TalkTorial 1 - T1_ChEMBL - Step 24 about teachopencadd

[dominiquesydow]

Hi @amitindore,

Thank you very much for your interest in TeachOpenCADD!

You are most welcome to use and adapt the material. When doing so please

• cite the TeachOpenCADD publication as well as link the repo and
• grant the same or more permissive license to your material,

as pointed out by @jaimergp (LICENSE).

Also, we would be happy if you and your students would star those repositories they consider useful for their learning activities during your course.

Thanks a lot and good luck with your course!

[jaimergp]

Hi! Can you provide some more information about the error? Is there any traceback you can paste here or just a silent/wrong result? Thanks!

[Farabotti]

Hi, I will try to explain myself:
the really first line would be:
from chembl_webresource_client.new_client import new_client import pandas as pd import math from rdkit.Chem import PandasTools

but when I try to enter it I receive:
`---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
in
2 import pandas as pd
3 import math
----> 4 from rdkit.Chem import PandasTools

ModuleNotFoundError: No module named 'rdkit'`

So I used:
pip install chembl_webresource_client

and it worked but when I tried to enter line 24:
PandasTools.AddMoleculeColumnToFrame(output_df, smilesCol='smiles')

I get:

`---------------------------------------------------------------------------
NameError Traceback (most recent call last)
in
----> 1 PandasTools.AddMoleculeColumnToFrame(output_df, smilesCol='smiles')

NameError: name 'PandasTools' is not defined
`

I hope this is the correct way to write everything.
Thanks a lot!

[jaimergp]

Have you created a conda environment with the dependencies specified in this file? That should take care of all the missing packages. More instructions can be found here.

[Farabotti]

I am actually working on Anaconda 3 on a mac. Shouldn't the CONDA env be already installed?
Thanks and sorry again for the very easy-level questions.

[jaimergp]

Anaconda will provide a default environment with the installation (called base), but you can create more with conda env create! The purpose of having multiple environments is the possibility of isolating dependencies and providing reproducible configurations. In our project, we provide a file environment.yml with the exact dependencies so you can use our notebooks without the kind of problems you are observing.

Let me know if there's anything else I can clarify!

[amitindore]

can i use these material and coding as such for an online course I am designing for pharmacy students ?

[jaimergp]

Hi @amitindore!

Please refer to the LICENSE to check whether the covered scenarios fit your case.

I am also tagging @AndreaVolkamer and @dominiquesydow in case they want to clarify further.

[amitindore]

Thanks a lot. This is nice gestures of yours. Would you be comfortable if we host a webinar of yours for entire pharma fraternity of India, on this topic?

…

On Tue, Jun 2, 2020 at 2:38 PM Dominique Sydow ***@***.***> wrote: Hi @amitindore <https://github.com/amitindore>, Thank you very much for your interest in TeachOpenCADD! You are most welcome to use and adapt the material. When doing so please - cite <https://github.com/volkamerlab/TeachOpenCADD/blob/master/README.md#citation> the TeachOpenCADD publication as well as link the repo and - grant the same or more permissive license to your material, as pointed out by @jaimergp <https://github.com/jaimergp> (LICENSE <https://github.com/volkamerlab/TeachOpenCADD/blob/master/LICENSE>). Also, we would be happy if you and your students would star <https://help.github.com/en/github/getting-started-with-github/saving-repositories-with-stars> those repositories they consider useful for their learning activities during your course. Thanks a lot and good luck with your course! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#15 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APUDGE2GNRIVVNFCCKSQH5DRUS6R7ANCNFSM4KGFLWCQ> .

[dominiquesydow]

Hi @amitindore,

My sincere apologies for my belated reply, it slipped my mind.

We ourselves cannot participate in such a seminar due to time constraints (in case you were also asking this), but you are absolutely welcome to use the TeachOpenCADD material for your seminar, complying with the license as discussed before.

We would be happy to hear about your experience from the course! Good luck!

[amitindore]

No, no. I am requesting you to deliver a seminar as per your convenience on this open tutorial. Meanwhile I would let you know that lot many images and infographics I have taken as such from your TeachopenCADD with full acknowledgement in my free online certificate course on AI and Drug Discovery. Once again I am thankful to you. Thanks.

…

On Thu, Jun 11, 2020 at 2:37 PM Dominique Sydow ***@***.***> wrote: Hi @amitindore <https://github.com/amitindore>, My sincere apologies for my belated reply, it slipped my mind. We ourselves cannot participate in such a seminar due to time constraints (in case you were also asking this), but you are absolutely welcome to use the TeachOpenCADD material for your seminar, complying with the license as discussed before. We would be happy to hear about your experience from the course! Good luck! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#15 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APUDGE6OAG7U5XQEIPLDHFDRWCNGTANCNFSM4KGFLWCQ> .

[AndreaVolkamer]

Hi @amitindore,
as my colleagues already stated, we can not offer such a seminar.
We provide the material here as an open resource meant to be used for self-study or your own class room training.
Happy to hear that the material was useful in your course and thanks for the acknowledgement.

[amitindore]

Okay sir. Thanks.

…

On Fri, 12 Jun 2020, 8:03 pm AndreaVolkamer, ***@***.***> wrote: Hi @amitindore <https://github.com/amitindore>, as my colleagues already stated, we can not offer such a seminar. We provide the material here as an open resource meant to be used for self-study or your own class room training. Happy to hear that the material was useful in your course and thanks for the acknowledgement. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#15 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APUDGE2HW5WYEBDTRHQEOZLRWI4CTANCNFSM4KGFLWCQ> .

[dominiquesydow]

I am closing this issue, since both questions - the initial issue on an installation problem and the second question on licenses - are answered.

@Farabotti, feel free to reopen this issue in case you still have installation problems.
We are currently working on a TeachOpenCADD package, which should make installing the resource much more convenient! We'll keep you posted.

@amitindore, I wish you all the best with your course!

For more license/usage (or any other) questions, please open a separate issue. Thank you!