[Cdk-commits] SF.net SVN: cdk: [10070] trunk/cdk/src/org/openscience/cdk/libio/cml/ Convertor.java

[<dr...@us...>]

Revision: 10070
          http://cdk.svn.sourceforge.net/cdk/?rev=10070&view=rev
Author:   drzz
Date:     2008-02-12 08:00:06 -0800 (Tue, 12 Feb 2008)

Log Message:
-----------
added a cmlMoleculetocdkAtomContainer method

Modified Paths:
--------------
    trunk/cdk/src/org/openscience/cdk/libio/cml/Convertor.java

Modified: trunk/cdk/src/org/openscience/cdk/libio/cml/Convertor.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/libio/cml/Convertor.java	2008-02-12 15:16:09 UTC (rev 10069)
+++ trunk/cdk/src/org/openscience/cdk/libio/cml/Convertor.java	2008-02-12 16:00:06 UTC (rev 10070)
@@ -25,6 +25,7 @@
 package org.openscience.cdk.libio.cml;
 
 import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.OptionalDataException;
@@ -54,6 +55,7 @@
 import org.openscience.cdk.interfaces.IPseudoAtom;
 import org.openscience.cdk.interfaces.IReaction;
 import org.openscience.cdk.interfaces.IReactionSet;
+import org.openscience.cdk.io.CMLReader;
 import org.openscience.cdk.protein.data.PDBPolymer;
 import org.openscience.cdk.tools.IDCreator;
 import org.openscience.cdk.tools.LoggingTool;
@@ -77,7 +79,6 @@
 import org.xmlcml.cml.element.CMLScalar;
 import org.xmlcml.cml.element.CMLSubstance;
 import org.xmlcml.cml.element.CMLSubstanceList;
-
 /**
  * @cdk.module       libiocml
  * @cdk.svnrev  $Revision$
@@ -385,7 +386,23 @@
        	}
         return cmlMolecule;
     }
+    public IMolecule cmlMoleculeTocdkAtomContainer(CMLMolecule mol) throws Exception {
+        String cmlString = "<!-- failed -->";
+        cmlString = mol.toXML();
+        
+        IMolecule roundTrippedMol = null;
+        logger.debug("CML string: ", cmlString);
+        CMLReader reader = new CMLReader(new ByteArrayInputStream(cmlString.getBytes()));
 
+        IChemFile file = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());
+        IChemSequence sequence = file.getChemSequence(0);
+        IChemModel chemModel = sequence.getChemModel(0);
+        IMoleculeSet moleculeSet = chemModel.getMoleculeSet();
+        roundTrippedMol = moleculeSet.getMolecule(0);
+        
+        return roundTrippedMol;
+    }
+
     public CMLMolecule cdkMoleculeToCMLMolecule(IMolecule structure) {
         return cdkMoleculeToCMLMolecule(structure, true);
     }


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