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Se atom type test cases added
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Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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@gilleain @egonw
gilleain authored and egonw committed Sep 8, 2011
1 parent ad7753a commit 55c6a83
Showing 1 changed file with 230 additions and 0 deletions.
230 changes: 230 additions & 0 deletions src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
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Expand Up @@ -3519,6 +3519,236 @@ public void testPine() throws Exception {
Assert.assertNotNull(type);
}
}


@Test
public void testSe_sp3d1_4() throws Exception {
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom a1 = builder.newInstance(IAtom.class, "Se");
a1.setFormalCharge(0);
mol.addAtom(a1);
IAtom a2 = builder.newInstance(IAtom.class, "C");
a2.setFormalCharge(0);
mol.addAtom(a2);
IAtom a3 = builder.newInstance(IAtom.class, "C");
a3.setFormalCharge(0);
mol.addAtom(a3);
IAtom a4 = builder.newInstance(IAtom.class, "C");
a4.setFormalCharge(0);
mol.addAtom(a4);
IAtom a5 = builder.newInstance(IAtom.class, "C");
a5.setFormalCharge(0);
mol.addAtom(a5);
IBond b1 = builder.newInstance(IBond.class, a1, a2, IBond.Order.SINGLE);
mol.addBond(b1);
IBond b2 = builder.newInstance(IBond.class, a1, a3, IBond.Order.SINGLE);
mol.addBond(b2);
IBond b3 = builder.newInstance(IBond.class, a1, a4, IBond.Order.SINGLE);
mol.addBond(b3);
IBond b4 = builder.newInstance(IBond.class, a1, a5, IBond.Order.SINGLE);
mol.addBond(b4);

String[] expectedTypes1 = {"Se.sp3d1.4", "C.sp3", "C.sp3", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes1, mol);
}

@Test
public void testSe_sp3_4() throws Exception {
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom a1 = builder.newInstance(IAtom.class, "Se");
a1.setFormalCharge(0);
mol.addAtom(a1);
IAtom a2 = builder.newInstance(IAtom.class, "C");
a2.setFormalCharge(0);
mol.addAtom(a2);
IAtom a3 = builder.newInstance(IAtom.class, "C");
a3.setFormalCharge(0);
mol.addAtom(a3);
IAtom a4 = builder.newInstance(IAtom.class, "C");
a4.setFormalCharge(0);
mol.addAtom(a4);
IAtom a5 = builder.newInstance(IAtom.class, "C");
a5.setFormalCharge(0);
mol.addAtom(a5);
IBond b1 = builder.newInstance(IBond.class, a1, a2, IBond.Order.SINGLE);
mol.addBond(b1);
IBond b2 = builder.newInstance(IBond.class, a1, a3, IBond.Order.SINGLE);
mol.addBond(b2);
IBond b3 = builder.newInstance(IBond.class, a1, a4, IBond.Order.DOUBLE);
mol.addBond(b3);
IBond b4 = builder.newInstance(IBond.class, a1, a5, IBond.Order.DOUBLE);
mol.addBond(b4);

String[] expectedTypes = {"Se.sp3.4", "C.sp3", "C.sp3", "C.sp2", "C.sp2"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}

@Test
public void testSe_sp2_2() throws Exception {
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom a1 = builder.newInstance(IAtom.class, "Se");
a1.setFormalCharge(0);
mol.addAtom(a1);
IAtom a2 = builder.newInstance(IAtom.class, "C");
a2.setFormalCharge(0);
mol.addAtom(a2);
IAtom a3 = builder.newInstance(IAtom.class, "C");
a3.setFormalCharge(0);
mol.addAtom(a3);
IBond b1 = builder.newInstance(IBond.class, a1, a2, IBond.Order.DOUBLE);
mol.addBond(b1);
IBond b2 = builder.newInstance(IBond.class, a1, a3, IBond.Order.DOUBLE);
mol.addBond(b2);

String[] expectedTypes2 = {"Se.sp2.2", "C.sp2", "C.sp2"};
assertAtomTypes(testedAtomTypes, expectedTypes2, mol);
}

@Test
public void testSe_1() throws Exception {
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom a1 = builder.newInstance(IAtom.class, "C");
a1.setFormalCharge(0);
mol.addAtom(a1);
IAtom a2 = builder.newInstance(IAtom.class, "Se");
a2.setFormalCharge(0);
mol.addAtom(a2);
IBond b1 = builder.newInstance(IBond.class, a1, a2, IBond.Order.DOUBLE);
mol.addBond(b1);

String[] expectedTypes3 = {"C.sp2", "Se.1"};
assertAtomTypes(testedAtomTypes, expectedTypes3, mol);
}

