Use covalent radii of the atoms inside the check_distance function

[jonathan-schoeps]

Current status

check_distance in generate_molecule.py checks all inter-atomic distances based on a global threshold from ConfigClass.

• Atoms with very small radii like hydrogen are not put close together, while super large atoms like Pb might be placed too close to each other.

How to improve

Take the covalent radii from refinement.py and use it to calculate the distance threshold between the atom pairs.