Removed field declarations of Molecule

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Dec 11, 2011 · 88a2935 · 88a2935
1 parent 436dba5
commit 88a2935
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Showing 4 changed files with 18 additions and 12 deletions.
diff --git a/src/main/org/openscience/cdk/io/inchi/INChIHandler.java b/src/main/org/openscience/cdk/io/inchi/INChIHandler.java
@@ -58,7 +58,7 @@ public class INChIHandler extends DefaultHandler {
     private ChemSequence chemSequence;
     private ChemModel chemModel;
     private IAtomContainerSet setOfMolecules;
-    private Molecule tautomer;
+    private IAtomContainer tautomer;
 
     /** Used to store all chars between two tags */
     private String currentChars;

diff --git a/src/main/org/openscience/cdk/isomorphism/IsomorphismTester.java b/src/main/org/openscience/cdk/isomorphism/IsomorphismTester.java
@@ -29,7 +29,7 @@
 import org.openscience.cdk.exception.NoSuchAtomException;
 import org.openscience.cdk.graph.invariant.MorganNumbersTools;
 import org.openscience.cdk.interfaces.IAtom;
-import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.interfaces.IAtomContainer;
 
 import java.util.Arrays;
 
@@ -61,8 +61,8 @@ public class IsomorphismTester implements java.io.Serializable
 	long[] sortedBaseTable;
 	long[] compareTable;
 	long[] sortedCompareTable;
-	IMolecule base = null;
-	IMolecule compare = null;
+	IAtomContainer base = null;
+	IAtomContainer compare = null;
 
 
 	/**
@@ -74,7 +74,7 @@ public IsomorphismTester() { }
 	/**
 	 *  Constructor for the IsomorphismTester object
 	 */
-	public IsomorphismTester(IMolecule mol) throws NoSuchAtomException
+	public IsomorphismTester(IAtomContainer mol) throws NoSuchAtomException
 	{
 		setBaseTable(mol);
 	}
@@ -89,7 +89,7 @@ public IsomorphismTester(IMolecule mol) throws NoSuchAtomException
 	 * @return                          True, if the two molecules are isomorphic
 	 */
     @TestMethod("testIsIsomorphic_IMolecule_IMolecule")
-    public boolean isIsomorphic(IMolecule mol1, IMolecule mol2) {
+    public boolean isIsomorphic(IAtomContainer mol1, IAtomContainer mol2) {
 		setBaseTable(mol1);
 		return isIsomorphic(mol2);
 	}
@@ -103,7 +103,7 @@ public boolean isIsomorphic(IMolecule mol1, IMolecule mol2) {
 	 * @return                          True, if the two molecules are isomorphic 
 	 */
     @TestMethod("testIsIsomorphic_IMolecule")
-    public boolean isIsomorphic(IMolecule mol2) {
+    public boolean isIsomorphic(IAtomContainer mol2) {
 		boolean found;
 		IAtom atom1 = null;
 		IAtom atom2 = null;
@@ -146,7 +146,7 @@ public boolean isIsomorphic(IMolecule mol2) {
 	 *
 	 * @param  mol                      The new BaseTable value
 	 */
-	private void setBaseTable(IMolecule mol) {
+	private void setBaseTable(IAtomContainer mol) {
 		this.base = mol;
 		this.baseTable = MorganNumbersTools.getMorganNumbers(base);
 		sortedBaseTable = new long[baseTable.length];
@@ -160,7 +160,7 @@ private void setBaseTable(IMolecule mol) {
 	 *
 	 * @param  mol                      The new CompareTable value
 	 */
-	private void setCompareTable(IMolecule mol) {
+	private void setCompareTable(IAtomContainer mol) {
 		this.compare = mol;
 		this.compareTable = MorganNumbersTools.getMorganNumbers(compare);
 		sortedCompareTable = new long[compareTable.length];

diff --git a/src/test/org/openscience/cdk/graph/PathToolsTest.java b/src/test/org/openscience/cdk/graph/PathToolsTest.java
@@ -26,7 +26,13 @@
 import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
-import org.openscience.cdk.*;
+import org.openscience.cdk.Atom;
+import org.openscience.cdk.AtomContainer;
+import org.openscience.cdk.Bond;
+import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.CDKTestCase;
+import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.Molecule;
 import org.openscience.cdk.exception.InvalidSmilesException;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
@@ -46,7 +52,7 @@
  * @cdk.module test-core
  */
 public class PathToolsTest extends CDKTestCase {
-    private static Molecule molecule;
+    private static IAtomContainer molecule;
     private static SmilesParser sp;
 
     @BeforeClass

diff --git a/src/test/org/openscience/cdk/isomorphism/IsomorphismTesterTest.java b/src/test/org/openscience/cdk/isomorphism/IsomorphismTesterTest.java
@@ -45,7 +45,7 @@
  */
 public class IsomorphismTesterTest extends CDKTestCase
 {
-	Molecule pinene_1 = null, pinene_2 = null, pinene_non = null;
+	IAtomContainer pinene_1 = null, pinene_2 = null, pinene_non = null;
 	public IsomorphismTesterTest()
 	{
 		super();