/**
* Create a benzene molecule with 2 residues and 2 charge groups
*
* @return
*/
public MDMolecule makeMDBenzene() {
MDMolecule mol = new MDMolecule();
mol.addAtom(new Atom("C")); // 0
mol.addAtom(new Atom("C")); // 1
mol.addAtom(new Atom("C")); // 2
mol.addAtom(new Atom("C")); // 3
mol.addAtom(new Atom("C")); // 4
mol.addAtom(new Atom("C")); // 5
mol.addBond(0, 1, IBond.Order.SINGLE); // 1
mol.addBond(1, 2, IBond.Order.DOUBLE); // 2
mol.addBond(2, 3, IBond.Order.SINGLE); // 3
mol.addBond(3, 4, IBond.Order.DOUBLE); // 4
mol.addBond(4, 5, IBond.Order.SINGLE); // 5
mol.addBond(5, 0, IBond.Order.DOUBLE); // 6
// Create 2 residues
AtomContainer ac = new AtomContainer();
ac.addAtom(mol.getAtom(0));
ac.addAtom(mol.getAtom(1));
ac.addAtom(mol.getAtom(2));
Residue res1 = new Residue(ac, 0, mol);
res1.setName("myResidue1");
mol.addResidue(res1);
AtomContainer ac2 = new AtomContainer();
ac2.addAtom(mol.getAtom(3));
ac2.addAtom(mol.getAtom(4));
ac2.addAtom(mol.getAtom(5));
Residue res2 = new Residue(ac2, 1, mol);
res2.setName("myResidue2");
mol.addResidue(res2);
// Create 2 chargegroups
AtomContainer ac3 = new AtomContainer();
ac3.addAtom(mol.getAtom(0));
ac3.addAtom(mol.getAtom(1));
ChargeGroup chg1 = new ChargeGroup(ac3, 2, mol);
chg1.setSwitchingAtom(mol.getAtom(1));
mol.addChargeGroup(chg1);
AtomContainer ac4 = new AtomContainer();
ac4.addAtom(mol.getAtom(2));
ac4.addAtom(mol.getAtom(3));
ac4.addAtom(mol.getAtom(4));
ac4.addAtom(mol.getAtom(5));
ChargeGroup chg2 = new ChargeGroup(ac4, 3, mol);
chg2.setSwitchingAtom(mol.getAtom(4));
mol.addChargeGroup(chg2);
return mol;
}
