Skip to content
Browse files

Removed field declarations of Molecule

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
  • Loading branch information...
1 parent 436dba5 commit 88a2935f28c181b59f08f4f8bfbdeefa2e0cbbe7 @rajarshi rajarshi committed with egonw Dec 11, 2011
View
2 src/main/org/openscience/cdk/io/inchi/INChIHandler.java
@@ -58,7 +58,7 @@
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;
View
16 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 @@
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];
View
10 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
View
2 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();

0 comments on commit 88a2935

Please sign in to comment.
Something went wrong with that request. Please try again.