Integration feature and bug fixes

[knaegle]

Description

Integration of PDB and Uniprot currently works for the most part. However there are a series of bugs and requested features

Screenshots

See Ticket #27 about mutation issues

Tasks

Include specific tasks in the order they need to be done in. Include links to specific lines of code where the task should happen at, if known

• [x] Update integration column names to be clear they come from the reference integration. We decided that all of these column names will begin with IntRef:
• [x] See and resolve Ticket #27 about differences in mutation data.
• [x] For entities not found in the reference file, we want to still report the sequence (using pdbx_seq_one_letter_code_can and setting the reference range to be 1-rcsb_sample_sequence_length+1)
• [x] 'reference range' and 'struct/ref sequence' columns have empty cells for structures that do not have a reference available (like ligands). Replace these empty cells with 'not found'. --- ignored, this was fixed in another ticket by copying the sequence and designating range where record is not in reference. All other fields are N/A

[knaegle]

Note, that the reference integration columns are preceded by ref:

[knaegle]

Note that the last