Automation in Bept (auto)

Bept provides a way to automate your commands and save them for future references. This is done through the auto command in Bept. The auto command has the following features.

1. Run one PDB2PQR and APBS at a time

Say you just want to run your given pdb2pqr or apbs command, you can run the following command to execute and save the command to history.

# For pdb2pqr
bept auto -p protein.pdb

# For apbs
bept auto -a apbs_input.in

You can provide the --interactive | -i flag to run the command interactively.

2. Run series of PDB2PQR and APBS commands

Say you want to run a series of pdb2pqr and apbs commands, you can make a text file containing the commands and run the following command to execute and save the commands to history, using --file-load or -f flag. Here is example -

bept auto -f commands.txt

The format of the commands.txt file should be as follows:

  • Each line should be in itself a command executable

  • The file paths should be correct w.r.t the current working directory

[!Tip] We have given an example of the commands.txt file at the bottom of this page.

You can interactively run each command one by one by adding the interactive flag -i to the command.

bept auto -f commands.txt -i

If you want to say halt the execution of the commands at any command specified, you can add :? in between any command in the file, the execution will go into interactive mode just for that command. Example - apbs :? protein.in.

Note that the :? token is meant to be edited. It is not a command line flag in itself. However for pdb2pqr command, if you run pdb2pqr --your-flags protein.pdb :?, it will still work, since pdb2pqr will interpret it as the output path for pqr file.

3. Save the commands to history

All the commands will be saved to history and can be viewed using the history command. All the apbs_input files generated will be saved in the cache directory. See history docs for more information.

Example for commands.txt file.

This file should be a simple .txt or non executable file. Here is an example containing various examples for you to run.

# This is an example of a simple pdb2pqr command. This line is commented out.
pdb2pqr --ff=AMBER --apbs-input=2gmo.in --keep-chain --whitespace --drop-water --titration-state-method=propka --with-ph=7 2gmo.pdb 2gmo.pqr

# Above is an empty line, which is allowed.
apbs 2gmo.in
# To halt the command in between automation, you can add :? in between the command. Please edit `:?` else it will be considered as a part of the command.
pdb2pqr --ff=AMBER --apbs-input=7y6i.in --keep-chain --whitespace 7y6i.pdb 7y6i.pqr :?
apbs 7y6i.in

Important Note:

  1. You can have an empty line in between the commands.

  2. To write commands in the file, you can use the # symbol in the beginning of the line.

If you have any other issues, feel free to raise an issue on the repository.