[Cdk-commits] CVS: cdk/src/org/openscience/cdk/test AtomTest.java,1.18,1.19 ChemSequenceTest.java,1.10,1.11 CrystalTest.java,1.13,1.14

[Egon Willighagen <egonw@us...>]

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/test
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv29321/src/org/openscience/cdk/test

Modified Files:
	AtomTest.java ChemSequenceTest.java CrystalTest.java 
Log Message:
More work on core module coverage... bla bla

Index: AtomTest.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/test/AtomTest.java,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -r1.18 -r1.19
--- AtomTest.java	29 Dec 2004 08:45:34 -0000	1.18
+++ AtomTest.java	29 Dec 2004 21:06:58 -0000	1.19
@@ -235,6 +235,13 @@
         assertEquals(point3d.y, a.getPoint3d().y, 0.001);
         assertEquals(point3d.z, a.getPoint3d().z, 0.001);
     }
+    public void testSetPoint3d_Point3d() {
+        Point3d point3d = new Point3d(1.0, 2.0, 3.0);
+        
+        Atom a = new Atom("C");
+        a.setPoint3d(point3d);
+        assertEquals(point3d, a.getPoint3d());
+    }
     
     /**
      * Method to test the set[XY]2D() methods.
@@ -273,10 +280,17 @@
         Point2d point2d = new Point2d(1.0, 2.0);
         
         Atom a = new Atom("C", point2d);
-	assertNotNull(a.getPoint2d());
+        assertNotNull(a.getPoint2d());
         assertEquals(point2d.x, a.getPoint2d().x, 0.001);
         assertEquals(point2d.y, a.getPoint2d().y, 0.001);
     }
+    public void testSetPoint2d_Point2d() {
+        Point2d point2d = new Point2d(1.0, 2.0);
+        
+        Atom a = new Atom("C");
+        a.setPoint2d(point2d);
+        assertEquals(point2d, a.getPoint2d());
+    }
 
     /**
      * Method to test the get/setHydrogenCount() methods.
@@ -288,11 +302,14 @@
         a.setStereoParity(parity);
         assertEquals(parity, a.getStereoParity());
     }
+    public void testGetStereoParity() {
+        testSetStereoParity_int();
+    }
     
     /**
      * Method to test the compare() method.
      */
-    public void testCompare() {
+    public void testCompare_Object() {
         Atom atom = new Atom("C");
         assertTrue(atom.compare(atom));
         Atom hydrogen = new Atom("H");

Index: ChemSequenceTest.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/test/ChemSequenceTest.java,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- ChemSequenceTest.java	28 Dec 2004 11:21:31 -0000	1.10
+++ ChemSequenceTest.java	29 Dec 2004 21:06:58 -0000	1.11
@@ -84,6 +84,16 @@
         assertEquals(3, cs.getChemModelCount());
     }
 
+    public void testGetChemModel_int() {
+        ChemSequence cs = new ChemSequence();
+        cs.addChemModel(new ChemModel());
+        ChemModel second = new ChemModel();
+        cs.addChemModel(second);
+        cs.addChemModel(new ChemModel());
+        
+        assertEquals(second, cs.getChemModel(1));
+    }
+
     public void testGetChemModels() {
         ChemSequence cs = new ChemSequence();
         cs.addChemModel(new ChemModel());

Index: CrystalTest.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/test/CrystalTest.java,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- CrystalTest.java	28 Dec 2004 15:02:07 -0000	1.13
+++ CrystalTest.java	29 Dec 2004 21:06:58 -0000	1.14
@@ -50,6 +50,8 @@
         return new TestSuite(CrystalTest.class);
     }
 
+    
+    
     public void testSetA_Vector3d() {
         Crystal crystal = new Crystal();
         

[Cdk-commits] CVS: cdk/src/org/openscience/cdk/test AtomContainerTest.java,1.22,1.23 AtomTest.java,1.17,1.18 ChemFileTest.java,1.7,1.8 MoleculeTest.java,1.7,1.8

[Egon Willighagen <egonw@us...>]

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/test
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv25109/src/org/openscience/cdk/test

Modified Files:
	AtomContainerTest.java AtomTest.java ChemFileTest.java 
	MoleculeTest.java 
Log Message:
Another more JUnit testing for the core module

