--cache_templates for mk_prepare_receptor.py

[rwxayheee]

This is an alternate to #209. Instead of caching CIF files (which are not really useful for other functions in Meeko), the encoded residue chem templates will be cached.

[rwxayheee]

New argument added:

  --cache_templates [CACHE_TEMPLATES]
                        Turns on caching of ResidueChemTemplates (default is OFF) by this option and (optionally) a
                        provided JSON filename. Default cache filename is: $HOME/.meeko_residue_chem_templates_cached.json)
                        When the caching is ON, the templates for polymer construction will be read from the specified
                        cache file and updates may be made to the same file in a cumulative manner.

Usage note:

(1) Creates, updates cumulatively and uses default cached templates

mk_prepare_receptor.py -i 6O4W.pdb -o some_output --cache_templates

This usage creates and updates the cached templates at $HOME/.meeko_residue_chem_templates_cached.json, with a message:
--cache_templates is turned on, but a name is not provided. The default filename ($HOME/.meeko_residue_chem_templates_cached.json) will be used.

(2) Specifies a destination or re-uses an existing cache

mk_prepare_receptor.py -i 6O4W.pdb -o some_output --cache_templates hohoho.json

This usage creates and updates the cached templates at the given name.