@Test public void testNewAminoAcid() { IChemObjectBuilder builder = rootObject.getBuilder(); IAminoAcid aa = builder.newInstance(IAminoAcid.class); Assert.assertNotNull(aa); }
@Test public void testNewAtomType_String_String() { IChemObjectBuilder builder = rootObject.getBuilder(); IAtomType type = builder.newInstance(IAtomType.class, "C", "C.sp2"); Assert.assertNotNull(type); }
@Test public void testNewPDBMonomer() { IChemObjectBuilder builder = rootObject.getBuilder(); IPDBMonomer monomer = builder.newInstance(IPDBMonomer.class); Assert.assertNotNull(monomer); }
@Test public void testNewRing() { IChemObjectBuilder builder = rootObject.getBuilder(); IRing ring = builder.newInstance(IRing.class); Assert.assertNotNull(ring); }
@Test public void testNewMoleculeSet() { IChemObjectBuilder builder = rootObject.getBuilder(); IAtomContainerSet set = builder.newInstance(IAtomContainerSet.class); Assert.assertNotNull(set); }
@Test public void testNewReactionScheme() { IChemObjectBuilder builder = rootObject.getBuilder(); IReactionScheme scheme = builder.newInstance(IReactionScheme.class); Assert.assertNotNull(scheme); }
@Test public void testNewFragmentAtom() { IChemObjectBuilder builder = rootObject.getBuilder(); IFragmentAtom fragAtom = builder.newInstance(IFragmentAtom.class); Assert.assertNotNull(fragAtom); }
@Test @Override public void testCompare_Object() { IChemObject object = newChemObject(); IAtom c = object.getBuilder().newInstance(IAtom.class, "C"); IAtom o = object.getBuilder().newInstance(IAtom.class, "O"); IBond b = new Bond(c, o, IBond.Order.DOUBLE); // C=O bond IBond b2 = new Bond(c, o, IBond.Order.DOUBLE); // same C=O bond Assert.assertTrue(b.compare(b2)); }
@Test public void testNewLonePair_IAtom() { IChemObjectBuilder builder = rootObject.getBuilder(); ILonePair lonePair = builder.newInstance(ILonePair.class, builder.newInstance(IAtom.class)); Assert.assertNotNull(lonePair); }
@Test public void testNewPDBAtom_String_Point3D() { IChemObjectBuilder builder = rootObject.getBuilder(); IPDBAtom atom = builder.newInstance(IPDBAtom.class, "O", new Point3d(1, 2, 3)); Assert.assertNotNull(atom); }
@Test public void testNewMolecularFormulaSet_IMolecularFormula() { IChemObjectBuilder builder = rootObject.getBuilder(); IMolecularFormulaSet mfSet = builder.newInstance(IMolecularFormulaSet.class, builder.newInstance(IMolecularFormula.class)); Assert.assertNotNull(mfSet); }
@Test public void testNewAdductFormula_IMolecularFormula() { IChemObjectBuilder builder = rootObject.getBuilder(); IAdductFormula af = builder.newInstance(IAdductFormula.class, builder.newInstance(IMolecularFormula.class)); Assert.assertNotNull(af); }
@Test public void testPDBAtom_IElement() { IElement element = newChemObject().getBuilder().newInstance(IElement.class); IAtom a = new PDBAtom(element); Assert.assertNotNull(a); }
@Test public void testAtomType_IElement() { IElement element = newChemObject().getBuilder().newInstance(IElement.class, "C"); IAtomType at = new AtomType(element); Assert.assertEquals("C", at.getSymbol()); }
@Test public void testDebugBond_IAtom_IAtom() { IChemObject object = newChemObject(); IAtom c = object.getBuilder().newInstance(IAtom.class, "C"); IAtom o = object.getBuilder().newInstance(IAtom.class, "O"); IBond bond = new DebugBond(c, o); Assert.assertEquals(2, bond.getAtomCount()); Assert.assertEquals(c, bond.getBegin()); Assert.assertEquals(o, bond.getEnd()); Assert.assertEquals(IBond.Order.SINGLE, bond.getOrder()); Assert.assertEquals(IBond.Stereo.NONE, bond.getStereo()); }
@Test public void testDebugBond_IAtom_IAtom_IBond_Order() { IChemObject object = newChemObject(); IAtom c = object.getBuilder().newInstance(IAtom.class, "C"); IAtom o = object.getBuilder().newInstance(IAtom.class, "O"); IBond bond = new DebugBond(c, o, IBond.Order.DOUBLE); Assert.assertEquals(2, bond.getAtomCount()); Assert.assertEquals(c, bond.getBegin()); Assert.assertEquals(o, bond.getEnd()); Assert.assertTrue(bond.getOrder() == IBond.Order.DOUBLE); Assert.assertEquals(IBond.Stereo.NONE, bond.getStereo()); }
@Test public void testBond_IAtom_IAtom() { IChemObject object = newChemObject(); IAtom c = object.getBuilder().newInstance(IAtom.class, "C"); IAtom o = object.getBuilder().newInstance(IAtom.class, "O"); IBond bond = new Bond(c, o); Assert.assertEquals(2, bond.getAtomCount()); Assert.assertEquals(c, bond.getBegin()); Assert.assertEquals(o, bond.getEnd()); Assert.assertEquals(IBond.Order.SINGLE, bond.getOrder()); Assert.assertEquals(IBond.Stereo.NONE, bond.getStereo()); }
@Test public void testPseudoAtom_IElement() { IElement element = newChemObject().getBuilder().newInstance(IElement.class); IPseudoAtom a = new PseudoAtom(element); Assert.assertEquals("R", a.getSymbol()); Assert.assertNull(a.getPoint3d()); Assert.assertNull(a.getPoint2d()); Assert.assertNull(a.getFractionalPoint3d()); }
@Test public void testDebugPseudoAtom_IElement() { IElement element = newChemObject().getBuilder().newInstance(IElement.class); IPseudoAtom a = new DebugPseudoAtom(element); Assert.assertEquals("R", a.getSymbol()); Assert.assertNull(a.getPoint3d()); Assert.assertNull(a.getPoint2d()); Assert.assertNull(a.getFractionalPoint3d()); }
@Test public void testRing_IAtomContainer() { IAtomContainer container = newChemObject().getBuilder().newInstance(IAtomContainer.class); container.addAtom(container.getBuilder().newInstance(IAtom.class, "C")); container.addAtom(container.getBuilder().newInstance(IAtom.class, "C")); IRing ring = new Ring(container); Assert.assertNotNull(ring); Assert.assertEquals(2, ring.getAtomCount()); Assert.assertEquals(0, ring.getBondCount()); }