@Test
public void testDebugPDBPolymer() {
IPDBPolymer pdbPolymer = new DebugPDBPolymer();
Assert.assertNotNull(pdbPolymer);
Assert.assertEquals(pdbPolymer.getMonomerCount(), 0);
IStrand oStrand1 = pdbPolymer.getBuilder().newInstance(IStrand.class);
oStrand1.setStrandName("A");
IStrand oStrand2 = pdbPolymer.getBuilder().newInstance(IStrand.class);
oStrand2.setStrandName("B");
IMonomer oMono1 = pdbPolymer.getBuilder().newInstance(IMonomer.class);
oMono1.setMonomerName(new String("TRP279"));
IMonomer oMono2 = pdbPolymer.getBuilder().newInstance(IMonomer.class);
oMono2.setMonomerName(new String("HOH"));
IMonomer oMono3 = pdbPolymer.getBuilder().newInstance(IMonomer.class);
oMono3.setMonomerName(new String("GLYA16"));
IPDBAtom oPDBAtom1 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C1");
IPDBAtom oPDBAtom2 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C2");
IPDBAtom oPDBAtom3 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C3");
IPDBAtom oPDBAtom4 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C4");
IPDBAtom oPDBAtom5 = pdbPolymer.getBuilder().newInstance(IPDBAtom.class, "C5");
pdbPolymer.addAtom(oPDBAtom1);
pdbPolymer.addAtom(oPDBAtom2, oStrand1);
pdbPolymer.addAtom(oPDBAtom3, oMono1, oStrand1);
pdbPolymer.addAtom(oPDBAtom4, oMono2, oStrand2);
pdbPolymer.addAtom(oPDBAtom5, oMono3, oStrand2);
Assert.assertNotNull(pdbPolymer.getAtom(0));
Assert.assertNotNull(pdbPolymer.getAtom(1));
Assert.assertNotNull(pdbPolymer.getAtom(2));
Assert.assertNotNull(pdbPolymer.getAtom(3));
Assert.assertNotNull(pdbPolymer.getAtom(4));
Assert.assertEquals(oPDBAtom1, pdbPolymer.getAtom(0));
Assert.assertEquals(oPDBAtom2, pdbPolymer.getAtom(1));
Assert.assertEquals(oPDBAtom3, pdbPolymer.getAtom(2));
Assert.assertEquals(oPDBAtom4, pdbPolymer.getAtom(3));
Assert.assertEquals(oPDBAtom5, pdbPolymer.getAtom(4));
Assert.assertNull(pdbPolymer.getMonomer("0815", "A"));
Assert.assertNull(pdbPolymer.getMonomer("0815", "B"));
Assert.assertNull(pdbPolymer.getMonomer("0815", ""));
Assert.assertNull(pdbPolymer.getStrand(""));
Assert.assertNotNull(pdbPolymer.getMonomer("TRP279", "A"));
Assert.assertEquals(oMono1, pdbPolymer.getMonomer("TRP279", "A"));
Assert.assertEquals(pdbPolymer.getMonomer("TRP279", "A").getAtomCount(), 1);
Assert.assertNotNull(pdbPolymer.getMonomer("HOH", "B"));
Assert.assertEquals(oMono2, pdbPolymer.getMonomer("HOH", "B"));
Assert.assertEquals(pdbPolymer.getMonomer("HOH", "B").getAtomCount(), 1);
Assert.assertEquals(pdbPolymer.getStrand("B").getAtomCount(), 2);
Assert.assertEquals(pdbPolymer.getStrand("B").getMonomerCount(), 2);
Assert.assertNull(pdbPolymer.getStrand("C"));
Assert.assertNotNull(pdbPolymer.getStrand("B"));
}
@Test
public void testStrand() {
IStrand oStrand = new Strand();
Assert.assertNotNull(oStrand);
Assert.assertEquals(oStrand.getMonomerCount(), 0);
IMonomer oMono1 = oStrand.getBuilder().newInstance(IMonomer.class);
oMono1.setMonomerName(new String("TRP279"));
IMonomer oMono2 = oStrand.getBuilder().newInstance(IMonomer.class);
oMono2.setMonomerName(new String("HOH"));
IMonomer oMono3 = oStrand.getBuilder().newInstance(IMonomer.class);
oMono3.setMonomerName(new String("GLYA16"));
IAtom oAtom1 = oStrand.getBuilder().newInstance(IAtom.class, "C1");
IAtom oAtom2 = oStrand.getBuilder().newInstance(IAtom.class, "C2");
IAtom oAtom3 = oStrand.getBuilder().newInstance(IAtom.class, "C3");
IAtom oAtom4 = oStrand.getBuilder().newInstance(IAtom.class, "C4");
IAtom oAtom5 = oStrand.getBuilder().newInstance(IAtom.class, "C5");
oStrand.addAtom(oAtom1);
oStrand.addAtom(oAtom2);
oStrand.addAtom(oAtom3, oMono1);
oStrand.addAtom(oAtom4, oMono2);
oStrand.addAtom(oAtom5, oMono3);
Assert.assertNotNull(oStrand.getAtom(0));
Assert.assertNotNull(oStrand.getAtom(1));
Assert.assertNotNull(oStrand.getAtom(2));
Assert.assertNotNull(oStrand.getAtom(3));
Assert.assertNotNull(oStrand.getAtom(4));
Assert.assertEquals(oAtom1, oStrand.getAtom(0));
Assert.assertEquals(oAtom2, oStrand.getAtom(1));
Assert.assertEquals(oAtom3, oStrand.getAtom(2));
Assert.assertEquals(oAtom4, oStrand.getAtom(3));
Assert.assertEquals(oAtom5, oStrand.getAtom(4));
Assert.assertNull(oStrand.getMonomer("0815"));
Assert.assertNotNull(oStrand.getMonomer(""));
Assert.assertNotNull(oStrand.getMonomer("TRP279"));
Assert.assertEquals(oMono1, oStrand.getMonomer("TRP279"));
Assert.assertEquals(oStrand.getMonomer("TRP279").getAtomCount(), 1);
Assert.assertNotNull(oStrand.getMonomer("HOH"));
Assert.assertEquals(oMono2, oStrand.getMonomer("HOH"));
Assert.assertEquals(oStrand.getMonomer("HOH").getAtomCount(), 1);
Assert.assertEquals(oStrand.getMonomer("").getAtomCount(), 2);
Assert.assertEquals(oStrand.getAtomCount(), 5);
Assert.assertEquals(oStrand.getMonomerCount(), 3);
}
/**
* Adds the atom oAtom to a specified Monomer. Additionally, it keeps record of the iCode.
*
* @param oAtom The IPDBAtom to add
* @param oMonomer The monomer the atom belongs to
*/
public void addAtom(IPDBAtom oAtom, IMonomer oMonomer) {
super.addAtom(oAtom, oMonomer);
if (!sequentialListOfMonomers.contains(oMonomer.getMonomerName()))
sequentialListOfMonomers.add(oMonomer.getMonomerName());
}
/**
* Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand. Additionally, it keeps
* record of the iCode.
*
* @param oAtom The IPDBAtom to add
* @param oMonomer The monomer the atom belongs to
*/
@Override
public void addAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand) {
super.addAtom(oAtom, oMonomer, oStrand);
if (!sequentialListOfMonomers.contains(oMonomer.getMonomerName()))
sequentialListOfMonomers.add(oMonomer.getMonomerName());
}