fixed bug: 3220

Added method for adding molecule entry to SDF file
bioclipse · Jun 13, 2012 · a8bdf2a · a8bdf2a
1 parent b1cafdb
commit a8bdf2a
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Showing 3 changed files with 67 additions and 2 deletions.
diff --git a/...e.cdk.business.test/src/net/bioclipse/cdk/business/test/AbstractCDKManagerPluginTest.java b/...e.cdk.business.test/src/net/bioclipse/cdk/business/test/AbstractCDKManagerPluginTest.java
@@ -55,6 +55,7 @@
 import net.bioclipse.ui.business.IUIManager;
 
 import org.eclipse.core.resources.IFile;
+import org.eclipse.core.resources.IProject;
 import org.eclipse.core.resources.IResource;
 import org.eclipse.core.resources.ResourcesPlugin;
 import org.eclipse.core.resources.WorkspaceJob;
@@ -1377,6 +1378,35 @@ public void testSaveMDLMolfile() throws Exception {
         assertEquals("CCC", mol.toSMILES(
         ));
     }
+
+    @Test
+    public void testAppendToSDF() throws Exception {
+
+        IProject project = ResourcesPlugin.getWorkspace().getRoot().getProject( "testAppendToSDF" );
+        try {
+            project.create( new NullProgressMonitor() );
+            project.open( new NullProgressMonitor() );
+            final ICDKMolecule propane  = cdk.fromSMILES("CCC");
+
+            ICDKMolecule ethane  = cdk.fromSMILES("CC");
+            String path = "/testAppendToSDF/testSaveSDF" + propane.hashCode() + ".mol";
+            cdk.saveSDFile( path, new ArrayList() {{add(propane);}} );
+
+            assertEquals(1, cdk.loadMolecules(path).size());
+
+            cdk.appendToSDF( path, ethane );
+
+            List<ICDKMolecule> molecules = cdk.loadMolecules(path);
+            assertEquals( "CCC",
+                          cdk.calculateSMILES( molecules.get( 0 ) ) );
+
+            assertEquals( "CC",
+                          cdk.calculateSMILES( molecules.get(1) ) );
+        }
+        finally {
+            project.delete( true, new NullProgressMonitor() );
+        }
+    }
 
     @Test
     public void testSaveCML() throws Exception {

diff --git a/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/CDKManager.java b/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/CDKManager.java
@@ -1,6 +1,6 @@
 /*******************************************************************************
  * Copyright (c) 2008-2009  Ola Spjuth
- *               2008-2010  Jonathan Alvarsson
+ *               2008-2012  Jonathan Alvarsson
  *               2008-2009  Stefan Kuhn
  *               2008-2009  Egon Willighagen <egonw@users.sf.net>
  *
@@ -17,6 +17,8 @@
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
 import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
@@ -2156,6 +2158,30 @@ public String determineFormat( String path ) throws IOException,
         );
         return format == null ? "Unknown" : format.getFormatName();
     }
+
+    public void appendToSDF( IFile sdFile, ICDKMolecule molecule ) throws BioclipseException {
+        try {
+            SDFWriter writer 
+                = new SDFWriter( EFS.getStore(sdFile.getLocationURI())
+                                    .openOutputStream( 
+                                         EFS.APPEND, 
+                                         new NullProgressMonitor() ) );
+            try {
+                writer.write( molecule.getAtomContainer() );
+                writer.close();
+            } catch ( CDKException e ) {
+                throw new BioclipseException(
+                              "Failed in writing molecule to file", e );
+            } catch ( IOException e ) {
+                throw new BioclipseException(
+                              "Failed in writing molecule to file", e );
+            }
+        } catch ( CoreException e ) {
+            throw new BioclipseException( "Could not open file: " + sdFile 
+                                          + " for writing.",
+                                          e );
+        }
+    }
 
       public void saveSDFile(final IFile file, List<? extends IMolecule> entries,
               IProgressMonitor monitor)

diff --git a/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/ICDKManager.java b/plugins/net.bioclipse.cdk.business/src/net/bioclipse/cdk/business/ICDKManager.java
@@ -1186,5 +1186,14 @@ public void saveSDFile( IFile molFile, List<? extends IMolecule> mols,
     public List<List<IMolecule>> randomSplit2parts(List<IMolecule> mols_in, double firstRatio);
 
     public List<ICDKMolecule> loadSMILESFile( IFile file,
-                                              IProgressMonitor monitor );    
+                                              IProgressMonitor monitor );
+
+    @Recorded
+    @PublishedMethod(
+         params="String sdFile, ICDKMolecule molecule",
+         methodSummary="Append a molecule at the end of a given sd file."
+    )
+    public void appendToSDF( String sdFile, ICDKMolecule molecule ) throws BioclipseException;
+
+    public void appendToSDF( IFile sdFile, ICDKMolecule molecule ) throws BioclipseException;
 }