cdk-commits
|
From: <egonw@us...> - 2007-01-28 19:30:48
|
Revision: 7772
http://svn.sourceforge.net/cdk/?rev=7772&view=rev
Author: egonw
Date: 2007-01-28 11:30:44 -0800 (Sun, 28 Jan 2007)
Log Message:
-----------
Let JUnit catch the exception.
Modified Paths:
--------------
trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java
Modified: trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java 2007-01-28 14:15:33 UTC (rev 7771)
+++ trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java 2007-01-28 19:30:44 UTC (rev 7772)
@@ -76,403 +76,364 @@
assertTrue(reader.accepts(ChemFile.class));
}
- public void testPDBFileCoffein() {
+ public void testPDBFileCoffein() throws Exception {
String filename = "data/pdb/coffeine.pdb";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
- try {
- IChemObjectReader oReader = new PDBReader(ins);
- assertNotNull(oReader);
- IChemFile oChemFile = (IChemFile)oReader.read(new NNChemFile());
- assertNotNull(oChemFile);
- assertEquals(oChemFile.getChemSequenceCount(), 1);
+ IChemObjectReader oReader = new PDBReader(ins);
+ assertNotNull(oReader);
- IChemSequence oSeq = oChemFile.getChemSequence(0);
- assertNotNull(oSeq);
- assertEquals(oSeq.getChemModelCount(), 1);
+ IChemFile oChemFile = (IChemFile)oReader.read(new NNChemFile());
+ assertNotNull(oChemFile);
+ assertEquals(oChemFile.getChemSequenceCount(), 1);
- IChemModel oModel = oSeq.getChemModel(0);
- assertNotNull(oModel);
- assertEquals(1, oModel.getMoleculeSet().getMoleculeCount());
+ IChemSequence oSeq = oChemFile.getChemSequence(0);
+ assertNotNull(oSeq);
+ assertEquals(oSeq.getChemModelCount(), 1);
- IAtomContainer container = oModel.getMoleculeSet().getMolecule(0);
- assertFalse(container instanceof IBioPolymer);
- assertTrue(container instanceof IAtomContainer);
- IAtomContainer oMol = (IAtomContainer)container;
- assertNotNull(oMol);
- assertEquals(oMol.getAtomCount(), 14);
+ IChemModel oModel = oSeq.getChemModel(0);
+ assertNotNull(oModel);
+ assertEquals(1, oModel.getMoleculeSet().getMoleculeCount());
- IAtom nAtom = oMol.getFirstAtom();
- assertNotNull(nAtom);
- assertTrue(nAtom instanceof PDBAtom);
- PDBAtom oAtom = (PDBAtom)nAtom;
- assertEquals(new String("C"), oAtom.getSymbol());
- assertEquals(1, oAtom.getSerial());
- assertEquals("C1", oAtom.getName());
- assertEquals("MOL", oAtom.getResName());
- assertEquals("1", oAtom.getResSeq());
- assertEquals(1.0, oAtom.getOccupancy(), 0);
- assertEquals(0.0, oAtom.getTempFactor(), 0);
+ IAtomContainer container = oModel.getMoleculeSet().getMolecule(0);
+ assertFalse(container instanceof IBioPolymer);
+ assertTrue(container instanceof IAtomContainer);
+ IAtomContainer oMol = (IAtomContainer)container;
+ assertNotNull(oMol);
+ assertEquals(oMol.getAtomCount(), 14);
- nAtom = oMol.getAtom(3);
- assertNotNull(nAtom);
- assertTrue(nAtom instanceof PDBAtom);
- oAtom = (PDBAtom)nAtom;
- assertEquals("O", oAtom.getSymbol());
- assertEquals(4, oAtom.getSerial());
- assertEquals("O4", oAtom.getName());
- assertEquals("MOL", oAtom.getResName());
- assertEquals("1", oAtom.getResSeq());
- assertEquals(1.0, oAtom.getOccupancy(), 0);
- assertEquals(0.0, oAtom.getTempFactor(), 0);
+ IAtom nAtom = oMol.getFirstAtom();
+ assertNotNull(nAtom);
+ assertTrue(nAtom instanceof PDBAtom);
+ PDBAtom oAtom = (PDBAtom)nAtom;
+ assertEquals(new String("C"), oAtom.getSymbol());
+ assertEquals(1, oAtom.getSerial());
+ assertEquals("C1", oAtom.getName());
+ assertEquals("MOL", oAtom.getResName());
+ assertEquals("1", oAtom.getResSeq());
+ assertEquals(1.0, oAtom.getOccupancy(), 0);
+ assertEquals(0.0, oAtom.getTempFactor(), 0);
- nAtom = oMol.getLastAtom();
- assertNotNull(nAtom);
- assertTrue(nAtom instanceof PDBAtom);
- oAtom = (PDBAtom)nAtom;
- assertEquals("N", oAtom.getSymbol());
- assertEquals(14, oAtom.getSerial());
- assertEquals("N14", oAtom.getName());
- assertEquals("MOL", oAtom.getResName());
- assertEquals("1", oAtom.getResSeq());
- assertEquals(1.0, oAtom.getOccupancy(), 0);
- assertEquals(0.0, oAtom.getTempFactor(), 0);
- } catch (Exception e) {
- fail(e.toString());
- }
+ nAtom = oMol.getAtom(3);
+ assertNotNull(nAtom);
+ assertTrue(nAtom instanceof PDBAtom);
+ oAtom = (PDBAtom)nAtom;
+ assertEquals("O", oAtom.getSymbol());
+ assertEquals(4, oAtom.getSerial());
+ assertEquals("O4", oAtom.getName());
+ assertEquals("MOL", oAtom.getResName());
+ assertEquals("1", oAtom.getResSeq());
+ assertEquals(1.0, oAtom.getOccupancy(), 0);
+ assertEquals(0.0, oAtom.getTempFactor(), 0);
+
+ nAtom = oMol.getLastAtom();
+ assertNotNull(nAtom);
+ assertTrue(nAtom instanceof PDBAtom);
+ oAtom = (PDBAtom)nAtom;
+ assertEquals("N", oAtom.getSymbol());
+ assertEquals(14, oAtom.getSerial());
+ assertEquals("N14", oAtom.getName());
+ assertEquals("MOL", oAtom.getResName());
+ assertEquals("1", oAtom.getResSeq());
+ assertEquals(1.0, oAtom.getOccupancy(), 0);
+ assertEquals(0.0, oAtom.getTempFactor(), 0);
}
- /**
- * Tests reading a protein PDB file.
