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cleaner patch for Fe atomtype test cases added
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Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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@asad @egonw
asad authored and egonw committed Aug 21, 2011
1 parent b92b8b1 commit ed3a554
Showing 1 changed file with 345 additions and 0 deletions.
345 changes: 345 additions & 0 deletions src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
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Expand Up @@ -4415,9 +4415,354 @@ public void test_As_5() throws Exception {

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

@Test
public void test_Fe_metallic() throws Exception {
String molName = "Fe_metallic";
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom a1 = builder.newInstance(IAtom.class, "Fe");
a1.setFormalCharge(0);
mol.addAtom(a1);
String[] expectedTypes = {"Fe.metallic"};
assertAtomTypes(testedAtomTypes, expectedTypes, mol);
}

@Test
public void test_Fe_plus() throws Exception {
String molName1 = "Fe_plus";
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, "C");
a2.setFormalCharge(0);
mol.addAtom(a2);
IAtom a3 = builder.newInstance(IAtom.class, "Fe");
a3.setFormalCharge(1);
mol.addAtom(a3);
IBond b1 = builder.newInstance(IBond.class, a2, a3, IBond.Order.SINGLE);
mol.addBond(b1);
IBond b2 = builder.newInstance(IBond.class, a1, a3, IBond.Order.SINGLE);
mol.addBond(b2);

String[] expectedTypes1 = {"C.sp3", "C.sp3", "Fe.plus"};
assertAtomTypes(testedAtomTypes, expectedTypes1, mol);
}

@Test
public void test_Fe_4() throws Exception {
String molName2 = "Fe_4";
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, "C");
a2.setFormalCharge(0);
mol.addAtom(a2);
IAtom a3 = builder.newInstance(IAtom.class, "Fe");
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, a2, a3, 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, a3, a4, IBond.Order.SINGLE);
mol.addBond(b3);
IBond b4 = builder.newInstance(IBond.class, a3, a5, IBond.Order.SINGLE);
mol.addBond(b4);
String[] expectedTypes2 = {"C.sp3", "C.sp3", "Fe.4", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes2, mol);
}

@Test
public void test_Fe_3minus() throws Exception {
String molName3 = "Fe_3minus";
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom a1 = builder.newInstance(IAtom.class, "Fe");
a1.setFormalCharge(-3);
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);
IAtom a7 = builder.newInstance(IAtom.class, "C");
a7.setFormalCharge(0);
mol.addAtom(a7);
IBond b1 = builder.newInstance(IBond.class, a1, a3, IBond.Order.SINGLE);
mol.addBond(b1);
IBond b2 = builder.newInstance(IBond.class, a1, a5, IBond.Order.SINGLE);
mol.addBond(b2);
IBond b3 = builder.newInstance(IBond.class, a1, a6, IBond.Order.SINGLE);
mol.addBond(b3);
IBond b4 = builder.newInstance(IBond.class, a1, a4, IBond.Order.SINGLE);
mol.addBond(b4);
IBond b5 = builder.newInstance(IBond.class, a1, a7, IBond.Order.SINGLE);
mol.addBond(b5);
IBond b6 = builder.newInstance(IBond.class, a1, a2, IBond.Order.SINGLE);
mol.addBond(b6);
String[] expectedTypes3 = {"Fe.3minus", "C.sp3", "C.sp3", "C.sp3", "C.sp3", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes3, mol);
}

@Test
public void test_Fe_2plus() throws Exception {
String molName4 = "Fe_2plus";
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom a1 = builder.newInstance(IAtom.class, "Fe");
a1.setFormalCharge(2);
mol.addAtom(a1);
String[] expectedTypes4 = {"Fe.2plus"};
assertAtomTypes(testedAtomTypes, expectedTypes4, mol);
}

