T003: mols2grid example added

[e-mayo]

Description

A simple introductory example of mols2grid.display function was added in the T003_compound_unwanted_substructures.

Todos

Notable points that this PR has either accomplished or will accomplish.

• Add an example of mols2grid

Reviewers:

• Download and checkout this branch locally (installation) and run notebook to check if everything runs as expected
• Check rendering on our website locally (instructions)
• Check if CI runs for all OS (Linux/Windows/MacOS) and Python versions (check if GitHub Action fails are connected to T003, if not ignore). > CI passes for T003
• Spellcheck and code review
• Do we need to update the Table of Content, i.e. were any new sections added in the Theory or Practical part?

Questions

• Question1

Status

• Ready to go

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[dominiquesydow]

Hi @e-mayo,

Thanks a lot for this addition to T003! 🚀
Introducing mols2grid here is super useful I think :)

I added a couple of TODOs for the reviewers to the PR description.
@yonghui-cc, would you like to take over some of the TODOs? Let me know if you have any questions!

We have a passing CI for T003 🥳

[yonghui-cc]

Hi @e-mayo,

Thanks a lot for this addition to T003! 🚀 Introducing mols2grid here is super useful I think :)

I added a couple of TODOs for the reviewers to the PR description. @yonghui-cc, would you like to take over some of the TODOs? Let me know if you have any questions!

We have a passing CI for T003 🥳

Hi, @dominiquesydow,
I'm glad to review the nice notebook, but I have a problem here:
I try to run the 'import mols2grid' code but failed, so I realized there is something wrong with my environment. Then I create the env by installation, but it still failed in the Pip subprocess.

'''

'''

It's on macOS and I will try to find what's wrong here with the environment.

[dominiquesydow]

Hi @yonghui-cc,

Thanks for looking into this! Can you please check if you can install this via conda?
conda install -c conda-forge mols2grid

Or you reinstall the full environment based on this file:
https://github.com/e-mayo/teachopencadd/blob/add-mols2grid/devtools/test_env.yml

Let me know if this works for you, thank you!

[yonghui-cc]

Hi, @dominiquesydow,

• For the install problem: it worked when I install mols2grid independently. But it still failed for the full environment install:

mamba env create -f https://raw.githubusercontent.com/volkamerlab/TeachOpenCADD/master/devtools/test_env.yml
Error message:

Although the error happened, the teachopencadd env could still be created without mols2grid package, maybe also others we don't know.

• For the code running: the notebook is great and worked well on my machine.

• For the task rendering on the website locally: It failed to run make html
  Error message:

this may help for the first error: https://www.mail-archive.com/qemu-devel@nongnu.org/msg894683.html
For the second error, I try to fix the missing module, but there are more and more missing, I guess it's the sphinx version problem. Which version of sphinx on your machine?

[e-mayo]

Hello, I will try to take a look at it this week. Best, Eduardo

…

On Thu, Nov 17, 2022 at 11:30 PM yonghui-cc ***@***.***> wrote: Hi, @dominiquesydow <https://github.com/dominiquesydow>, it worked when I install mols2grid independently. But it still failed for the full environment install: mamba env create -f https://raw.githubusercontent.com/volkamerlab/TeachOpenCADD/master/devtools/test_env.yml Error message: [image: image] <https://user-images.githubusercontent.com/26645421/202563202-656413c0-2bd2-4a4b-b7f1-75c44619ddbc.png> — Reply to this email directly, view it on GitHub <#279 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHYQADDEGZG2KKGKRLJLJLLWI2PV5ANCNFSM6AAAAAARH5MIEI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[yonghui-cc]

Eduardo

Hi, @e-mayo, I tried the environment installment command line on Unbuntu OS, but the same problem happen.

So, we know that it's not an OS problem.

[e-mayo]

Hello!!

I have generated a new yml file. This works on my computer Windows [Version 10.0.22621.819]
Please test it under your systems and let me know if it works now.

test_env.txt

[dominiquesydow]

Hi @e-mayo and @yonghui-cc,
Thanks a lot!
The environment file works well for me (macOS) as well, the CI is picking up mols2grid without problems for all systems as well.

@yonghui-cc, can you please try installing the environment from a local yml file instead of from the GitHub URL (it cannot install the teachopencadd package because you do not have it downloaded I think) -- i.e. clone the repo first, cd into the teachopencadd folder and then do mamba env create -f devtools/test_env.yml -n toc-mols2grid.

@e-mayo I finally added the code review for the new pieces in the notebook, please let me know if you find this reasonable, thanks!

EDIT: Website rendering works nicely :)

[dominiquesydow]

Please remove empty line before mols2grid as it is part of the third party import block (see the respective PEP).

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[dominiquesydow]

I suggest to move the whole mols2grid topic to the end of the Substructure statistics section and look at the three most frequent substructures:

• Michael-acceptor C=!@CC=[O,S]
• Aliphatic-long-chain  [R0&D2][R0&D2][R0&D2][R0&D2]
• Oxygen-nitrogen-single-bond [OR0,NR0][OR0,NR0]

Some minor text edits:

Dataframes > DataFrame

unwanted substructures, let's have a look

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[dominiquesydow]

Could you please run black-nb over this notebook (should streamline the formatting with the rest of the notebooks):

black-nb -l 99 teachopencadd/talktorials/T003_compound_unwanted_substructures/talktorial.ipynb

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[e-mayo]

I will be able to have a look at it only after the Friday. So expect some update by next week.