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Moved confs_to_mol_list function from isolated.py to formats.py module and generalised the calculations functions to be able to work with no matter which kind of calculation
Changed logging of formats.py from info to debug severity level.
Disabled the removal of hydrogens when using rdkit sdl mol file reader. Now, rdkit mol object contain hydrogens explicitly.
Moved logger to a global variable
Changed the read_coords.py module name to formats.py which states more clearly the purpose of the module.