@Test
public void testSe_3() throws Exception {
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom a1 = builder.newInstance(IAtom.class, "Se");
a1.setFormalCharge(0);
mol.addAtom(a1);
IAtom a2 = builder.newInstance(IAtom.class, "C");
a2.setFormalCharge(0);
mol.addAtom(a2);
IAtom a3 = builder.newInstance(IAtom.class, "C");
a3.setFormalCharge(0);
mol.addAtom(a3);
IBond b1 = builder.newInstance(IBond.class, a1, a2, IBond.Order.SINGLE);
mol.addBond(b1);
IBond b2 = builder.newInstance(IBond.class, a1, a3, IBond.Order.SINGLE);
mol.addBond(b2);

String[] expectedTypes4 = {"Se.3", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes4, mol);
}

@Test
public void testSe_sp3_3() throws Exception {
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom a1 = builder.newInstance(IAtom.class, "C");
a1.setFormalCharge(0);
mol.addAtom(a1);
IAtom a2 = builder.newInstance(IAtom.class, "Se");
a2.setFormalCharge(0);
mol.addAtom(a2);
IAtom a3 = builder.newInstance(IAtom.class, "C");
a3.setFormalCharge(0);
mol.addAtom(a3);
IAtom a4 = builder.newInstance(IAtom.class, "C");
a4.setFormalCharge(0);
mol.addAtom(a4);
IBond b1 = builder.newInstance(IBond.class, a1, a2, IBond.Order.SINGLE);
mol.addBond(b1);
IBond b2 = builder.newInstance(IBond.class, a2, a3, IBond.Order.SINGLE);
mol.addBond(b2);
IBond b3 = builder.newInstance(IBond.class, a2, a4, IBond.Order.DOUBLE);
mol.addBond(b3);

String[] expectedTypes5 = {"C.sp3", "Se.sp3.3", "C.sp3", "C.sp2"};
assertAtomTypes(testedAtomTypes, expectedTypes5, mol);
}

@Test
public void testSe_4plus() throws Exception {
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom a1 = builder.newInstance(IAtom.class, "Se");
a1.setFormalCharge(4);
mol.addAtom(a1);

String[] expectedTypes6 = {"Se.4plus"};
assertAtomTypes(testedAtomTypes, expectedTypes6, mol);
}

@Test
public void testSe_plus_3() throws Exception {
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom a1 = builder.newInstance(IAtom.class, "C");
a1.setFormalCharge(0);
mol.addAtom(a1);
IAtom a2 = builder.newInstance(IAtom.class, "Se");
a2.setFormalCharge(1);
mol.addAtom(a2);
IAtom a3 = builder.newInstance(IAtom.class, "C");
a3.setFormalCharge(0);
mol.addAtom(a3);
IAtom a4 = builder.newInstance(IAtom.class, "C");
a4.setFormalCharge(0);
mol.addAtom(a4);
IBond b1 = builder.newInstance(IBond.class, a1, a2, IBond.Order.SINGLE);
mol.addBond(b1);
IBond b2 = builder.newInstance(IBond.class, a2, a3, IBond.Order.SINGLE);
mol.addBond(b2);
IBond b3 = builder.newInstance(IBond.class, a2, a4, IBond.Order.SINGLE);
mol.addBond(b3);

String[] expectedTypes7 = {"C.sp3", "Se.plus.3", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes7, mol);
}

@Test
public void testSe_5() throws Exception {
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom a1 = builder.newInstance(IAtom.class, "Se");
a1.setFormalCharge(0);
mol.addAtom(a1);
IAtom a2 = builder.newInstance(IAtom.class, "C");
a2.setFormalCharge(0);
mol.addAtom(a2);
IAtom a3 = builder.newInstance(IAtom.class, "C");
a3.setFormalCharge(0);
mol.addAtom(a3);
IAtom a4 = builder.newInstance(IAtom.class, "C");
a4.setFormalCharge(0);
mol.addAtom(a4);
IAtom a5 = builder.newInstance(IAtom.class, "C");
a5.setFormalCharge(0);
mol.addAtom(a5);
IAtom a6 = builder.newInstance(IAtom.class, "C");
a6.setFormalCharge(0);
mol.addAtom(a6);
IBond b1 = builder.newInstance(IBond.class, a1, a2, IBond.Order.DOUBLE);
mol.addBond(b1);
IBond b2 = builder.newInstance(IBond.class, a1, a3, IBond.Order.SINGLE);
mol.addBond(b2);
IBond b3 = builder.newInstance(IBond.class, a1, a4, IBond.Order.SINGLE);
mol.addBond(b3);
IBond b4 = builder.newInstance(IBond.class, a1, a5, IBond.Order.SINGLE);
mol.addBond(b4);
IBond b5 = builder.newInstance(IBond.class, a1, a6, IBond.Order.SINGLE);
mol.addBond(b5);

String[] expectedTypes8 = {"Se.5", "C.sp2", "C.sp3", "C.sp3", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes8, mol);
}


/**
* @cdk.inchi InChI=1S/H2Te/h1H2
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