Fix Cl and Br atom issue in atomMapping

[k-ujihara]

The Cl atom is incorrectly converted to C by "pmx atomMapping" due to a misimplementation in the writeFormatPDB method.
As a result, the script below should output two "CCl", but it outputs two "CC" instead. Br atom also has the same problem.
This PR fixes the issue.

python -c "from rdkit.Chem.AllChem import *; m = MolFromSmiles('ClC'); EmbedMolecule(m); MolToPDBFile(m, 'm1.pdb')"
python -c "from rdkit.Chem.AllChem import *; m = MolFromSmiles('ClC'); EmbedMolecule(m); MolToPDBFile(m, 'm2.pdb')"
pmx atomMapping -i1 m1.pdb -i2 m2.pdb -opdb1 pdb1.pdb -opdb2 pdb2.pdb
python -c "from rdkit.Chem.AllChem import *; m = MolFromPDBFile('pdb1.pdb'); print(MolToSmiles(m));"
python -c "from rdkit.Chem.AllChem import *; m = MolFromPDBFile('pdb2.pdb'); print(MolToSmiles(m));"