[Cdk-commits] CVS: cdk/src/org/openscience/cdk/tools ChemFileManipulator.java,1.1,1.2 ChemModelManipulator.java,1.4,1.5 ChemSequenceManipulator.java,1.1,1.2 ReactionManipulator.java,1.7,1.8 SetOfMoleculesManipulator.java,1.3,1.4 SetOfReactionsManipulator.java,1.4,1.5

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

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/tools
In directory sc8-pr-cvs1:/tmp/cvs-serv24826

Modified Files:
	ChemFileManipulator.java ChemModelManipulator.java 
	ChemSequenceManipulator.java ReactionManipulator.java 
	SetOfMoleculesManipulator.java SetOfReactionsManipulator.java 
Log Message:
Added a getAllAtomContainers() to Manipulators

Index: ChemFileManipulator.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/tools/ChemFileManipulator.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- ChemFileManipulator.java	27 Aug 2003 17:42:04 -0000	1.1
+++ ChemFileManipulator.java	30 Sep 2003 10:40:43 -0000	1.2
@@ -24,11 +24,13 @@
  * 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., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
- *  */
+ */
 package org.openscience.cdk.tools;
 
 import org.openscience.cdk.*;
 import org.openscience.cdk.exception.*;
+import java.util.Vector;
+import java.util.Enumeration;
 
 /**
  * Class with convenience methods that provide methods from
@@ -51,6 +53,32 @@
             container.add(ChemSequenceManipulator.getAllInOneContainer(sequence));
         }
         return container;
+    }
+
+    /**
+     * Returns all the AtomContainer's of a ChemFile.
+     */
+    public static AtomContainer[] getAllAtomContainers(ChemFile file) {
+        ChemSequence[] sequences = file.getChemSequences();
+        int acCount = 0;
+        Vector acArrays = new Vector();
+        for (int i=0; i<sequences.length; i++) {
+            AtomContainer[] sequenceContainers = ChemSequenceManipulator.
+                getAllAtomContainers(sequences[i]);
+            acArrays.addElement(sequenceContainers);
+            acCount += sequenceContainers.length;
+        }
+        AtomContainer[] containers = new AtomContainer[acCount];
+        int arrayOffset = 0;
+        for (Enumeration acArraysElements = acArrays.elements(); 
+             acArraysElements.hasMoreElements(); ) {
+            AtomContainer[] modelContainers = (AtomContainer[])acArraysElements.nextElement();
+            System.arraycopy(modelContainers, 0,
+                             containers, arrayOffset,
+                             modelContainers.length);
+            arrayOffset += modelContainers.length;
+        }
+        return containers;
     }
 }
 

Index: ChemModelManipulator.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/tools/ChemModelManipulator.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- ChemModelManipulator.java	2 Jul 2003 12:00:00 -0000	1.4
+++ ChemModelManipulator.java	30 Sep 2003 10:40:43 -0000	1.5
@@ -157,5 +157,23 @@
         // This should never happen.
         return createNewMolecule(chemModel);
     }
+
+    /**
+     * Returns all the AtomContainer's of a ChemModel.
+     */
+    public static AtomContainer[] getAllAtomContainers(ChemModel chemModel) {
+        SetOfMolecules moleculeSet = new SetOfMolecules();
+        if (chemModel.getSetOfMolecules() != null) {
+            moleculeSet.add(chemModel.getSetOfMolecules());
+        }
+        if (chemModel.getSetOfReactions() != null) {
+            moleculeSet.add(
+                SetOfReactionsManipulator.getAllMolecules(
+                    chemModel.getSetOfReactions()
+                )
+            );
+        }
+        return SetOfMoleculesManipulator.getAllAtomContainers(moleculeSet);
+    }
 }
 

Index: ChemSequenceManipulator.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/tools/ChemSequenceManipulator.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- ChemSequenceManipulator.java	27 Aug 2003 17:42:04 -0000	1.1
+++ ChemSequenceManipulator.java	30 Sep 2003 10:40:43 -0000	1.2
@@ -29,6 +29,8 @@
 
 import org.openscience.cdk.*;
 import org.openscience.cdk.exception.*;
+import java.util.Vector;
+import java.util.Enumeration;
 
 /**
  * Class with convenience methods that provide methods from
@@ -51,6 +53,32 @@
             container.add(ChemModelManipulator.getAllInOneContainer(model));
         }
         return container;
+    }
+    
+    /**
+     * Returns all the AtomContainer's of a ChemSequence.
+     */
+    public static AtomContainer[] getAllAtomContainers(ChemSequence sequence) {
+        ChemModel[] models = sequence.getChemModels();
+        int acCount = 0;
+        Vector acArrays = new Vector();
+        for (int i=0; i<models.length; i++) {
+            AtomContainer[] modelContainers = ChemModelManipulator.
+                getAllAtomContainers(models[i]);
+            acArrays.addElement(modelContainers);
+            acCount += modelContainers.length;
+        }
+        AtomContainer[] containers = new AtomContainer[acCount];
+        int arrayOffset = 0;
+        for (Enumeration acArraysElements = acArrays.elements(); 
+             acArraysElements.hasMoreElements(); ) {
+            AtomContainer[] modelContainers = (AtomContainer[])acArraysElements.nextElement();
+            System.arraycopy(modelContainers, 0,
+                             containers, arrayOffset,
+                             modelContainers.length);
+            arrayOffset += modelContainers.length;
+        }
+        return containers;
     }
 }
 

Index: ReactionManipulator.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/tools/ReactionManipulator.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- ReactionManipulator.java	13 Aug 2003 18:31:58 -0000	1.7
+++ ReactionManipulator.java	30 Sep 2003 10:40:43 -0000	1.8
@@ -125,4 +125,14 @@
         }
         return reversedReaction;
     }
+    
+    /**
+     * Returns all the AtomContainer's of a Reaction.
+     */
+    public static AtomContainer[] getAllAtomContainers(Reaction reaction) {
+		return SetOfMoleculesManipulator.getAllAtomContainers(
+            getAllMolecules(reaction)
+        );
+    }
+    
 }

Index: SetOfMoleculesManipulator.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/tools/SetOfMoleculesManipulator.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- SetOfMoleculesManipulator.java	11 Mar 2003 11:40:37 -0000	1.3
+++ SetOfMoleculesManipulator.java	30 Sep 2003 10:40:43 -0000	1.4
@@ -72,5 +72,17 @@
         }
         return container;
     }
+    
+    /**
+     * Returns all the AtomContainer's of a SetOfMolecules.
+     */
+    public static AtomContainer[] getAllAtomContainers(SetOfMolecules set) {
+        int acCount = set.getMoleculeCount();
+		AtomContainer[] container = new AtomContainer[acCount];
+        Molecule[] mols = set.getMolecules();
+		System.arraycopy(mols, 0, container, 0, acCount);
+		return container;
+    }
+    
 }
 

Index: SetOfReactionsManipulator.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/tools/SetOfReactionsManipulator.java,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- SetOfReactionsManipulator.java	13 Aug 2003 18:31:58 -0000	1.4
+++ SetOfReactionsManipulator.java	30 Sep 2003 10:40:43 -0000	1.5
@@ -73,4 +73,12 @@
         return moleculeSet;
     }
     
+    /**
+     * Returns all the AtomContainer's of a Reaction.
+     */
+    public static AtomContainer[] getAllAtomContainers(SetOfReactions set) {
+		return SetOfMoleculesManipulator.getAllAtomContainers(
+            getAllMolecules(set)
+        );
+    }
 }