- */
- public void testProtein() {
- String filename = "data/pdb/Test-1crn.pdb";
- InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+ /**
+ * Tests reading a protein PDB file.
+ */
+ public void testProtein() throws Exception {
+ String filename = "data/pdb/Test-1crn.pdb";
+ InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
- try {
- IChemObjectReader reader = new PDBReader(ins);
- assertNotNull(reader);
+ IChemObjectReader reader = new PDBReader(ins);
+ assertNotNull(reader);
- ChemFile chemFile = (ChemFile) reader.read(new NNChemFile());
- assertNotNull(chemFile);
- assertEquals(1, chemFile.getChemSequenceCount());
+ ChemFile chemFile = (ChemFile) reader.read(new NNChemFile());
+ assertNotNull(chemFile);
+ assertEquals(1, chemFile.getChemSequenceCount());
- org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
- assertNotNull(seq);
- assertEquals(1, seq.getChemModelCount());
-
- IChemModel model = seq.getChemModel(0);
- assertNotNull(model);
- assertEquals(1, model.getMoleculeSet().getMoleculeCount());
+ org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
+ assertNotNull(seq);
+ assertEquals(1, seq.getChemModelCount());
- IAtomContainer container = model.getMoleculeSet().getMolecule(0);
- assertTrue(container instanceof IBioPolymer);
- IBioPolymer mol = (IBioPolymer)container;
- assertNotNull(mol);
- assertEquals(327, mol.getAtomCount());
- assertEquals(46, mol.getMonomerCount());
- assertNotNull(mol.getMonomer("THRA1", "A"));
- assertEquals(7, mol.getMonomer("THRA1", "A").getAtomCount());
- assertNotNull(mol.getMonomer("ILEA7", "A"));
- assertEquals(8, mol.getMonomer("ILEA7", "A").getAtomCount());
-
- IAtom nAtom = mol.getAtom(94);
- assertNotNull(nAtom);
- assertTrue(nAtom instanceof PDBAtom);
- PDBAtom atom = (PDBAtom)nAtom;
- assertEquals("C", atom.getSymbol());
- assertEquals(95, atom.getSerial());
- assertEquals("CZ", atom.getName());
- assertEquals("PHE", atom.getResName());
- assertEquals("13", atom.getResSeq());
- assertEquals(1.0, atom.getOccupancy(), 0.001);
- assertEquals(6.84, atom.getTempFactor(), 0.001);
-
- } catch (Exception ex) {
- ex.printStackTrace();
- fail(ex.toString());
- }
- }
+ IChemModel model = seq.getChemModel(0);
+ assertNotNull(model);
+ assertEquals(1, model.getMoleculeSet().getMoleculeCount());
+
+ IAtomContainer container = model.getMoleculeSet().getMolecule(0);
+ assertTrue(container instanceof IBioPolymer);
+ IBioPolymer mol = (IBioPolymer)container;
+ assertNotNull(mol);
+ assertEquals(327, mol.getAtomCount());
+ assertEquals(46, mol.getMonomerCount());
+ assertNotNull(mol.getMonomer("THRA1", "A"));
+ assertEquals(7, mol.getMonomer("THRA1", "A").getAtomCount());
+ assertNotNull(mol.getMonomer("ILEA7", "A"));
+ assertEquals(8, mol.getMonomer("ILEA7", "A").getAtomCount());
+
+ IAtom nAtom = mol.getAtom(94);
+ assertNotNull(nAtom);
+ assertTrue(nAtom instanceof PDBAtom);
+ PDBAtom atom = (PDBAtom)nAtom;
+ assertEquals("C", atom.getSymbol());
+ assertEquals(95, atom.getSerial());
+ assertEquals("CZ", atom.getName());
+ assertEquals("PHE", atom.getResName());
+ assertEquals("13", atom.getResSeq());
+ assertEquals(1.0, atom.getOccupancy(), 0.001);
+ assertEquals(6.84, atom.getTempFactor(), 0.001);
+
+ }
- public void test114D() {
+ public void test114D() throws Exception {
String filename = "data/pdb/114D.pdb";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
- try {
- IChemObjectReader reader = new PDBReader(ins);
- assertNotNull(reader);
+ IChemObjectReader reader = new PDBReader(ins);
+ assertNotNull(reader);
- IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
- assertNotNull(chemFile);
- assertEquals(1, chemFile.getChemSequenceCount());
+ IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
+ assertNotNull(chemFile);
+ assertEquals(1, chemFile.getChemSequenceCount());
- org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
- assertNotNull(seq);
- assertEquals(1, seq.getChemModelCount());
-
- IChemModel model = seq.getChemModel(0);
- assertNotNull(model);
- assertEquals(1, model.getMoleculeSet().getMoleculeCount());
+ org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
+ assertNotNull(seq);
+ assertEquals(1, seq.getChemModelCount());
- IAtomContainer container = model.getMoleculeSet().getMolecule(0);
- assertTrue(container instanceof IBioPolymer);
- IBioPolymer polymer = (IBioPolymer)container;
+ IChemModel model = seq.getChemModel(0);
+ assertNotNull(model);
+ assertEquals(1, model.getMoleculeSet().getMoleculeCount());
+
+ IAtomContainer container = model.getMoleculeSet().getMolecule(0);
+ assertTrue(container instanceof IBioPolymer);
+ IBioPolymer polymer = (IBioPolymer)container;
+
+ // chemical validation
