[Cdk-commits] SF.net SVN: cdk:[14566] cdk-xws/trunk/xws-cdk-services/src

[<eg...@us...>]

Revision: 14566
          http://cdk.svn.sourceforge.net/cdk/?rev=14566&view=rev
Author:   egonw
Date:     2009-04-25 06:23:01 +0000 (Sat, 25 Apr 2009)

Log Message:
-----------
Added method to generate 2D coordinates

Modified Paths:
--------------
    cdk-xws/trunk/xws-cdk-services/src/net/bioclipse/xws/component/functions/Functions.java

Added Paths:
-----------
    cdk-xws/trunk/xws-cdk-services/src/org/openscience/cdk/xws/services/Generate2DCoordinates.java

Modified: cdk-xws/trunk/xws-cdk-services/src/net/bioclipse/xws/component/functions/Functions.java
===================================================================
--- cdk-xws/trunk/xws-cdk-services/src/net/bioclipse/xws/component/functions/Functions.java	2009-04-24 09:19:37 UTC (rev 14565)
+++ cdk-xws/trunk/xws-cdk-services/src/net/bioclipse/xws/component/functions/Functions.java	2009-04-25 06:23:01 UTC (rev 14566)
@@ -24,16 +24,18 @@
  */
 package net.bioclipse.xws.component.functions;
 
+import org.openscience.cdk.xws.services.Generate2DCoordinates;
 import org.openscience.cdk.xws.services.SomeCDKFunctionOne;
 import org.openscience.cdk.xws.services.SomeCDKFunctionTwo;
 
 public class Functions implements IFunctions {
     
     public Class[] getFunctions() {
-        Class[] functions = new Class[2];
+        Class[] functions = new Class[3];
 
         functions[0] = SomeCDKFunctionOne.class;
         functions[1] = SomeCDKFunctionTwo.class;
+        functions[2] = Generate2DCoordinates.class;
 
         return functions;
     }

Added: cdk-xws/trunk/xws-cdk-services/src/org/openscience/cdk/xws/services/Generate2DCoordinates.java
===================================================================
--- cdk-xws/trunk/xws-cdk-services/src/org/openscience/cdk/xws/services/Generate2DCoordinates.java	                        (rev 0)
+++ cdk-xws/trunk/xws-cdk-services/src/org/openscience/cdk/xws/services/Generate2DCoordinates.java	2009-04-25 06:23:01 UTC (rev 14566)
@@ -0,0 +1,107 @@
+/* $Revision: 6707 $ $Author: egonw $ $Date: 2006-07-30 16:38:18 -0400 (Sun, 30 Jul 2006) $
+ * 
+ * Copyright (C) 2008  Egon Willighagen <eg...@us...>
+ * 
+ * Contact: cdk...@li...
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ * All we ask is that proper credit is given for our work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may distribute
+ * with programs based on this work.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.cdk.xws.services;
+
+import java.io.ByteArrayInputStream;
+
+import net.bioclipse.xws.JavaDOMTools;
+import net.bioclipse.xws.component.adhoc.function.FunctionInformation;
+import net.bioclipse.xws.component.adhoc.function.IFunction;
+import net.bioclipse.xws.component.xmpp.process.IProcessStatus;
+
+import org.openscience.cdk.interfaces.IChemFile;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.io.CMLReader;
+import org.openscience.cdk.layout.StructureDiagramGenerator;
+import org.openscience.cdk.libio.cml.Convertor;
+import org.openscience.cdk.nonotify.NNChemFile;
+import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
+import org.openscience.cdk.xws.ResourceAsStringTool;
+import org.w3c.dom.Element;
+import org.xmlcml.cml.element.CMLMolecule;
+
+public class Generate2DCoordinates implements IFunction {
+	
+    private static final String FUNCTION_NAME = "generate2Dcoordinates";
+    private static final String FUNCTION_DESCRIPTION = "Generates a 2D schema for the input molecule.";
+    private static final String FUNCTION_DETAILS = "A full-connected molecular structure in CML.";
+    
+    private final static String SCHEMATA =
+        ResourceAsStringTool.getAsString("org/openscience/cdk/xws/schema/cml.xml");
+
+    private static StructureDiagramGenerator sdg;
+    private static Convertor convertor = new Convertor(true, null);
+    
+    private FunctionInformation info = null;
+    
+    public FunctionInformation getFunctionInformation() {
+        if (info == null) {
+            info = new FunctionInformation(
+                    FUNCTION_NAME,
+                    FUNCTION_DESCRIPTION,
+                    FUNCTION_DETAILS,
+                    SCHEMATA,
+                    SCHEMATA,
+                    true
+            );
+        }
+
+        return info;
+    }
+
+    public void run(IProcessStatus ps, Element input) {
+        Element output = null;
+        if ("http://www.xml-cml.org/schema".equals(input.getNamespaceURI()) &&
+            "molecule".equals(input.getLocalName())) {
+            String cmlString = JavaDOMTools.w3cElementToString(input);
+            System.out.println("CML: " + cmlString);
+            CMLReader reader = new CMLReader(new ByteArrayInputStream(cmlString.getBytes()));
+            try {
+                IChemFile file = (IChemFile)reader.read(new NNChemFile());
+                if (sdg == null) {
+                    sdg = new StructureDiagramGenerator();
+                }
+                IMolecule mol = file.getBuilder().newMolecule(
+                    ChemFileManipulator.getAllAtomContainers(file).get(0)
+                );
+                sdg.setMolecule(mol);
+                sdg.generateCoordinates();
+                mol = sdg.getMolecule();
+                CMLMolecule cmlMol = convertor.cdkAtomContainerToCMLMolecule(mol);
+                String outputString = cmlMol.toXML();
+                output = JavaDOMTools.string2Element(outputString);
+            } catch (Exception e) {
+                // TODO Auto-generated catch block
+                e.printStackTrace();
+                ps.setError(e.getMessage());
+            }
+        } else {
+            System.out.println("Expected CML but got: " + input.getNamespaceURI());
+            ps.setError("Expected CML input.");
+        }
+
+        ps.setResult(output, "Done");
+    }
+}
\ No newline at end of file


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