The PDB columns that are really important are hard to understand from the titles, and they are misspelled (cannonical instead of canonical, but canonical as a phrase is unclear in this context). Hence, let's take this opportunity to identify a better way to refer to what is currently: CANNONICAL_REF_SEQ and CANNONICAL_SEQ_BEG_POSITION
Files
PDB reference file and derivatives.
Expected behavior
PDB_SEQ - sequence of the PDB
UNIPROT_SEQ - sequence of the reference (Uniprot) - let's change this to REF_SEQ
CANNONICAL_REF_SEQ - let's change this to PDB_REF_SEQ (i.e. the intersection of PDB and REF seq)
PDB_SEQ_BEG_POSITION - can keep this the same
CANNONICAL_SEQ_BEG_POSITION - let's change this to REF_SEQ_BEG_POSITION
Tasks
[x] Change the PDB generator to rename these columns.
[x] Update dependent code in the integration and anywhere else these columns are used
[x] Update the References.md documentation
[x] Update the figure that References.md uses (@knaegle will have to do this).
knaegle
commented
1 year ago
Description
The PDB columns that are really important are hard to understand from the titles, and they are misspelled (cannonical instead of canonical, but canonical as a phrase is unclear in this context). Hence, let's take this opportunity to identify a better way to refer to what is currently: CANNONICAL_REF_SEQ and CANNONICAL_SEQ_BEG_POSITION
Files
PDB reference file and derivatives.
Expected behavior
PDB_SEQ - sequence of the PDB UNIPROT_SEQ - sequence of the reference (Uniprot) - let's change this to REF_SEQ CANNONICAL_REF_SEQ - let's change this to PDB_REF_SEQ (i.e. the intersection of PDB and REF seq) PDB_SEQ_BEG_POSITION - can keep this the same CANNONICAL_SEQ_BEG_POSITION - let's change this to REF_SEQ_BEG_POSITION
Tasks