+ assertEquals(552, ChemFileManipulator.getAtomCount(chemFile));
+ assertEquals(2, polymer.getStrandCount());
+ assertEquals(24, polymer.getMonomerCount());
+
+ assertTrue(polymer instanceof PDBPolymer);
+ PDBPolymer pdb = (PDBPolymer)polymer;
+
+ // PDB validation
+ assertEquals(0, pdb.getStructures().size());
- // chemical validation
- assertEquals(552, ChemFileManipulator.getAtomCount(chemFile));
- assertEquals(2, polymer.getStrandCount());
- assertEquals(24, polymer.getMonomerCount());
-
- assertTrue(polymer instanceof PDBPolymer);
- PDBPolymer pdb = (PDBPolymer)polymer;
-
- // PDB validation
- assertEquals(0, pdb.getStructures().size());
-
- } catch (Exception ex) {
- fail(ex.toString());
- }
}
- public void test1SPX() {
+ public void test1SPX() throws Exception {
String filename = "data/pdb/1SPX.pdb";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
- try {
- IChemObjectReader reader = new PDBReader(ins);
- assertNotNull(reader);
+ IChemObjectReader reader = new PDBReader(ins);
+ assertNotNull(reader);
- IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
- assertNotNull(chemFile);
- assertEquals(1, chemFile.getChemSequenceCount());
+ IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
+ assertNotNull(chemFile);
+ assertEquals(1, chemFile.getChemSequenceCount());
- org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
- assertNotNull(seq);
- assertEquals(1, seq.getChemModelCount());
-
- IChemModel model = seq.getChemModel(0);
- assertNotNull(model);
- assertEquals(1, model.getMoleculeSet().getMoleculeCount());
+ org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
+ assertNotNull(seq);
+ assertEquals(1, seq.getChemModelCount());
- IAtomContainer container = model.getMoleculeSet().getMolecule(0);
- assertTrue(container instanceof IBioPolymer);
- IBioPolymer polymer = (IBioPolymer)container;
-
- // chemical validation
- assertEquals(1904, ChemFileManipulator.getAtomCount(chemFile));
- assertEquals(1, polymer.getStrandCount());
- assertEquals(237, polymer.getMonomerCount());
+ IChemModel model = seq.getChemModel(0);
+ assertNotNull(model);
+ assertEquals(1, model.getMoleculeSet().getMoleculeCount());
- assertTrue(polymer instanceof PDBPolymer);
- PDBPolymer pdb = (PDBPolymer)polymer;
+ IAtomContainer container = model.getMoleculeSet().getMolecule(0);
+ assertTrue(container instanceof IBioPolymer);
+ IBioPolymer polymer = (IBioPolymer)container;
+
+ // chemical validation
+ assertEquals(1904, ChemFileManipulator.getAtomCount(chemFile));
+ assertEquals(1, polymer.getStrandCount());
+ assertEquals(237, polymer.getMonomerCount());
+
+ assertTrue(polymer instanceof PDBPolymer);
+ PDBPolymer pdb = (PDBPolymer)polymer;
+
+ // PDB validation
+ assertEquals(19, pdb.getStructures().size());
- // PDB validation
- assertEquals(19, pdb.getStructures().size());
-
- } catch (Exception ex) {
- fail(ex.toString());
- }
}
- public void test1XKQ() {
+ public void test1XKQ() throws Exception {
String filename = "data/pdb/1XKQ.pdb";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
- try {
- IChemObjectReader reader = new PDBReader(ins);
- assertNotNull(reader);
+ IChemObjectReader reader = new PDBReader(ins);
+ assertNotNull(reader);
- IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
- assertNotNull(chemFile);
- assertEquals(1, chemFile.getChemSequenceCount());
+ IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
+ assertNotNull(chemFile);
+ assertEquals(1, chemFile.getChemSequenceCount());
- org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
- assertNotNull(seq);
- assertEquals(1, seq.getChemModelCount());
-
- IChemModel model = seq.getChemModel(0);
- assertNotNull(model);
- assertEquals(1, model.getMoleculeSet().getMoleculeCount());
+ org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
+ assertNotNull(seq);
+ assertEquals(1, seq.getChemModelCount());
- IAtomContainer container = model.getMoleculeSet().getMolecule(0);
- assertTrue(container instanceof IBioPolymer);
- IBioPolymer polymer = (IBioPolymer)container;
-
- // chemical validation
- assertEquals(8955, ChemFileManipulator.getAtomCount(chemFile));
- assertEquals(4, polymer.getStrandCount());
- assertEquals(1085, polymer.getMonomerCount());
+ IChemModel model = seq.getChemModel(0);
+ assertNotNull(model);
+ assertEquals(1, model.getMoleculeSet().getMoleculeCount());
- assertTrue(polymer instanceof PDBPolymer);
- PDBPolymer pdb = (PDBPolymer)polymer;
+ IAtomContainer container = model.getMoleculeSet().getMolecule(0);
+ assertTrue(container instanceof IBioPolymer);
+ IBioPolymer polymer = (IBioPolymer)container;
+
+ // chemical validation
+ assertEquals(8955, ChemFileManipulator.getAtomCount(chemFile));
+ assertEquals(4, polymer.getStrandCount());
