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Various fixes to tests

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1 parent 850fd1a commit 592b920a7f7e0ebe6d93af14e4b7db4a87de0e3c @gilleain gilleain committed with egonw Jun 17, 2010
@@ -25,8 +25,7 @@
import java.util.HashMap;
import java.util.Map;
-import junit.framework.Assert;
-
+import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.openscience.cdk.interfaces.IAtom;
@@ -54,7 +53,6 @@ public void setUp() {
atomSignature = new AtomSignature(0, atomContainer);
}
-
@Test
public void getIntLabelTest() {
atomContainer.getAtom(0).setMassNumber(12);
@@ -76,46 +74,36 @@ public void getVertexSymbolTest() {
Assert.assertEquals("C", atomSignature.getVertexSymbol(0));
}
- @Test
- public void integerInvariantsTest() {
- IMolecule isotopeChiralMol = builder.newInstance(IMolecule.class);
- isotopeChiralMol.addAtom(builder.newInstance(IAtom.class, "C"));
-
- IAtom s32 = builder.newInstance(IAtom.class, "S");
- s32.setMassNumber(32);
- isotopeChiralMol.addAtom(s32);
-
- IAtom s33 = builder.newInstance(IAtom.class, "S");
- s33.setMassNumber(33);
- isotopeChiralMol.addAtom(s33);
-
- IAtom s34 = builder.newInstance(IAtom.class, "S");
- s34.setMassNumber(34);
- isotopeChiralMol.addAtom(s34);
-
- IAtom s36 = builder.newInstance(IAtom.class, "S");
- s36.setMassNumber(36);
- isotopeChiralMol.addAtom(s36);
-
-
- }
-
- @Test
- public void heightTest() {
- IMolecule benzene = makeBenzene();
- AtomSignature atomSignature = new AtomSignature(0, 1, benzene);
- System.out.println(atomSignature.toCanonicalString());
- }
-
- @Test
- public void cubaneHeightTest() {
- IMolecule cubane = AbstractSignatureTest.makeCubane();
- moleculeIsCarbon3Regular(cubane);
- int height = 3;
- AtomSignature atomSignature = new AtomSignature(0, height, cubane);
- String canonicalString = atomSignature.toCanonicalString();
- System.out.println(canonicalString);
- }
+// @Test
+// public void integerInvariantsTest() {
+// IMolecule isotopeChiralMol = builder.newInstance(IMolecule.class);
+// isotopeChiralMol.addAtom(builder.newInstance(IAtom.class, "C"));
+//
+// IAtom s32 = builder.newInstance(IAtom.class, "S");
+// s32.setMassNumber(32);
+//
+// IAtom s33 = builder.newInstance(IAtom.class, "S");
+// s33.setMassNumber(33);
+//
+// IAtom s34 = builder.newInstance(IAtom.class, "S");
+// s34.setMassNumber(34);
+//
+// IAtom s36 = builder.newInstance(IAtom.class, "S");
+// s36.setMassNumber(36);
+//
+// isotopeChiralMol.addAtom(s36);
+// isotopeChiralMol.addAtom(s34);
+// isotopeChiralMol.addAtom(s33);
+// isotopeChiralMol.addAtom(s32);
+//
+// isotopeChiralMol.addBond(0, 1, IBond.Order.SINGLE);
+// isotopeChiralMol.addBond(0, 2, IBond.Order.SINGLE);
+// isotopeChiralMol.addBond(0, 3, IBond.Order.SINGLE);
+// isotopeChiralMol.addBond(0, 4, IBond.Order.SINGLE);
+//
+// MoleculeSignature molSig = new MoleculeSignature(isotopeChiralMol);
+// System.out.println(molSig.toCanonicalString());
+// }
@Test
public void cuneaneCubaneHeightTest() {
@@ -126,8 +114,6 @@ public void cuneaneCubaneHeightTest() {
AtomSignature cubaneSignature = new AtomSignature(0, height, cubane);
String cuneaneSigString = cuneaneSignature.toCanonicalString();
String cubaneSigString = cubaneSignature.toCanonicalString();
- System.out.println(cuneaneSigString);
- System.out.println(cubaneSigString);
Assert.assertEquals(cuneaneSigString, cubaneSigString);
}
@@ -174,18 +160,7 @@ public void allEqualAtHeightTest(IMolecule molecule, int height) {
} else {
sigfreq.put(canonicalSignature, 1);
}
-// System.out.println(i + " " + canonicalSignature);
}
-// for (String key : sigfreq.keySet()) { System.out.println(key + " " + sigfreq.get(key));}
Assert.assertEquals(1, sigfreq.keySet().size());
}
-
- @Test
- public void testNonZeroRootForSubsignature() {
- IMolecule cubane = makeCubane();
- AtomSignature atomSignature = new AtomSignature(1, 2, cubane);
- String canonicalSignature = atomSignature.toCanonicalString();
- System.out.println(canonicalSignature);
- }
-
}
@@ -22,8 +22,7 @@
*/
package org.openscience.cdk.signature;
-import junit.framework.Assert;
-
+import org.junit.Assert;
import org.junit.Test;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
@@ -22,14 +22,11 @@
*/
package org.openscience.cdk.signature;
-import java.io.IOException;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import junit.framework.Assert;
