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…etter - added more identifiers in gap_letter (a,b..AA, AB.. - Added warning message for when a structure has to get additional identifiers (AA, AB)
…hat includes information about problematic chains in a structure
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Pull request overview
This PR aims to address residue renumbering failures when the “gap tracker” exceeds the available alternate identifier set by introducing a generated gap-label scheme and surfacing warnings for structures/chains with many gaps during MSA-based renumbering.
Changes:
- Added
get_gap_letter()to generate gap alternate identifiers beyond the previous fixed list. - Added tracking/reporting of structures/chains that require multi-character alternate identifiers.
- Added a warning output file listing affected
structure:chainpairs.
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| for freq in gaps: # accepted gap percentage based on user defined occupancy threshold | ||
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| # Changing the functionality of gap_letter | ||
| #freq_tracker = 1 | ||
| #gap_tracker = 0 |
Changed output file type from txt -> csv Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
updated the logic behind the assignment of function get_gap_letter(n) Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
This takes into consideration the 0-9 identifiers that we included into gap_letter
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Solved issue #201, I updated the code to output a CSV file containing information regarding problematic chains in a structure