Index: AtomContainerTest.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/test/AtomContainerTest.java,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -r1.22 -r1.23
--- AtomContainerTest.java	28 Dec 2004 16:18:16 -0000	1.22
+++ AtomContainerTest.java	29 Dec 2004 08:45:33 -0000	1.23
@@ -423,6 +423,30 @@
         acetone.addBond(b3);
         
         AtomContainer container = new AtomContainer(acetone);
+        assertEquals(4, container.getAtomCount());
+        assertEquals(3, container.getBondCount());
+    }
+    
+    public void testAdd_AtomContainer() {
+        Molecule acetone = new Molecule();
+        Atom c1 = new Atom("C");
+        Atom c2 = new Atom("C");
+        Atom o = new Atom("O");
+        Atom c3 = new Atom("C");
+        acetone.addAtom(c1);
+        acetone.addAtom(c2);
+        acetone.addAtom(c3);
+        acetone.addAtom(o);
+        Bond b1 = new Bond(c1, c2,1);
+        Bond b2 = new Bond(c1, o, 2);
+        Bond b3 = new Bond(c1, c3,1);
+        acetone.addBond(b1);
+        acetone.addBond(b2);
+        acetone.addBond(b3);
+        
+        AtomContainer container = new AtomContainer();
+        container.add(acetone);
+        assertEquals(4, container.getAtomCount());
         assertEquals(3, container.getBondCount());
     }
     
@@ -625,6 +649,53 @@
         assertEquals(4, counter);
     }
 
+    public void testContains_Atom() {
+        // acetone molecule
+        Molecule acetone = new Molecule();
+        Atom c1 = new Atom("C");
+        Atom c2 = new Atom("C");
+        Atom o = new Atom("O");
+        Atom c3 = new Atom("C");
+        acetone.addAtom(c1);
+        acetone.addAtom(c2);
+        acetone.addAtom(c3);
+        acetone.addAtom(o);
+        
+        assertTrue(acetone.contains(c1));
+        assertTrue(acetone.contains(c2));
+        assertTrue(acetone.contains(o));
+        assertTrue(acetone.contains(c3));
+    }
+
+    public void testContains_ElectronContainer() {
+        // acetone molecule
+        Molecule acetone = new Molecule();
+        Atom c1 = new Atom("C");
+        Atom c2 = new Atom("C");
+        Atom o = new Atom("O");
+        Atom c3 = new Atom("C");
+        acetone.addAtom(c1);
+        acetone.addAtom(c2);
+        acetone.addAtom(c3);
+        acetone.addAtom(o);
+        Bond b1 = new Bond(c1, c2,1);
+        Bond b2 = new Bond(c1, o, 2);
+        Bond b3 = new Bond(c1, c3,1);
+        acetone.addBond(b1);
+        acetone.addBond(b2);
+        acetone.addBond(b3);
+        LonePair lp1 = new LonePair(o);
+        LonePair lp2 = new LonePair(o);
+        acetone.addElectronContainer(lp1);
+        acetone.addElectronContainer(lp2);
+        
+        assertTrue(acetone.contains(b1));
+        assertTrue(acetone.contains(b2));
+        assertTrue(acetone.contains(b3));
+        assertTrue(acetone.contains(lp1));
+        assertTrue(acetone.contains(lp2));
+    }
+
     public void testGetElectronContainers() {
         // acetone molecule
         Molecule acetone = new Molecule();
@@ -650,6 +721,32 @@
         assertEquals(5, acetone.getElectronContainers().length);
     }
     
+    public void testGetLonePairs() {
+        // acetone molecule
+        Molecule acetone = new Molecule();
+        Atom c1 = new Atom("C");
+        Atom c2 = new Atom("C");
+        Atom o = new Atom("O");
+        Atom c3 = new Atom("C");
+        acetone.addAtom(c1);
+        acetone.addAtom(c2);
+        acetone.addAtom(c3);
+        acetone.addAtom(o);
+        Bond b1 = new Bond(c1, c2,1);
+        Bond b2 = new Bond(c1, o, 2);
+        Bond b3 = new Bond(c1, c3,1);
+        acetone.addBond(b1);
+        acetone.addBond(b2);
+        acetone.addBond(b3);
+        LonePair lp1 = new LonePair(o);
+        LonePair lp2 = new LonePair(o);
+        acetone.addElectronContainer(lp1);
+        acetone.addElectronContainer(lp2);
+        
+        assertNotNull(acetone.getLonePairs());
+        assertEquals(2, acetone.getLonePairs().length);
+    }
+    
     public void testGetBonds() {
         // acetone molecule
         Molecule acetone = new Molecule();
@@ -697,7 +794,7 @@
         assertEquals("H", container.getLastAtom().getSymbol());
     }
     