+ assertEquals(1085, polymer.getMonomerCount());
+
+ assertTrue(polymer instanceof PDBPolymer);
+ PDBPolymer pdb = (PDBPolymer)polymer;
+
+ // PDB validation
+ assertEquals(90, pdb.getStructures().size());
- // PDB validation
- assertEquals(90, pdb.getStructures().size());
-
- } catch (Exception ex) {
- fail(ex.toString());
- }
}
- public void test1A00() {
+ public void test1A00() throws Exception {
String filename = "data/pdb/1A00.pdb";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
- try {
- IChemObjectReader reader = new PDBReader(ins);
- assertNotNull(reader);
+ IChemObjectReader reader = new PDBReader(ins);
+ assertNotNull(reader);
- IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
- assertNotNull(chemFile);
- assertEquals(1, chemFile.getChemSequenceCount());
+ IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
+ assertNotNull(chemFile);
+ assertEquals(1, chemFile.getChemSequenceCount());
- org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
- assertNotNull(seq);
- assertEquals(1, seq.getChemModelCount());
-
- IChemModel model = seq.getChemModel(0);
- assertNotNull(model);
- assertEquals(1, model.getMoleculeSet().getMoleculeCount());
+ org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
+ assertNotNull(seq);
+ assertEquals(1, seq.getChemModelCount());
- IAtomContainer container = model.getMoleculeSet().getMolecule(0);
- assertTrue(container instanceof IBioPolymer);
- IBioPolymer polymer = (IBioPolymer)container;
-
- // chemical validation
- assertEquals(4770, ChemFileManipulator.getAtomCount(chemFile));
- assertEquals(4, polymer.getStrandCount());
- assertEquals(574, polymer.getMonomerCount());
+ IChemModel model = seq.getChemModel(0);
+ assertNotNull(model);
+ assertEquals(1, model.getMoleculeSet().getMoleculeCount());
- assertTrue(polymer instanceof PDBPolymer);
- PDBPolymer pdb = (PDBPolymer)polymer;
+ IAtomContainer container = model.getMoleculeSet().getMolecule(0);
+ assertTrue(container instanceof IBioPolymer);
+ IBioPolymer polymer = (IBioPolymer)container;
+
+ // chemical validation
+ assertEquals(4770, ChemFileManipulator.getAtomCount(chemFile));
+ assertEquals(4, polymer.getStrandCount());
+ assertEquals(574, polymer.getMonomerCount());
+
+ assertTrue(polymer instanceof PDBPolymer);
+ PDBPolymer pdb = (PDBPolymer)polymer;
+
+ // PDB validation
+ assertEquals(35, pdb.getStructures().size());
- // PDB validation
- assertEquals(35, pdb.getStructures().size());
-
- } catch (Exception ex) {
- fail(ex.toString());
- }
}
- public void test1BOQ() {
+ public void test1BOQ() throws Exception {
String filename = "data/pdb/1BOQ.pdb";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
- try {
- IChemObjectReader reader = new PDBReader(ins);
- assertNotNull(reader);
+ IChemObjectReader reader = new PDBReader(ins);
+ assertNotNull(reader);
- IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
- assertNotNull(chemFile);
- assertEquals(1, chemFile.getChemSequenceCount());
+ IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
+ assertNotNull(chemFile);
+ assertEquals(1, chemFile.getChemSequenceCount());
- org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
- assertNotNull(seq);
- assertEquals(1, seq.getChemModelCount());
-
- IChemModel model = seq.getChemModel(0);
- assertNotNull(model);
- assertEquals(1, model.getMoleculeSet().getMoleculeCount());
+ org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
+ assertNotNull(seq);
+ assertEquals(1, seq.getChemModelCount());
- IAtomContainer container = model.getMoleculeSet().getMolecule(0);
- assertTrue(container instanceof IBioPolymer);
- IBioPolymer polymer = (IBioPolymer)container;
-
- // chemical validation
- assertEquals(1538, ChemFileManipulator.getAtomCount(chemFile));
- assertEquals(1, polymer.getStrandCount());
- assertEquals(198, polymer.getMonomerCount());
+ IChemModel model = seq.getChemModel(0);
+ assertNotNull(model);
+ assertEquals(1, model.getMoleculeSet().getMoleculeCount());
- assertTrue(polymer instanceof PDBPolymer);
- PDBPolymer pdb = (PDBPolymer)polymer;
+ IAtomContainer container = model.getMoleculeSet().getMolecule(0);
+ assertTrue(container instanceof IBioPolymer);
+ IBioPolymer polymer = (IBioPolymer)container;
+
+ // chemical validation
+ assertEquals(1538, ChemFileManipulator.getAtomCount(chemFile));
+ assertEquals(1, polymer.getStrandCount());
+ assertEquals(198, polymer.getMonomerCount());
+
+ assertTrue(polymer instanceof PDBPolymer);
+ PDBPolymer pdb = (PDBPolymer)polymer;
+
+ // PDB validation
+ assertEquals(21, pdb.getStructures().size());
- // PDB validation
- assertEquals(21, pdb.getStructures().size());
-
- } catch (Exception ex) {
- fail(ex.toString());
