mmCIF chain names

[Eric Pettersen]

Need the pdbx_poly_seq_scheme records extruded into the structure metadata in order to show descriptive names for chains

[Greg Couch]

Separate email from Eric says: "The tables I need are ‘pdbx_poly_seq_scheme’, ‘entity’, and ‘entity_name_com’."

As noted in #175, parsing the pdbx_poly_seq_scheme table slows down parsing of 3j3q by ~3.4% and that information needed is already available from the other tables that are read. The entity table is already read. So, it would be inexpensive to add reading the entity_name_com table and call a C/C++ API that sets the descriptive names for chains. Extruding the tables into the metadata is possible, but would be much slower.

[Greg Couch]

Interim solution: For the pdbx_poly_seq_scheme information, added a Residue.mmcif_chain_id, and structure.metadatachain_entity_map. And put the entity table into the metadata. The additional information should help any code that looks at other mmCIF tables.

[Eric Pettersen]

Well, a little prematurely closed, but now the new Residue attr is saved/restored/copied, and the metadata is used to set the descriptive chain names, so it is "actually" closed as of now. :-)