matching of fragemnt sets implemented

2 files changed, 222 insertions, 63 deletions

diff --git a/application.rb b/application.rb
index b8b1d04..e0e469d 100644
--- a/application.rb
+++ b/application.rb
@@ -10,81 +10,86 @@ require 'rjb'
 gem "opentox-ruby-api-wrapper", "= 1.6.0"
 require 'opentox-ruby-api-wrapper'
 
-get %r{/smiles/(.+)/smarts/(.*)} do |smiles,smarts| 
-		content_type "image/png"
-		attachment "#{smiles}.png"
-    #LOGGER.debug "SMILES: #{smiles}, SMARTS: #{smarts}"
-    s = Rjb::import('Structure').new(smiles,200)
-    s.match(smarts)
-    s.show
+post "/display" do
+  content_type "image/png"
+  attachment "#{params["smiles"]}.png"
+  s = Rjb::import('Structure').new(params["smiles"],200)
+  s.match_activating(params["smarts"])
+  s.match_deactivating(["CC"])
+  s.show
 end
 
+get %r{/smiles/(.+)/smarts/(.*)} do |smiles,smarts| 
+  content_type "image/png"
+  attachment "#{smiles}.png"
+  s = Rjb::import('Structure').new(smiles,200)
+  s.match(smarts)
+  s.show
+end
 
 get %r{/smiles/(.+)} do |smiles| 
-		content_type "image/png"
-		attachment "#{smiles}.png"
-    Rjb::import('Structure').new(smiles,200).show
+  content_type "image/png"
+  attachment "#{smiles}.png"
+  Rjb::import('Structure').new(smiles,200).show
 end
 
 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('Structure').new(smiles,200).show
-
+   smiles = OpenTox::Compound.new(:inchi => inchi).smiles
+   content_type "image/png"
+   attachment "#{smiles}.png"
+   Rjb::import('Structure').new(smiles,200).show
 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, ..."
-	case request.env['HTTP_ACCEPT']
-	when "*/*"
-		response['Content-Type'] = "chemical/x-daylight-smiles"
-		OpenTox::Compound.new(:inchi => inchi).smiles
-	when "chemical/x-daylight-smiles"
-		response['Content-Type'] = "chemical/x-daylight-smiles"
-		OpenTox::Compound.new(:inchi => inchi).smiles
-	when "chemical/x-inchi"
-		response['Content-Type'] = "chemical/x-inchi"
-		inchi 
-	when "chemical/x-mdl-sdfile"
-		response['Content-Type'] = "chemical/x-mdl-sdfile"
-		OpenTox::Compound.new(:inchi => inchi).sdf
-	when "image/gif"
-		response['Content-Type'] = "image/gif"
-		OpenTox::Compound.new(:inchi => inchi).gif
-	when "image/png"
-		response['Content-Type'] = "image/png"
-		OpenTox::Compound.new(:inchi => inchi).png
-	when "text/plain"
-		response['Content-Type'] = "text/plain"
-		uri = File.join @@cactus_uri,inchi,"names"
-		RestClient.get(uri).body
-	else
-		halt 400, "Unsupported MIME type '#{request.env['HTTP_ACCEPT']}'"
-	end
+  inchi = URI.unescape request.env['REQUEST_URI'].sub(/^\//,'').sub(/.*compound\//,'') # hack to avoid sinatra's URI/CGI unescaping, splitting, ..."
+  case request.env['HTTP_ACCEPT']
+  when "*/*"
+    response['Content-Type'] = "chemical/x-daylight-smiles"
+    OpenTox::Compound.new(:inchi => inchi).smiles
+  when "chemical/x-daylight-smiles"
+    response['Content-Type'] = "chemical/x-daylight-smiles"
+    OpenTox::Compound.new(:inchi => inchi).smiles
+  when "chemical/x-inchi"
+    response['Content-Type'] = "chemical/x-inchi"
+    inchi 
+  when "chemical/x-mdl-sdfile"
+    response['Content-Type'] = "chemical/x-mdl-sdfile"
+    OpenTox::Compound.new(:inchi => inchi).sdf
+  when "image/gif"
+    response['Content-Type'] = "image/gif"
+    OpenTox::Compound.new(:inchi => inchi).gif
+  when "image/png"
+    response['Content-Type'] = "image/png"
+    OpenTox::Compound.new(:inchi => inchi).png
+  when "text/plain"
+    response['Content-Type'] = "text/plain"
+    uri = File.join @@cactus_uri,inchi,"names"
+    RestClient.get(uri).body
+  else
+    halt 400, "Unsupported MIME type '#{request.env['HTTP_ACCEPT']}'"
+  end
 end
 
 post '/?' do 
 
-	input =	request.env["rack.input"].read
-	response['Content-Type'] = 'text/uri-list'
-	begin
-		case request.content_type
-		when /chemical\/x-daylight-smiles/
-			OpenTox::Compound.new(:smiles => input).uri + "\n"
-		when /chemical\/x-inchi/
-			OpenTox::Compound.new(:inchi => input).uri + "\n"
-		when /chemical\/x-mdl-sdfile|chemical\/x-mdl-molfile/
-			OpenTox::Compound.new(:sdf => input).uri + "\n"
-		when /text\/plain/
-			OpenTox::Compound.new(:name => input).uri + "\n"
-		else
-			status 400
-			"Unsupported MIME type '#{request.content_type}'"
-		end
-	rescue
-		status 400
-		"Cannot process request '#{input}' for content type '#{request.content_type}'"
-	end
+  input = request.env["rack.input"].read
+  response['Content-Type'] = 'text/uri-list'
+  begin
+    case request.content_type
+    when /chemical\/x-daylight-smiles/
+      OpenTox::Compound.new(:smiles => input).uri + "\n"
+    when /chemical\/x-inchi/
+      OpenTox::Compound.new(:inchi => input).uri + "\n"
+    when /chemical\/x-mdl-sdfile|chemical\/x-mdl-molfile/
+      OpenTox::Compound.new(:sdf => input).uri + "\n"
+    when /text\/plain/
+      OpenTox::Compound.new(:name => input).uri + "\n"
+    else
+      status 400
+      "Unsupported MIME type '#{request.content_type}'"
+    end
+  rescue
+    status 400
+    "Cannot process request '#{input}' for content type '#{request.content_type}'"
+  end
 end
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();
+    }
+
+  }
+
+}