- }
}
- public void test1TOH() {
+ public void test1TOH() throws Exception {
String filename = "data/pdb/1TOH.pdb";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
- try {
- IChemObjectReader reader = new PDBReader(ins);
- assertNotNull(reader);
+ IChemObjectReader reader = new PDBReader(ins);
+ assertNotNull(reader);
- IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
- assertNotNull(chemFile);
- assertEquals(1, chemFile.getChemSequenceCount());
+ IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
+ assertNotNull(chemFile);
+ assertEquals(1, chemFile.getChemSequenceCount());
- org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
- assertNotNull(seq);
- assertEquals(1, seq.getChemModelCount());
-
- IChemModel model = seq.getChemModel(0);
- assertNotNull(model);
- assertEquals(1, model.getMoleculeSet().getMoleculeCount());
+ org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
+ assertNotNull(seq);
+ assertEquals(1, seq.getChemModelCount());
- IAtomContainer container = model.getMoleculeSet().getMolecule(0);
- assertTrue(container instanceof IBioPolymer);
- IBioPolymer polymer = (IBioPolymer)container;
-
- // chemical validation
- assertEquals(2804, ChemFileManipulator.getAtomCount(chemFile));
- assertEquals(1, polymer.getStrandCount());
- assertEquals(325, polymer.getMonomerCount());
+ IChemModel model = seq.getChemModel(0);
+ assertNotNull(model);
+ assertEquals(1, model.getMoleculeSet().getMoleculeCount());
- assertTrue(polymer instanceof PDBPolymer);
- PDBPolymer pdb = (PDBPolymer)polymer;
-
- // PDB validation
- assertEquals(23, pdb.getStructures().size());
-
- } catch (Exception ex) {
- fail(ex.toString());
- }
+ IAtomContainer container = model.getMoleculeSet().getMolecule(0);
+ assertTrue(container instanceof IBioPolymer);
+ IBioPolymer polymer = (IBioPolymer)container;
+
+ // chemical validation
+ assertEquals(2804, ChemFileManipulator.getAtomCount(chemFile));
+ assertEquals(1, polymer.getStrandCount());
+ assertEquals(325, polymer.getMonomerCount());
+
+ assertTrue(polymer instanceof PDBPolymer);
+ PDBPolymer pdb = (PDBPolymer)polymer;
+
+ // PDB validation
+ assertEquals(23, pdb.getStructures().size());
}
- public void test1CKV() {
+ public void test1CKV() throws Exception {
String filename = "data/pdb/1CKV.pdb";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
- try {
- IChemObjectReader reader = new PDBReader(ins);
- assertNotNull(reader);
+ IChemObjectReader reader = new PDBReader(ins);
+ assertNotNull(reader);
- IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
- assertNotNull(chemFile);
- assertEquals(1, chemFile.getChemSequenceCount());
+ IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
+ assertNotNull(chemFile);
+ assertEquals(1, chemFile.getChemSequenceCount());
- org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
- assertNotNull(seq);
- assertEquals(14, seq.getChemModelCount());
-
- IChemModel model = seq.getChemModel(0);
- assertNotNull(model);
- assertEquals(1, model.getMoleculeSet().getMoleculeCount());
+ org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
+ assertNotNull(seq);
+ assertEquals(14, seq.getChemModelCount());
- IAtomContainer container = model.getMoleculeSet().getMolecule(0);
- assertTrue(container instanceof IBioPolymer);
- IBioPolymer polymer = (IBioPolymer)container;
-
- // chemical validation
- assertEquals(31066, ChemFileManipulator.getAtomCount(chemFile));
- assertEquals(1, polymer.getStrandCount());
- // TODO: get the next tests going
- assertEquals(141, polymer.getMonomerCount());
+ IChemModel model = seq.getChemModel(0);
+ assertNotNull(model);
+ assertEquals(1, model.getMoleculeSet().getMoleculeCount());
- assertTrue(polymer instanceof PDBPolymer);
- PDBPolymer pdb = (PDBPolymer)polymer;
-
- // PDB validation
- assertEquals(9, pdb.getStructures().size());
-
- } catch (Exception ex) {
- fail(ex.toString());
- }
+ IAtomContainer container = model.getMoleculeSet().getMolecule(0);
+ assertTrue(container instanceof IBioPolymer);
+ IBioPolymer polymer = (IBioPolymer)container;
+
+ // chemical validation
+ assertEquals(31066, ChemFileManipulator.getAtomCount(chemFile));
+ assertEquals(1, polymer.getStrandCount());
+ assertEquals(141, polymer.getMonomerCount());
+
+ assertTrue(polymer instanceof PDBPolymer);
+ PDBPolymer pdb = (PDBPolymer)polymer;
+
+ // PDB validation
+ assertEquals(9, pdb.getStructures().size());
}
}
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From: <egonw@us...> - 2007-02-07 21:00:11
|
Revision: 7888
http://svn.sourceforge.net/cdk/?rev=7888&view=rev
Author: egonw
Date: 2007-02-07 13:00:01 -0800 (Wed, 07 Feb 2007)
Log Message:
-----------
Cleaned up header, and removed unused import.
