[Cdk-commits] CVS: cdk/src/org/openscience/cdk/io MDLWriter.java,1.57,1.58

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

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/io
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv18733

Modified Files:
	MDLWriter.java 
Log Message:
Applied patch by Uli, so that writeMolecule() can be called repetively.

Index: MDLWriter.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/MDLWriter.java,v
retrieving revision 1.57
retrieving revision 1.58
diff -u -r1.57 -r1.58
--- MDLWriter.java	27 Jun 2005 10:53:23 -0000	1.57
+++ MDLWriter.java	28 Jun 2005 08:32:10 -0000	1.58
@@ -60,14 +60,6 @@
  * writer.close();
  * </pre>
  *
- * <p>The <code>write(Molecule)</code> method cannot be used to write a MDL SDF
- * file. Then you have to use code like this:
- * <pre>
- * MDLWriter writer = new MDLWriter(new FileWriter(new File("output.sdf")));
- * writer.write((SetOfMolecules)moleculeSet);
- * writer.close();
- * </pre>
- *
  * See {@cdk.cite DAL92}.
  *
  * @cdk.module io
@@ -79,6 +71,7 @@
     private BufferedWriter writer;
     private LoggingTool logger;
     private IsotopeFactory isotopeFactory = null;
+    private int moleculeNumber;
     public Map sdFields=null;
 
     /**
@@ -128,6 +121,7 @@
                 throw new CDKException("Failed to initiate isotope factory: " + exception.getMessage());
             }
         }
+        this.moleculeNumber = 1;
     }
 
     /**
@@ -185,23 +179,10 @@
 	private void writeSetOfMolecules(SetOfMolecules som)
 	{
 		Molecule[] molecules = som.getMolecules();
-			try
-			{
-        boolean[] isVisible=new boolean[molecules[0].getAtomCount()];
-        for(int i=0;i<isVisible.length;i++){
-          isVisible[i]=true;
-        }
-        writeMolecule(molecules[0], isVisible);
-			}
-			catch (Exception exc)
-			{
-			}
-		for (int i = 1; i <= som.getMoleculeCount() - 1; i++)
+		for (int i = 0; i < som.getMoleculeCount(); i++)
 		{
 			try
 			{
-			    writer.write("$$$$");
-				writer.newLine();
         boolean[] isVisible=new boolean[molecules[i].getAtomCount()];
         for(int k=0;k<isVisible.length;k++){
           isVisible[k]=true;
@@ -240,7 +221,12 @@
     public void writeMolecule(Molecule molecule, boolean[] isVisible) throws Exception {
         int Bonorder, stereo;
         String line = "";
-        
+        // taking care of the $$$$ signs:
+        // we do not write such a sign at the end of the first molecule, thus we have to write on BEFORE the second molecule
+        if(moleculeNumber == 2) {
+          writer.write("$$$$");
+          writer.newLine();
+        }
         // write header block
         // lines get shortened to 80 chars, that's in the spec
         String title = (String)molecule.getProperty(CDKConstants.TITLE);
@@ -397,6 +383,13 @@
             writer.newLine();
           }
         }
+        // taking care of the $$$$ signs:
+        // we write such a sign at the end of all except the first molecule
+        if(moleculeNumber != 1) {
+          writer.write("$$$$");
+          writer.newLine();
+        }
+        moleculeNumber++;
         writer.flush();
     }