Clean up hydrated docking scripts

[rwxayheee]

Some minor problems (about line-ending characters and to strip them before parsing atomic information out of them) were reported regarding the hydrated docking scripts. If we want to continue supporting hydrated docking we might want to do a small clean up of the scripts.

[diogomart]

What do you think of moving dry.py into mk_export.py? Then drying wouldn't require an additional step.

[rwxayheee]

Hi @diogomart, Yes, we could relocate the functions to mk_export.py. We currently don't have a parser for map files in Meeko (?) but it would be great to have one. Feel free to relocate this issue as needed