Add the ability to use a toml file as input.

[joanimato]

This PR adds the option to use a .toml file as an input file. The .toml file can store command line options for reproducibility. For example, instead of running

scrub.py "c1cc[nH]c(=O)c1" -o scrubbed.sdf --pH 5 --skip_gen3d

you can create a input.toml file with the following options:

input = "c1cc[nH]c(=O)c1"
out_fname = "scrubbed.sdf"
ph = 5
skip_gen3d = true

and then run scrub.py input.toml. This makes it easier to create reproducible runs when testing the software. The toml input also allows the user to input multiple SMILES strings (similar to a .smi file).

CLI options can still be passed to the script and will override anything that's in the toml file.

[diogomart]

Thanks for this feature, I think it's useful. I have two comments:

1. It looks easy to add bugs if we add options in the future to argparse and forget to update the list of expected keywords in the override function, which is in a different file.
2. If we have a typo in an option in toml there is no error, it fails silently. It should error.

Similar functionality is implemented in meeko's mk_prepare_ligand.py, by setting the defaults of argparse based on the configuration file. This happens here:
https://github.com/forlilab/Meeko/blob/07a38f8bac4aa9eef4ef30aa8e67475b15d517aa/meeko/cli/mk_prepare_ligand.py#L276

and the defaults that are used for options that are passed neither in the config file or through argparse are read directly from the class:
https://github.com/forlilab/Meeko/blob/07a38f8bac4aa9eef4ef30aa8e67475b15d517aa/meeko/cli/mk_prepare_ligand.py#L50

Do you think that would make sense here?

[joanimato]

Sounds good, I will make the modifications.

[joanimato]

@diogomart

The new commit should address your issues. I did not want to make any major modifications just yet. We can decide any major regactors (as well as adding a test suite) later.