Update nucleotide templates, add NAKB_templates.json

[rwxayheee]

This PR includes two changes:

• Minor updates in nucleotide templates residue_chem_templates.json
  The phosphate capping groups (p), and the two molecular (ligand) forms of nucleotides are dropped. They aren't currently used for template matching.

• Add NAKB_templates.json
  This is a ready to use additional chemical template file. It includes up to four variants of the 5',3'-linking fragments for individual standard and nonstandard nucleotides.

Currently the additional JSON file has 1778 templates for 453 residues

All nucleotides (824) from the NAKB modified nucleotide pool were considered. The Python script to make is here. A nonstandard nucleotide / a template is dropped if:

• Is tagged not mappable by NAKB
• Contains unsupported elements
• Has a bad definition CIF file, and created rdkit molecule can't be sanitized or has implicit hydrogens
• Does not fall within some safe nets to ensure the uniqueness of matching and deleterious editing
• Is redundant (has the same smiles and atom_name) under the same parent
• Won't pass Meeko template check for other reasons (very very few cases)

Without further optimization it takes about 0.15 seconds per nucleotide to fetch the definition, process and write a template file (1-4 variants) on a Mac. It might be possible to integrate the process with prepare_receptor in future. But for the time being, I hope the additional chemical template file can help users who work with RNA/DNA systems where nonstandard nucleotides are present

08d7575 Added a few templates that went missing because of network issue

[diogomart]

Looks great. If I understand correctly these new templates aren't automatically loaded. Should we add a command line and Python option for that?

[rwxayheee]

Hi @diogomart
The new template file can be used by --add_templates in mk_receptor_preparation.py. I added it to meeko/data so that it's distributed with Meeko. What do you think?

I haven't checked the name conflicts, but will do some more work, and make sure it's not overwriting the existing templates.

[rwxayheee]

898a29c Regenerated the templates with new codes. Checked the name conflicts. Fixed some incorrect templates, added some templates that didn't go through because of mistakes in check. Re-counted the number of templates & residues.

This should be ready to merge. But again it's not urgent.

[rwxayheee]

merging the edited template + additional template