-    public void testGetAtomNumber() {
+    public void testGetAtomNumber_Atom() {
         Molecule acetone = new Molecule();
         Atom c1 = new Atom("C");
         Atom c2 = new Atom("C");
@@ -830,7 +927,7 @@
         assertEquals(2, acetone.getLonePairCount());
     }
 
-    public void testGetBondCount_Atom() {
+    public void testGetLonePairCount_Atom() {
         Molecule acetone = new Molecule();
         Atom c1 = new Atom("C");
         Atom c2 = new Atom("C");
@@ -847,13 +944,48 @@
         acetone.addBond(b2);
         acetone.addBond(b3);
         
-        assertEquals(3, acetone.getBondCount(c1));
-        assertEquals(1, acetone.getBondCount(c2));
-        assertEquals(1, acetone.getBondCount(c3));
-        assertEquals(1, acetone.getBondCount(o));
+        // add lone pairs on oxygen
+        LonePair lp1 = new LonePair(o);
+        LonePair lp2 = new LonePair(o);
+        acetone.addElectronContainer(lp1);
+        acetone.addElectronContainer(lp2);
+        
+        assertEquals(2, acetone.getLonePairCount(o));
+        assertEquals(0, acetone.getLonePairCount(c2));
+        assertEquals(0, acetone.getLonePairCount(c3));
+        assertEquals(0, acetone.getLonePairCount(c1));
+    }
+
+    public void testGetBondOrderSum_Atom() {
+        Molecule acetone = new Molecule();
+        Atom c1 = new Atom("C");
+        Atom c2 = new Atom("C");
+        Atom o = new Atom("O");
+        Atom c3 = new Atom("C");
+        acetone.addAtom(c1);
+        acetone.addAtom(c2);
+        acetone.addAtom(c3);
+        acetone.addAtom(o);
+        Bond b1 = new Bond(c1, c2,1);
+        Bond b2 = new Bond(c1, o, 2);
+        Bond b3 = new Bond(c1, c3,1);
+        acetone.addBond(b1);
+        acetone.addBond(b2);
+        acetone.addBond(b3);
+        
+        // add lone pairs on oxygen
+        LonePair lp1 = new LonePair(o);
+        LonePair lp2 = new LonePair(o);
+        acetone.addElectronContainer(lp1);
+        acetone.addElectronContainer(lp2);
+        
+        assertEquals(4.0, acetone.getBondOrderSum(c1), 0.00001);
+        assertEquals(1.0, acetone.getBondOrderSum(c2), 0.00001);
+        assertEquals(1.0, acetone.getBondOrderSum(c3), 0.00001);
+        assertEquals(2.0, acetone.getBondOrderSum(o), 0.00001);
     }
     
-    public void testGetLonePairCount_Atom() {
+    public void testGetBondCount_Atom() {
         Molecule acetone = new Molecule();
         Atom c1 = new Atom("C");
         Atom c2 = new Atom("C");
@@ -876,13 +1008,13 @@
         acetone.addElectronContainer(lp1);
         acetone.addElectronContainer(lp2);
         
-        assertEquals(2, acetone.getLonePairCount(o));
-        assertEquals(0, acetone.getLonePairCount(c2));
-        assertEquals(0, acetone.getLonePairCount(c3));
-        assertEquals(0, acetone.getLonePairCount(c1));
+        assertEquals(3, acetone.getBondCount(c1));
+        assertEquals(1, acetone.getBondCount(c2));
+        assertEquals(1, acetone.getBondCount(c3));
+        assertEquals(1, acetone.getBondCount(o));
     }
-
-    public void testGetBondOrderSum_Atom() {
+    
+    public void testGetBondCount_int() {
         Molecule acetone = new Molecule();
         Atom c1 = new Atom("C");
         Atom c2 = new Atom("C");
@@ -905,10 +1037,10 @@
         acetone.addElectronContainer(lp1);
         acetone.addElectronContainer(lp2);
         
