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MutantAutoMate

  • The script getPDB.py will find the isoform of a gene and mutant of interest and find and download the relevant PDB.
  • The script getPDF2.py will generate a PDF with relevant descriptions of a given mutant.
  • The script snapshot.sh will produce an image of your mutant structure.

Download dependencies after cloning repository with

pip install -e.

Call snapshot.sh through the terminal by:

./snapshot.sh 'file1' 'file2'

To run a code in the src folder:

python -m mutantautomate getPDB.py

This code for NRXN1 for residue P89 will give the output(isoforms list):

P55196 Q62765 Q62889 Q8N2Q7 Q07666 Q9NZ94 Q99K10 Q91V33 Q60749 O35889 Q9QZQ1 P55196-5 P55196-1 P55196-2 P55196-3 P55196-6 Q62765-3 Q62765-2 Q62765-4 Q62889-2 Q62889-4 Q62889-3

Examples

docker compose run python bash
cd src/mutantautomate
python ./final.py --gene-name NLGN1 --residue1 D --position 140 --residue2 Y --top-isoforms True

Frontend / Web Server

app2.py is a Flask app that serves a single index page, index2.html.

The Flask app uses process.py and pdb_helpers.py to do the back-end processing. process.py has a process function which is a Python generator. The front-end opens up an EventSource, and the process function yields JSON events back to the browser.

The front-end uses Preact and other JS libraries to render the front end. There is no build step, everything is rendered in-browser and fetched from the JS CDN called esm.sh.