Constant openbabel/pybel problem during installation

[iwonaa.go...@gmail.com]

Hi,

I have all the requirements installed, but I can't run oddt_cli. I have installed open babel, which runs from terminal as obabel, lastest 3.0.0 version. 

I get this error message:

I will be grateful for any hints how to solve this problem.

Kind regards,

Iwona

[Maciek Wójcikowski]

Dear Iwona,

It seems that Openbabel is not available in Python modules. How did you install it? On the screenshot I can see that you are most probably using conda environment, while ODDT is installed in user folders instead of the conda environment. Let me know your setup first, figuring it will probably reveal the problem.

Can you also provide the locations of obabel and python binaries? `which obabel` and `which python` bash commands.

Best,

Maciek

----
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Maciek Wójcikowski
mac...@wojcikowski.pl

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[iwonaa.go...@gmail.com]

Dear Maciek,

I managed to run oddt_cli, while installed by pip install -U --no-deps oddt

Earlier I had all the latest versions of dependencies and obabel, pybel installed with pip3 and conda. 

I had also build obabel and it runned from command line properly.

(tf_gpu) ➜  ~ which obabel

/home/iwona/anaconda3/envs/tf_gpu/bin/obabel

(tf_gpu) ➜  ~ which python 

/home/iwona/anaconda3/envs/tf_gpu/bin/python

Thank You for such a quick reply, I will have in mind env differencies, while future installations.

Kind regards,

Iwona

On Friday, December 27, 2019 at 9:44:14 PM UTC+1, Maciek Wójcikowski wrote:

Dear Iwona,

It seems that Openbabel is not available in Python modules. How did you install it? On the screenshot I can see that you are most probably using conda environment, while ODDT is installed in user folders instead of the conda environment. Let me know your setup first, figuring it will probably reveal the problem.

Can you also provide the locations of obabel and python binaries? `which obabel` and `which python` bash commands.

Best,

Maciek

----
Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

pt., 27 gru 2019 o 13:55 <iwonaa.g...@gmail.com> napisał(a):

Hi,

I have all the requirements installed, but I can't run oddt_cli. I have installed open babel, which runs from terminal as obabel, lastest 3.0.0 version. 

I get this error message:

I will be grateful for any hints how to solve this problem.

Kind regards,

Iwona

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To unsubscribe from this group and stop receiving emails from it, send an email to od...@googlegroups.com.

[Maciek Wójcikowski]

I'm glad it worked for you. If you run into problems you also need to check if oddt_cli is in fact in the same environment (`which oddt_cli`). I always recommend installing all dependencies using conda, but your solution is also valid.

To install oddt via conda run:

conda install -c oddt oddt

This unfortunately does not install toolkits, that you can install from conda forge

conda install -c conda-forge rdkit openbabel

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Maciek Wójcikowski
mac...@wojcikowski.pl

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[Bruna Katiele de Paula Sousa]

Hi everyone 

Im having the same problem, but I tried to install using  pip install -U --no-deps oddt  and didnt worked.

I will be grateful for any hints how to solve this problem.

Kind regards,

Bruna

[Maciek Wójcikowski]

Hi Bruna,

While it is fine to install oddt using PIP, you cannot do it for the OB or RDKit. You have to install either of them using conda or system package manager.

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Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

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[Bruna Katiele de Paula Sousa]

Many thanks Maciek! I tried at ubuntu and worked hehe 

Thanks in advance!