@Test
public void test_Fe_4minus() throws Exception {
String molName5 = "Fe_4minus";
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom a1 = builder.newInstance(IAtom.class, "Fe");
a1.setFormalCharge(-4);
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);
IAtom a7 = builder.newInstance(IAtom.class, "C");
a7.setFormalCharge(0);
mol.addAtom(a7);
IBond b1 = builder.newInstance(IBond.class, a1, a3, IBond.Order.SINGLE);
mol.addBond(b1);
IBond b2 = builder.newInstance(IBond.class, a1, a5, IBond.Order.SINGLE);
mol.addBond(b2);
IBond b3 = builder.newInstance(IBond.class, a1, a6, IBond.Order.SINGLE);
mol.addBond(b3);
IBond b4 = builder.newInstance(IBond.class, a1, a4, IBond.Order.SINGLE);
mol.addBond(b4);
IBond b5 = builder.newInstance(IBond.class, a1, a7, IBond.Order.SINGLE);
mol.addBond(b5);
IBond b6 = builder.newInstance(IBond.class, a1, a2, IBond.Order.SINGLE);
mol.addBond(b6);

String[] expectedTypes5 = {"Fe.4minus", "C.sp3", "C.sp3", "C.sp3", "C.sp3", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes5, mol);
}

@Test
public void test_Fe_5() throws Exception {
String molNameFe5 = "Fe_5";
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom a1 = builder.newInstance(IAtom.class, "Fe");
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.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);
IBond b5 = builder.newInstance(IBond.class, a1, a6, IBond.Order.SINGLE);
mol.addBond(b5);
String[] expectedTypesFe5 = {"Fe.5", "C.sp3", "C.sp3", "C.sp3", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypesFe5, mol);
}

@Test
public void test_Fe_6() throws Exception {
String molName7 = "Fe_6";
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom a1 = builder.newInstance(IAtom.class, "Fe");
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);
IAtom a7 = builder.newInstance(IAtom.class, "C");
a7.setFormalCharge(0);
mol.addAtom(a7);
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);
IBond b5 = builder.newInstance(IBond.class, a1, a6, IBond.Order.SINGLE);
mol.addBond(b5);
IBond b6 = builder.newInstance(IBond.class, a1, a7, IBond.Order.SINGLE);
mol.addBond(b6);
String[] expectedTypes7 = {"Fe.6", "C.sp3", "C.sp3", "C.sp3", "C.sp3", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes7, mol);
}

@Test
public void test_Fe_2minus() throws Exception {
String molName8 = "Fe_2minus";
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom a1 = builder.newInstance(IAtom.class, "Fe");
a1.setFormalCharge(-2);
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);
IAtom a7 = builder.newInstance(IAtom.class, "C");
a7.setFormalCharge(0);
mol.addAtom(a7);
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);
IBond b5 = builder.newInstance(IBond.class, a1, a6, IBond.Order.SINGLE);
mol.addBond(b5);
IBond b6 = builder.newInstance(IBond.class, a1, a7, IBond.Order.SINGLE);
mol.addBond(b6);
String[] expectedTypes8 = {"Fe.2minus", "C.sp3", "C.sp3", "C.sp3", "C.sp3", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypes8, mol);
}

@Test
public void test_Fe_3plus() throws Exception {
String molName9 = "Fe_3plus";
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom a1 = builder.newInstance(IAtom.class, "Fe");
a1.setFormalCharge(3);
mol.addAtom(a1);
String[] expectedTypes9 = {"Fe.3plus"};
assertAtomTypes(testedAtomTypes, expectedTypes9, mol);
}

@Test
public void test_Fe_2() throws Exception {
String molNameA = "Fe_2";
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, "Fe");
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, a2, a3, IBond.Order.SINGLE);
mol.addBond(b2);
String[] expectedTypesA = {"C.sp3", "Fe.2", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypesA, mol);
}

@Test
public void test_Fe_3() throws Exception {
String molNameB = "Fe_3";
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
IMolecule mol = builder.newInstance(IMolecule.class);
IAtom a1 = builder.newInstance(IAtom.class, "Fe");
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);
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);
String[] expectedTypesB = {"Fe.3", "C.sp3", "C.sp3", "C.sp3"};
assertAtomTypes(testedAtomTypes, expectedTypesB, mol);
}

/*
* This method *must* be the last method in the class.
*/
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