Modified Paths:
--------------
trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java
Modified: trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java 2007-02-07 20:20:37 UTC (rev 7887)
+++ trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java 2007-02-07 21:00:01 UTC (rev 7888)
@@ -1,7 +1,4 @@
-/* $RCSfile$
- * $Author$
- * $Date$
- * $Revision$
+/* $Revision$ $Author$ $Date$
*
* Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project
*
@@ -37,7 +34,6 @@
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBioPolymer;
-import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemSequence;
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From: <ospjuth@us...> - 2007-04-20 14:23:55
|
Revision: 8218
http://svn.sourceforge.net/cdk/?rev=8218&view=rev
Author: ospjuth
Date: 2007-04-20 07:23:51 -0700 (Fri, 20 Apr 2007)
Log Message:
-----------
Added test to verify that ID's is read in the PDBReader. Test currently fails, even though PDBReader actually stores ID. I suspect a bug deeper in the CDK hierarchy.
Modified Paths:
--------------
trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java
Modified: trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java 2007-04-20 08:55:56 UTC (rev 8217)
+++ trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java 2007-04-20 14:23:51 UTC (rev 8218)
@@ -25,23 +25,29 @@
package org.openscience.cdk.test.io;
import java.io.InputStream;
+import java.util.Collection;
+import java.util.List;
import junit.framework.Test;
import junit.framework.TestCase;
import junit.framework.TestSuite;
import org.openscience.cdk.ChemFile;
+import org.openscience.cdk.Monomer;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBioPolymer;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemSequence;
+import org.openscience.cdk.interfaces.IMonomer;
+import org.openscience.cdk.interfaces.IStrand;
import org.openscience.cdk.io.IChemObjectReader;
import org.openscience.cdk.io.PDBReader;
import org.openscience.cdk.nonotify.NNChemFile;
import org.openscience.cdk.protein.data.PDBAtom;
import org.openscience.cdk.protein.data.PDBPolymer;
+import org.openscience.cdk.protein.data.PDBStrand;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
/**
@@ -201,6 +207,14 @@
assertTrue(container instanceof IBioPolymer);
IBioPolymer polymer = (IBioPolymer)container;
+ if (!(polymer.getStrand("A") instanceof PDBStrand)) fail("Strand A is not a PDBStrand");
+ PDBStrand strandA=(PDBStrand)polymer.getStrand("A");
+ List lst=(List)strandA.getMonomerNamesInSequentialOrder();
+ String monomer1=(String)lst.get(0);
+ IMonomer mono1=strandA.getMonomer(monomer1);
+ assertTrue(mono1.getID()!=null);
+
+
// chemical validation
assertEquals(552, ChemFileManipulator.getAtomCount(chemFile));
assertEquals(2, polymer.getStrandCount());
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From: <egonw@us...> - 2007-04-20 23:07:56
|
Revision: 8220
http://svn.sourceforge.net/cdk/?rev=8220&view=rev
Author: egonw
Date: 2007-04-20 16:07:54 -0700 (Fri, 20 Apr 2007)
Log Message:
-----------
Rewrote test, and getID() should be getMonomerName() (closes #1704386)
Modified Paths:
--------------
trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java
Modified: trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java 2007-04-20 23:01:17 UTC (rev 8219)
+++ trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java 2007-04-20 23:07:54 UTC (rev 8220)
@@ -25,7 +25,6 @@
package org.openscience.cdk.test.io;
import java.io.InputStream;
-import java.util.Collection;
import java.util.List;
import junit.framework.Test;
@@ -33,7 +32,6 @@
import junit.framework.TestSuite;
import org.openscience.cdk.ChemFile;
-import org.openscience.cdk.Monomer;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBioPolymer;
@@ -41,7 +39,6 @@
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.interfaces.IMonomer;
-import org.openscience.cdk.interfaces.IStrand;
import org.openscience.cdk.io.IChemObjectReader;
import org.openscience.cdk.io.PDBReader;
import org.openscience.cdk.nonotify.NNChemFile;
@@ -207,14 +204,17 @@
assertTrue(container instanceof IBioPolymer);
IBioPolymer polymer = (IBioPolymer)container;
- if (!(polymer.getStrand("A") instanceof PDBStrand)) fail("Strand A is not a PDBStrand");
+ assertTrue(
+ "Strand A is not a PDBStrand",
+ polymer.getStrand("A") instanceof PDBStrand
+ );
PDBStrand strandA=(PDBStrand)polymer.getStrand("A");
List lst=(List)strandA.getMonomerNamesInSequentialOrder();
String monomer1=(String)lst.get(0);
IMonomer mono1=strandA.getMonomer(monomer1);
- assertTrue(mono1.getID()!=null);
+ assertNotNull(mono1);
+ assertNotNull(mono1.getMonomerName());
-
// chemical validation
assertEquals(552, ChemFileManipulator.getAtomCount(chemFile));
assertEquals(2, polymer.getStrandCount());
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From: <ospjuth@us...> - 2007-04-21 20:43:35
|
Revision: 8232
http://svn.sourceforge.net/cdk/?rev=8232&view=rev
Author: ospjuth
Date: 2007-04-21 13:43:32 -0700 (Sat, 21 Apr 2007)
Log Message:
-----------
Added PDBReaderTest test1D66. Fails to extract Strands and Monomers. Don't understand why...
