# README create_db_scripts/
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## Setup
Before creating the database, you must:
- Download the PDB structures listed in the file
- Download the whole AFDB human proteome
- Run AIUPred on all the structures and store the results in one text file
- Edit the locations.sh with all the necessary paths to data directories and files


## Usage
bash create_db.sh


## File description

- check_requirements.sh
	Checks the existence of the files and directories contained in requirements.sh

- compare-af2rsa-disprot.py
	Creates a complete list of residues that are annotated as disordered in DisProt
	but have secondary structure for AlphaFold2

- create_db.sh
	Main script.
	1. Checks the requirements are fulfilled
	2. Runs scripts to generate the different parts of the database
	3. Create an equilibrated dataset making a random selection

- find-unconfirmed-disorder.py
	Creates a complete list of residues that are predicted as not disordered by AIUPred
	but do not have secondary structure for AlphaFold2

- locations.sh
	User-set environment variables pointing to data folders (DisProt PDB files,
	AFDB predictions, DSSP executable, etc.)

- generate_equilibrated_dataset.sh
	Randomly creates the equilibrated dataset that will be used to train ABSTRAQT

- report_unphysical_SSEs.py
	Creates a complete list of secondary structure motifs whose backbone have uncommon
	planar and torsion angles

- requirements.sh
	List of scripts, files and directories that must be present to run these scripts 

- requirements_python.txt
	List of necessary python3 libraries