Add flags for optional t_atoms entries

Add flags for optional t_atoms entries

Instead of checking for (non-)NULL pointer, we can now determine
the presence of optional entries in t_atoms using booleans.
Moved the mass generation from confio.cpp to a function in atoms.cpp.
Most changes are caused by checking havePdbInfo iso pdbinfo!=NULL.

Change-Id: I6e2c8ffaa2240056f34da4c93f1713c40a00f391