Absolute path of download script

[zimb3l-priv]

Hey! I'm a bit confused as to what directory the "absolute path" in the documentation of the download script actually refers to. Because in OpenMM patch step the location ~/alphafold-2.2.0/ was referred to as the 'absolute path' but later in the directory structure the directories created by the script don't appear anywhere. Does this 'absolute path' for the script refer to ~/alphafold-2.2.0/alphafold instead then or is it simply an oversight that you didn't include said directories in the file structure?

[sanjaysrikakulam]

I am not sure where the following is mentioned in the readme

Because in OpenMM patch step the location ~/alphafold-2.2.0/ was referred to as the 'absolute path'

To simply run the script and download all databases that AF needs

bash download_db.sh -d /home/johndoe/alphafold_data

This command will download all databases to the folder /home/johndoe/alphafold_data.

Then for the -d option when executing the run_alphafold.sh use the above path /home/johndoe/alphafold_data

[zimb3l-priv]

Here it says
# $alphafold_path variable is set to the alphafold git repo directory (absolute path)
Ans later it refers to another download path for the databases but I just set the download directory as the ~/alphafold-2.2.0/ so this directory looks like this now

alphafold-2.2.0
├──alphafold
├──bfd
├──CONTRIBUTING.md
├──2022 docker
├──.dockerignore
├──imgs
├──LICENSE
├──mgnify
├──notebooks
├──params
├──pdb70
├──pdb_mmcif
├──pdb_seqres
├──README.md
├──requirements.txt
├──run_alphafold.py
├──run_alphafold_test.py
├──scripts
├──setup.py
├──uniclust30
├──uniprot
└── uniref90

And I am not sure whether this is correct, although the only thing this is impacting according to the documentation was that Docker would run slowly. Since this is the non-docker version this doesn't sound like it's a problem

[sanjaysrikakulam]

The alphafold_path variable refers to the AF2 git repo you download (also it is set here) and the download script asks you to provide a path to download the database (it can be anywhere, but just asks the user to provide a full path instead of a relative path to avoid any mishaps)

absolute path = Full path to a particular file or a folder.