Modified Paths:
--------------
trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java
Modified: trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java 2007-04-21 19:51:17 UTC (rev 8231)
+++ trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java 2007-04-21 20:43:32 UTC (rev 8232)
@@ -467,4 +467,194 @@
// PDB validation
assertEquals(9, pdb.getStructures().size());
}
+
+ public void test1D66() throws Exception {
+ String filename = "data/pdb/1D66.pdb";
+ InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+
+ IChemObjectReader reader = new PDBReader(ins);
+ assertNotNull(reader);
+
+ IChemFile chemFile = (IChemFile) reader.read(new NNChemFile());
+ assertNotNull(chemFile);
+ assertEquals(1, chemFile.getChemSequenceCount());
+
+ org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
+ assertNotNull(seq);
+ assertEquals(1, seq.getChemModelCount());
+
+ IChemModel model = seq.getChemModel(0);
+ assertNotNull(model);
+ assertEquals(1, model.getMoleculeSet().getMoleculeCount());
+
+ IAtomContainer container = model.getMoleculeSet().getMolecule(0);
+ assertTrue(container instanceof IBioPolymer);
+ IBioPolymer polymer = (IBioPolymer)container;
+
+ assertTrue(polymer instanceof PDBPolymer);
+ PDBPolymer pdb = (PDBPolymer)polymer;
+
+ assertTrue(polymer.getStrandNames().contains("D"));
+ assertTrue(polymer.getStrandNames().contains("E"));
+ assertTrue(polymer.getStrandNames().contains("A"));
+ assertTrue(polymer.getStrandNames().contains("B"));
+
+ assertTrue(
+ "Strand A is not a PDBStrand",
+ polymer.getStrand("D") instanceof PDBStrand
+ );
+ assertTrue(
+ "Strand A is not a PDBStrand",
+ polymer.getStrand("E") instanceof PDBStrand
+ );
+ assertTrue(
+ "Strand A is not a PDBStrand",
+ polymer.getStrand("A") instanceof PDBStrand
+ );
+ assertTrue(
+ "Strand A is not a PDBStrand",
+ polymer.getStrand("B") instanceof PDBStrand
+ );
+
+ //Check to pick up all 4 strands
+ assertEquals(polymer.getStrands().size(),4);
+
+ //The following check is to see that the first monomers in a strand
+ //can be accessed consecutively
+ //i.e. their resSeq numbering follows that in the File
+
+ //Strand A
+ PDBStrand strandA=(PDBStrand)polymer.getStrand("A");
+ List lst=(List)strandA.getMonomerNamesInSequentialOrder();
+
+ //Should be 57 monomers in strand A
+ assertEquals(57, lst.size());
+
+ String monomer1=(String)lst.get(0);
+ IMonomer mono1=strandA.getMonomer(monomer1);
+ assertNotNull(mono1);
+ assertNotNull(mono1.getMonomerName());
+ assertTrue(
+ "Monomer is not a PDBMonomer",
+ mono1 instanceof PDBMonomer
+ );
+ PDBMonomer pdbMonomer=(PDBMonomer)mono1;
+ assertEquals("A", pdbMonomer.getChainID());
+ assertEquals("8", pdbMonomer.getResSeq());
+
+ monomer1=(String)lst.get(1);
+ mono1=strandA.getMonomer(monomer1);
+ pdbMonomer=(PDBMonomer)mono1;
+ assertEquals("A", pdbMonomer.getChainID());
+ assertEquals("9", pdbMonomer.getResSeq());
+
+ monomer1=(String)lst.get(2);
+ mono1=strandA.getMonomer(monomer1);
+ pdbMonomer =(PDBMonomer)mono1;
+ assertEquals("A", pdbMonomer.getChainID());
+ assertEquals("10",pdbMonomer.getResSeq());
+
+ //Strand B
+ PDBStrand strandB=(PDBStrand)polymer.getStrand("B");
+ lst=(List)strandB.getMonomerNamesInSequentialOrder();
+
+ //Should be 57 monomers in strand B
+ assertEquals(57, lst.size());
+
+ monomer1=(String)lst.get(0);
+ mono1=strandB.getMonomer(monomer1);
+ assertNotNull(mono1);
+ assertNotNull(mono1.getMonomerName());
+ assertTrue(
+ "Monomer is not a PDBMonomer",
+ mono1 instanceof PDBMonomer
+ );
+ pdbMonomer=(PDBMonomer)mono1;
+ assertEquals("B", pdbMonomer.getChainID());
+ assertEquals("8", pdbMonomer.getResSeq());
+
+ monomer1=(String)lst.get(1);
+ mono1=strandB.getMonomer(monomer1);
+ pdbMonomer=(PDBMonomer)mono1;
+ assertEquals("B", pdbMonomer.getChainID());
+ assertEquals("9", pdbMonomer.getResSeq());
+
+ monomer1=(String)lst.get(2);
+ mono1=strandB.getMonomer(monomer1);
+ pdbMonomer =(PDBMonomer)mono1;
+ assertEquals("B", pdbMonomer.getChainID());
+ assertEquals("10",pdbMonomer.getResSeq());
+
+
+ //Strand E
+ PDBStrand strandE=(PDBStrand)polymer.getStrand("E");
+ lst=(List)strandE.getMonomerNamesInSequentialOrder();
+
