock, true
-CACTUS_URI="http://cactus.nci.nih.gov/chemical/structure/"
+#set :lock, true
+
+get %r{/(.+)/image} do |inchi| # catches all remaining get requests
+
+		smiles = OpenTox::Compound.new(:inchi => inchi).smiles
+		content_type "image/png"
+		attachment "#{smiles}.png"
+    Rjb::import('Display').new(smiles,600).image
+
+end
 
 get %r{/(.+)} do |inchi| # catches all remaining get requests
 	inchi = URI.unescape request.env['REQUEST_URI'].sub(/^\//,'').sub(/.*compound\//,'') # hack to avoid sinatra's URI/CGI unescaping, splitting, ..."
@@ -28,7 +44,7 @@ get %r{/(.+)} do |inchi| # catches all remaining get requests
 		OpenTox::Compound.new(:inchi => inchi).png
 	when "text/plain"
 		response['Content-Type'] = "text/plain"
-		uri = File.join CACTUS_URI,inchi,"names"
+		uri = File.join @@cactus_uri,inchi,"names"
 		RestClient.get(uri).body
 	else
 		halt 400, "Unsupported MIME type '#{request.env['HTTP_ACCEPT']}'"
diff --git a/public/java/Display.java b/public/java/Display.java
new file mode 100644
index 0000000..4a3e221
--- /dev/null
+++ b/public/java/Display.java
@@ -0,0 +1,125 @@
+import java.util.List;
+import java.util.Arrays;
+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.templates.*;
+import org.openscience.cdk.smiles.*;
+import org.openscience.cdk.smiles.smarts.*;
+import org.openscience.cdk.graph.*;
+import org.openscience.cdk.geometry.*;
+
+public class Display{
+
+	int size;
+	Rectangle drawArea;
+	IMolecule molecule = new Molecule();
+	IMoleculeSet moleculeSet;
+	IMolecule[] coordinated_mols;
+	StructureDiagramGenerator sdg = new StructureDiagramGenerator();
+	SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+	AtomContainer matches = new AtomContainer();
+	Vector<Integer> idlist = new Vector<Integer>();
+	List generators = new ArrayList();
+	Renderer renderer;
+	BufferedImage image;
+	Graphics2D g2;
+
+	ByteArrayOutputStream out = new ByteArrayOutputStream();
+
+	public Display (String smiles, int s) {
+
+		size = s; 
+		// generators make the image elements
+		generators.add(new BasicSceneGenerator());
+		generators.add(new BasicBondGenerator());
+		generators.add(new RingGenerator());
+		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.yellow);
+		g2.fillRect(0, 0, size, size);
+	}
+
+	public byte[] image() {
+		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);
+			renderer.paintMoleculeSet(moleculeSet, new AWTDrawVisitor(g2), drawArea, true);
+			//matchSmarts("NN",Color.green);
+			ImageIO.write(image, "png", out);
+		} catch (Exception ex) {
+				ex.printStackTrace();
+		}
+		return out.toByteArray();
+	}
+
+//	public Image match(String smiles, String smarts) {
+//	}
+	private void matchSmarts(String smarts, Color color) {
+		try {
+			// map smarts
+				SMARTSQueryTool querytool = new SMARTSQueryTool(smarts);
+				boolean status = querytool.matches(molecule);
+				if (status) {
+					List<List<java.lang.Integer>>	mappings = querytool.getMatchingAtoms();
+					int nmatch = querytool.countMatches();
+					for (int i = 0; i < nmatch; i++) {
+						List atomIndices = (List) mappings.get(i);
+						for (int n = 0; n < atomIndices.size(); n++) {
+							Integer atomID = (Integer) atomIndices.get(n);
+							idlist.add(atomID);
+						}
+					}
+				}
+
+				// get a unique list of bond ID's and add them to an AtomContainer
+				HashSet<Integer> hs = new HashSet<Integer>(idlist);
+				for (Integer h : hs) {
+					IAtom a = molecule.getAtom(h);
+					List bond_list = molecule.getConnectedBondsList(a);
+					for (int i = 0; i < bond_list.size(); i++) {
+						IBond b = (IBond) bond_list.get(i);
+						Integer connectedNr = molecule.getAtomNumber(b.getConnectedAtom(a));
+						//if (hs.contains(connectedNr)) renderer.getRenderer2DModel().getColorHash().put(b, color);
+					}
+				}
+
+		} catch (Exception exc) {
+				exc.printStackTrace();
+		}
+
+	}
+
+}
+