parse and use INDEX_MAP for flexible sidechains

[diogomart]

Meeko version v0.6.0 started adding and INDEX_MAP to flexible sidechains, allowing mk_export.py to write PDB files with docked sidecains positions for any sidechain, instead of being limited to the flexres templates stored in meeko's RDKitMolCreate class. Ringtail should parse the INDEX_MAP and use it, and call RDKitMolCreate.guess_flexres_smiles only if the INDEX_MAP is absent (for backwards compatibility with virtual screens prepared with meeko v0.5 and older).

[maylinnp]

Will deal with this once next major meeko release happens. Will most likely involve adding a column to the receptor table to store the polymer json produced by meeko, which contains additional information compared to the current receptor blob that is in the table.

Then, the method mentioned will just use the data from the new column (when available) instead of RDKitMolCreate.guess_flexres_smiles.