+ //Should be 19 monomers in strand E
+ assertEquals(19, lst.size());
+
+ monomer1=(String)lst.get(0);
+ mono1=strandE.getMonomer(monomer1);
+ assertNotNull(mono1);
+ assertNotNull(mono1.getMonomerName());
+ assertTrue(
+ "Monomer is not a PDBMonomer",
+ mono1 instanceof PDBMonomer
+ );
+ pdbMonomer=(PDBMonomer)mono1;
+ assertEquals("E", pdbMonomer.getChainID());
+ assertEquals("20", pdbMonomer.getResSeq());
+
+ monomer1=(String)lst.get(1);
+ mono1=strandE.getMonomer(monomer1);
+ pdbMonomer=(PDBMonomer)mono1;
+ assertEquals("E", pdbMonomer.getChainID());
+ assertEquals("21", pdbMonomer.getResSeq());
+
+ monomer1=(String)lst.get(2);
+ mono1=strandE.getMonomer(monomer1);
+ pdbMonomer =(PDBMonomer)mono1;
+ assertEquals("E", pdbMonomer.getChainID());
+ assertEquals("22",pdbMonomer.getResSeq());
+
+
+
+ //Chain D should be 1,2,3...19
+ PDBStrand strandD=(PDBStrand)polymer.getStrand("D");
+ lst=(List)strandD.getMonomerNamesInSequentialOrder();
+
+ //Should be 19 monomers in strand D
+ assertEquals(19, lst.size());
+
+ monomer1=(String)lst.get(0);
+ mono1=strandD.getMonomer(monomer1);
+ assertNotNull(mono1);
+ assertNotNull(mono1.getMonomerName());
+ assertTrue(
+ "Monomer is not a PDBMonomer",
+ mono1 instanceof PDBMonomer
+ );
+ pdbMonomer=(PDBMonomer)mono1;
+ assertEquals("D", pdbMonomer.getChainID());
+ assertEquals("1", pdbMonomer.getResSeq());
+
+ monomer1=(String)lst.get(1);
+ mono1=strandD.getMonomer(monomer1);
+ pdbMonomer=(PDBMonomer)mono1;
+ assertEquals("D", pdbMonomer.getChainID());
+ assertEquals("2", pdbMonomer.getResSeq());
+
+ monomer1=(String)lst.get(2);
+ mono1=strandD.getMonomer(monomer1);
+ pdbMonomer=(PDBMonomer)mono1;
+ assertEquals("D", pdbMonomer.getChainID());
+ assertEquals("3",pdbMonomer.getResSeq());
+
+ // PDB Structures validation
+ //Should have 6 helices
+ assertEquals(6, pdb.getStructures().size());
+
+ }
+
+
}
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From: <egonw@us...> - 2007-04-22 20:48:55
|
Revision: 8241
http://svn.sourceforge.net/cdk/?rev=8241&view=rev
Author: egonw
Date: 2007-04-22 13:48:51 -0700 (Sun, 22 Apr 2007)
Log Message:
-----------
Fixed error messages, reordered and added assertion on the strand count up front
Modified Paths:
--------------
trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java
Modified: trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java 2007-04-22 20:18:59 UTC (rev 8240)
+++ trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java 2007-04-22 20:48:51 UTC (rev 8241)
@@ -25,7 +25,6 @@
package org.openscience.cdk.test.io;
import java.io.InputStream;
-import java.util.Collection;
import java.util.List;
import junit.framework.Test;
@@ -33,7 +32,6 @@
import junit.framework.TestSuite;
import org.openscience.cdk.ChemFile;
-import org.openscience.cdk.Monomer;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBioPolymer;
@@ -41,7 +39,6 @@
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.interfaces.IMonomer;
-import org.openscience.cdk.interfaces.IStrand;
import org.openscience.cdk.io.IChemObjectReader;
import org.openscience.cdk.io.PDBReader;
import org.openscience.cdk.nonotify.NNChemFile;
@@ -493,26 +490,26 @@
assertTrue(polymer instanceof PDBPolymer);
PDBPolymer pdb = (PDBPolymer)polymer;
+ assertEquals(4, pdb.getStrandCount());
assertTrue(polymer.getStrandNames().contains("D"));
- assertTrue(polymer.getStrandNames().contains("E"));
- assertTrue(polymer.getStrandNames().contains("A"));
- assertTrue(polymer.getStrandNames().contains("B"));
-
assertTrue(
- "Strand A is not a PDBStrand",
+ "Strand D is not a PDBStrand",
polymer.getStrand("D") instanceof PDBStrand
);
+ assertTrue(polymer.getStrandNames().contains("E"));
assertTrue(
- "Strand A is not a PDBStrand",
+ "Strand E is not a PDBStrand",
polymer.getStrand("E") instanceof PDBStrand
);
+ assertTrue(polymer.getStrandNames().contains("A"));
assertTrue(
"Strand A is not a PDBStrand",
polymer.getStrand("A") instanceof PDBStrand
);
+ assertTrue(polymer.getStrandNames().contains("B"));
assertTrue(
- "Strand A is not a PDBStrand",
+ "Strand B is not a PDBStrand",
polymer.getStrand("B") instanceof PDBStrand
);
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