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Corrected bug when extracting the most stable conformer.
Corrected a typo and added info about the most stable structure on the log mesages if refinement.py.
Raise FileNotFoundError when no calculations finished normally.
Added log message to print the number of structures selected at the refinement step.
Adapted arguments due to changes in collect_coords in formats.py
Changed logger calls.
Added arguments due to the changes in collect_energies in formats.py
Change on function names and documentation.
Implemented check_finished_calcs which checks whether calculations are finished normally or not.
Included extra arguments for the proper working of special atoms.
Added logging entries at the beginning and end of each section.
Implemented refinement.py
Created a module for each stage of DockOnSurf and started developing the isolated one