Tutorials on readthedocs are contradictory to base installation instructions and ligand preparation basic use instructions

[bmp192529]

Hello,

I realize it may have been an oversight over the course of version changes, but the "Ligand preparation" sidebar instructions and "Getting started -> Installation" pages are contradicted by the "Tutorials -> Basic Docking" section of the readthedocs site. For instance, Molscrub is not mentioned on any of the pages other than the "Basic Docking" tutorial. Is molscrub required for meeko to function? Additionally, while it is implied in the "Basic ligand preparation" section that the pdbqt strings can be written to a file, how that is actually done is not explained. Is it as simple as writing the string as text in the .pdbqt file? Thank you for all the work you have done with this package.

Regards,
bmp192529

[rwxayheee]

Hi @bmp192529

This is how I view the planning of the current doc:

I realize it may have been an oversight over the course of version changes, but the "Ligand preparation" sidebar instructions and "Getting started -> Installation" pages are contradicted by the "Tutorials -> Basic Docking" section of the readthedocs site.

Basic docking was under tutorials, like materials for self-guided learning.
While the Ligand preparation & Receptor preparation are discussions over functionalities for the specific topics.
You will realize that Meeko is a library for molecule preparation, and there are always more than one ways to do a specific task. The tutorial shows you one basic docking pipeline and how Meeko can be integrated, but you're welcome to create your own.

For instance, Molscrub is not mentioned on any of the pages other than the "Basic Docking" tutorial. Is molscrub required for meeko to function?

No, but we have it as part of our sample docking pipeline. See here: https://meeko.readthedocs.io/en/release-doc/colab_examples.html

Additionally, while it is implied in the "Basic ligand preparation" section that the pdbqt strings can be written to a file, how that is actually done is not explained. Is it as simple as writing the string as text in the .pdbqt file?

Yes exactly. It would be great to have more examples! And if you would like to contribute please let us know.

Let us know if you have any further questions, thoughts about anything. Thanks!

[bmp192529]

The diagram "General Workflow of Docking Calculations" on the colab examples page made everything so much more clear and less fragmented for me, thank you! Perhaps you could put that diagram in a more central page on readthedocs, to explain the overall process more easily? Placing it on the overview pages for ligand preparation and receptor preparation might make the overall docking procedure much more clear to new users. Thank you all again for your work with this project.

[bmp192529]

One additional question:
When writing pdbqt strings to a file from the list generated by PDBQTWriterLegacy.write_string(mol), I have been skipping the last list item, which is usually the word "True" with nothing before or after. This would have been the line after the "TORSDOF" line towards the bottom of the file. Is that value important for the validity of the pdbqt file or instead a status/result report from the function?

[rwxayheee]

Hi @bmp192529
True (or False) indicates the status of the function. It's like a mini return code you can check for individual PDBQT writing attempt, when you're processing a large batch of the ligands. It doesn't need to be written to the PDBQT file though.