Shaoqz/refactor mutate stru

[shaoqx]

Basically finished mutation module refactoring:

• Finished tleap as engine of mutate_stru
• change Mutation name tuple to a class, added many methods
• add several function for List[Mutation] as a representation for mutant
• change run_command to match with functions in old_enzy_htp (mainly the retry)
• (TODO) Partially finished the topology check of mutated structure. (Need to finish init_connect of Structure)

Also contain some changes for the MultiEFdesign project

• mainly about assign_mutant function

[chrisjurich]

Code logic looks good. Primary thoughts are on need for:

• improved docstrings: In general they are not very descriptive and it is hard to tell what they actually do
• shorter function names: many function names are very long but do not provide much meaning

Please make changes and re-submit.

[chrisjurich]

Changes look good and are a step in the right direction. Will request more documentation when new release occurs.