Added pre-calculation of residue/atom positions in aligned structure-chain sequences at the data entry point. New property is called resaln, and specifies the position of the residue an atom belongs to relative to a specified alignment. This links atoms to sequence alignment positions so that atom-derived information can be displayed in the alignment framework of the explorer panels.
To activate this change you need to:
- Migrate:
python manage.py makemigrations explorer.python manage.py migrate explorer.
- Run the alignment table generator:
- Go to the structure alignment folder webCovidPortal/explorer/data/structure/alignment, note that the readme there has more detailed documentation of this process.
- Make sure that you have an existing
conformed_alignments.csvin webCovidPortal/explorer/data/structure/alignment and that these conformed sequences have successfully been imported using the manager commands. - Build the alignment table by running
build_alignment_table.py. - This will output a file called
conformed_alignment_table.csv.
- Import the results:
- Note that depending on how many atoms are defined, importing may take a minute or two.
- Go to webCovidPortal/ and import using
python manage.py import_structureresiduealignment explorer/data/structure/alignment/conformed_alignment_table.csv.
- Test:
- You can test by using the API directly with the following link: http://localhost:8000/explorer/structureresidueatoms?mesh_id=D064370&atom=CA&alignment=20200505&pdbchains=5X5B.A%2C5X5B.C