-        assertEquals(4.0, acetone.getBondOrderSum(c1), 0.00001);
-        assertEquals(1.0, acetone.getBondOrderSum(c2), 0.00001);
-        assertEquals(1.0, acetone.getBondOrderSum(c3), 0.00001);
-        assertEquals(2.0, acetone.getBondOrderSum(o), 0.00001);
+        assertEquals(3, acetone.getBondCount(0));
+        assertEquals(1, acetone.getBondCount(1));
+        assertEquals(1, acetone.getBondCount(2));
+        assertEquals(1, acetone.getBondCount(3));
     }
     
     public void testGetAtomParity_Atom() {
@@ -931,4 +1063,13 @@
         assertEquals(parity, copy);
     }
 
+    /** Test for RFC #9 */
+    public void testToString() {
+        AtomContainer container = new AtomContainer();
+        String description = container.toString();
+        for (int i=0; i< description.length(); i++) {
+            assertTrue(description.charAt(i) != '\n');
+            assertTrue(description.charAt(i) != '\r');
+        }
+    }
 }

Index: AtomTest.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/test/AtomTest.java,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -r1.17 -r1.18
--- AtomTest.java	28 Dec 2004 10:59:52 -0000	1.17
+++ AtomTest.java	29 Dec 2004 08:45:34 -0000	1.18
@@ -104,7 +104,10 @@
 
         Atom a = new Atom("C");
         a.setCharge(charge);
-        assertTrue(charge == a.getCharge());
+        assertEquals(charge, a.getCharge(), 0.001);
+    }
+    public void testGetCharge() {
+        testSetCharge_double();
     }
 
     /**
@@ -124,7 +127,7 @@
     /**
      * Method to test the setFractional3D() methods.
      */
-    public void testSetFractional3d_Point3d() {
+    public void testSetFractionalPoint3d_Point3d() {
         Atom a = new Atom("C");
         a.setFractionalPoint3d(new Point3d(0.5, 0.5, 0.5));
         Point3d fract = a.getFractionalPoint3d();
@@ -133,6 +136,9 @@
         assertEquals(0.5, fract.y, 0.001);
         assertEquals(0.5, fract.z, 0.001);
     }
+    public void testGetFractionalPoint3d() {
+        testSetFractionalPoint3d_Point3d();
+    }
     
     public void testGetFractX3d() {
         Atom a = new Atom("C");
@@ -233,21 +239,21 @@
     /**
      * Method to test the set[XY]2D() methods.
      */
-    public void testSetX2d() {
+    public void testSetX2d_double() {
 
         Atom a = new Atom("C");
         a.setX2d(1.0);
 
         assertNotNull(a.getPoint2d());
-	assertEquals(1.0, a.getPoint2d().x, 0.001);
+        assertEquals(1.0, a.getPoint2d().x, 0.001);
     }
-    public void testSetY2d() {
+    public void testSetY2d_double() {
 
         Atom a = new Atom("C");
         a.setY2d(2.0);
 
         assertNotNull(a.getPoint2d());
-	assertEquals(2.0, a.getPoint2d().y, 0.001);
+        assertEquals(2.0, a.getPoint2d().y, 0.001);
     }
     
     public void testGetX2d() {

Index: ChemFileTest.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/test/ChemFileTest.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- ChemFileTest.java	26 Feb 2004 13:12:55 -0000	1.7
+++ ChemFileTest.java	29 Dec 2004 08:45:34 -0000	1.8
@@ -51,7 +51,20 @@
         return new TestSuite(ChemFileTest.class);
     }
     
-    public void testAddChemSequence() {
+    public void testChemFile() {
+        ChemFile cs = new ChemFile();
+        assertNotNull(cs);
+    }
+
+    public void testAddChemSequence_ChemSequence() {
+        ChemFile cs = new ChemFile();
+        cs.addChemSequence(new ChemSequence());
+        cs.addChemSequence(new ChemSequence());
+        cs.addChemSequence(new ChemSequence());
+        assertEquals(3, cs.getChemSequenceCount());
+    }
+    
+    public void testGrowChemSequenceArray() {
         ChemFile cs = new ChemFile();
         cs.addChemSequence(new ChemSequence());
         cs.addChemSequence(new ChemSequence());
@@ -68,9 +81,18 @@
         cs.addChemSequence(new ChemSequence());
         cs.addChemSequence(new ChemSequence());
         cs.addChemSequence(new ChemSequence());
+
+        assertNotNull(cs.getChemSequences());
+        assertEquals(3, cs.getChemSequences().length);
+    }
+
+    public void testGetChemSequenceCount() {
+        ChemFile cs = new ChemFile();
+        cs.addChemSequence(new ChemSequence());
+        cs.addChemSequence(new ChemSequence());
+        cs.addChemSequence(new ChemSequence());
  