-
-import org.junit.Assume;
+import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.openscience.cdk.CDKTestCase;
@@ -41,7 +38,6 @@
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IMolecule;
-import org.openscience.cdk.io.MDLWriter;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.templates.MoleculeFactory;
@@ -109,21 +105,9 @@ public void toCanonicalSignatureStringTest() {
Assert.assertEquals("[C]", molSig.toCanonicalSignatureString(0));
}
- public void toMolfileString(IMolecule mol) {
- MDLWriter writer = new MDLWriter(System.out);
- try {
- writer.writeMolecule(mol);
- } catch (IOException ioe) {
- ioe.printStackTrace();
- } catch (Exception e) {
- e.printStackTrace();
- }
- }
-
public void fullPermutationTest(IMolecule mol) {
AtomContainerAtomPermutor permutor = new AtomContainerAtomPermutor(mol);
String expected = new MoleculeSignature(mol).toCanonicalString();
- System.out.println("canonical = " + expected);
int numberOfPermutationsTried = 0;
while (permutor.hasNext()) {
IAtomContainer permutation = permutor.next();
@@ -135,22 +119,6 @@ public void fullPermutationTest(IMolecule mol) {
}
}
- public void randomPermutationTest(IMolecule mol) {
- AtomContainerAtomPermutor permutor = new AtomContainerAtomPermutor(mol);
- String expected = new MoleculeSignature(mol).toCanonicalString();
- int numberOfPermutationsTried = 0;
- while (permutor.hasNext()) {
-// IAtomContainer permutation = permutor.randomNext();
-// String actual =
-// new MoleculeSignature(permutation).toCanonicalString();
- numberOfPermutationsTried++;
-// String msg = "Failed on permutation " + numberOfPermutationsTried;
-// Assert.assertEquals(msg, expected, actual);
- }
- System.out.println(expected);
- System.out.println("Tried " + numberOfPermutationsTried);
- }
-
public String canonicalStringFromSmiles(String smiles)
throws InvalidSmilesException {
IMolecule mol = parser.parseSmiles(smiles);
@@ -160,7 +128,6 @@ public String canonicalStringFromSmiles(String smiles)
public String canonicalStringFromMolecule(IMolecule molecule) {
MoleculeSignature signature = new MoleculeSignature(molecule);
-// return signature.toCanonicalString();
return signature.getGraphSignature();
}
@@ -301,9 +268,6 @@ public void testBridgedCycloButane() {
String expected = "[C]([C]([C,0])[C]([C,0])[C,0])";
IMolecule mol = AbstractSignatureTest.makeBridgedCyclobutane();
String signature = this.canonicalStringFromMolecule(mol);
- for (String atomicSignature : this.getAtomicSignatures(mol)) {
- System.out.println(atomicSignature);
- }
Assert.assertEquals(expected, signature);
}
@@ -411,23 +375,6 @@ public int findFirstAtomIndexForSymbol(
return -1;
}
- // XXX commented out this test for now, as it takes a long time - this
- // is a known weakness of the current implementation
- @Test
- public void testPolyPhenylMolecule() throws Exception {
- Assume.assumeTrue(runSlowTests());
- String smiles = "C1=CC=C(C=C1)P(C2=CC=CC=C2)(C3=CC=CC=C3)[RhH]" +
- "(P(C4=CC=CC=C4)(C5=CC=CC=C5)C6=CC=CC=C6)(P(C7=CC=CC=C7)" +
- "(C8=CC=CC=C8)C9=CC=CC=C9)P(C%10=CC=CC=C%10)" +
- "(C%11=CC=CC=C%11)C%12=CC=CC=C%12";
- IMolecule mol = parser.parseSmiles(smiles);
- int rhIndex = findFirstAtomIndexForSymbol(mol, "Rh");
-
- MoleculeSignature molSig = new MoleculeSignature(mol);
- String signatureForRh = molSig.signatureStringForVertex(rhIndex);
- System.out.println(signatureForRh);
- }
-
@Test
public void methylFerroceneTest() throws Exception {
String smiles = "CC12C3C4C5C1[Fe]23456789C%10C6C7C8C9%10";
@@ -25,8 +25,7 @@
import java.util.ArrayList;
import java.util.List;
-import junit.framework.Assert;
-
+import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
@@ -22,8 +22,8 @@
*/
package org.openscience.cdk.signature;
-import junit.framework.Assert;
+import org.junit.Assert;
import org.junit.Test;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
@@ -52,7 +52,6 @@ public void checkParameters(SignatureQuotientGraph qGraph,
int expectedVertexCount,
int expectedEdgeCount,
int expectedLoopEdgeCount) {
- System.out.println(qGraph);
Assert.assertEquals(expectedVertexCount, qGraph.getVertexCount());
Assert.assertEquals(expectedEdgeCount, qGraph.getEdgeCount());
Assert.assertEquals(expectedLoopEdgeCount, qGraph.numberOfLoopEdges());

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