         assertEquals(3, cs.getChemSequenceCount());
-        assertEquals(3, cs.getChemSequences().length);
     }
 
     /** Test for RFC #9 */

Index: MoleculeTest.java
===================================================================
RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/test/MoleculeTest.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- MoleculeTest.java	12 Feb 2004 10:11:20 -0000	1.7
+++ MoleculeTest.java	29 Dec 2004 08:45:34 -0000	1.8
@@ -28,8 +28,7 @@
 import junit.framework.Test;
 import junit.framework.TestCase;
 import junit.framework.TestSuite;
-
-import org.openscience.cdk.Molecule;
+import org.openscience.cdk.*;
 
 /**
  * Checks the funcitonality of the Molecule class.
@@ -56,4 +55,50 @@
         Molecule m = new Molecule();
         assertTrue(m != null);
     }
+
+    public void testMolecule_int_int() {
+        Molecule m = new Molecule(5,5);
+        assertTrue(m != null);
+        assertEquals(0, m.getAtoms().length);
+        assertEquals(0, m.getElectronContainers().length);
+    }
+
+    public void testMolecule_AtomContainer() {
+        AtomContainer acetone = new AtomContainer();
+        Atom c1 = new Atom("C");
+        Atom c2 = new Atom("C");
+        Atom o = new Atom("O");
+        Atom c3 = new Atom("C");
+        acetone.addAtom(c1);
+        acetone.addAtom(c2);
+        acetone.addAtom(c3);
+        acetone.addAtom(o);
+        Bond b1 = new Bond(c1, c2,1);
+        Bond b2 = new Bond(c1, o, 2);
+        Bond b3 = new Bond(c1, c3,1);
+        acetone.addBond(b1);
+        acetone.addBond(b2);
+        acetone.addBond(b3);
+        
+        Molecule m = new Molecule(acetone);
+        assertTrue(m != null);
+        assertEquals(4, m.getAtomCount());
+        assertEquals(3, m.getBondCount());
+    }
+
+	public void testClone() {
+        Molecule molecule = new Molecule();
+        Object clone = molecule.clone();
+        assertTrue(clone instanceof Molecule);
+    }    
+
+    /** Test for RFC #9 */
+    public void testToString() {
+        Molecule m = new Molecule();
+        String description = m.toString();
+        for (int i=0; i< description.length(); i++) {
+            assertTrue(description.charAt(i) != '\n');
+            assertTrue(description.charAt(i) != '\r');
+        }
+    }
 }

[Cdk-commits] CVS: cdk/src/org/openscience/cdk/modeling/forcefield ConjugateGradientMethod.java,1.1,NONE ForceField.java,1.2,NONE GeometricMinimizer.java,1.3,NONE

[Egon Willighagen <egonw@us...>]

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/modeling/forcefield
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19087/src/org/openscience/cdk/modeling/forcefield

Removed Files:
	ConjugateGradientMethod.java ForceField.java 
	GeometricMinimizer.java 
Log Message:
Removed broken files: non-ASCII chars make compile from CVS impossible. See email on devel list

--- ConjugateGradientMethod.java DELETED ---

--- ForceField.java DELETED ---

--- GeometricMinimizer.java DELETED ---

[Cdk-commits] CVS: cdk/src/org/openscience/cdk/test/modeling/forcefield ForceFieldTests.java,1.2,NONE

[Egon Willighagen <egonw@us...>]

Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/test/modeling/forcefield
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19087/src/org/openscience/cdk/test/modeling/forcefield

Removed Files:
	ForceFieldTests.java 
Log Message:
Removed broken files: non-ASCII chars make compile from CVS impossible. See email on devel list

--- ForceFieldTests.java DELETED ---