Ok, you aren't having problems with the RDKit install or with the RDKit and IPython; you are having problems with spyder + Ipython + the RDKit It would have been very, very helpful if you had mentioned that at the beginning so that I could have avoided wasting our time trying to diagnose rdkit + ipython problems.
I don't use spyder, but the things I told you to look at while trying to diagnose the rdkit+ipython problems may help you here. I won't be able to help any more. -greg On Wed, Apr 14, 2021 at 6:25 PM Andrés Sánchez Ruiz < andressanchezrui...@gmail.com> wrote: > Dear Christos, > > Yes, I activate my enviroment and start spyder from there but I get the > error. > > Thank you for answering. > > Best regards, > > Andrés > > El mié, 14 abr 2021 a las 18:20, Christos Kannas > (<chriskan...@gmail.com>) escribió: > > > > Hi Andres, > > > > Maybe Spyder runs on the base conda environment. > > Do you run Spyder from your activated environment? > > > > Kind regards, > > > > Christos > > > > On Wed, Apr 14, 2021, 17:52 Andrés Sánchez Ruiz < > andressanchezrui...@gmail.com> wrote: > >> > >> Dear Greg, > >> > >> It works! It seems I can call functions of RDKit from this console, > >> however, when I start spyder and try to run them I still get the > >> error. Could it be something related to the spyder interpreter? > >> > >> Best regards, > >> > >> Andrés > >> > >> El mié, 14 abr 2021 a las 17:38, Greg Landrum > >> (<greg.land...@gmail.com>) escribió: > >> > > >> > That looks good so far. > >> > So what happens in that exact same shell if you then start ipython > >> > and do "import rdkit"? > >> > > >> > -greg > >> > > >> > > >> > On Wed, Apr 14, 2021 at 5:33 PM Andrés Sánchez Ruiz < > andressanchezrui...@gmail.com> wrote: > >> >> > >> >> Dear Greg, > >> >> > >> >> After activating my enviroment (foodpains) I wrote the command " > >> >> ipython -c 'import IPython;import > >> >> rdkit;print(IPython.__file__,rdkit.__file__)' ". Right after getting > >> >> the output I wrote: " where ipython ". This is what I get: > >> >> > >> >> (foodpains) C:\Users\Andres Sanchez>ipython -c "import IPython;import > >> >> rdkit;print(IPython.__file__,rdkit.__file__)" > >> >> C:\Anaconda\envs\foodpains\lib\site-packages\IPython\__init__.py > >> >> C:\Anaconda\envs\foodpains\lib\site-packages\rdkit\__init__.py > >> >> > >> >> (foodpains) C:\Users\Andres Sanchez>where ipython > >> >> C:\Anaconda\envs\foodpains\Scripts\ipython.exe > >> >> C:\Anaconda\Scripts\ipython.exe > >> >> > >> >> Best regards, > >> >> > >> >> Andrés > >> >> > >> >> El mié, 14 abr 2021 a las 17:06, Greg Landrum > >> >> (<greg.land...@gmail.com>) escribió: > >> >> > > >> >> > That looks good. Please send the output of: > >> >> > ipython -c 'import IPython;import > rdkit;print(IPython.__file__,rdkit.__file__)' > >> >> > > >> >> > and we also need to figure out exactly which version of ipython > you are running. > >> >> > > >> >> > If you are running these commands in the command shell, that's > >> >> > where ipython > >> >> > > >> >> > in powershell: > >> >> > gcm ipython > >> >> > > >> >> > if you're using a bash shell: > >> >> > which ipython > >> >> > > >> >> > Please run the ipython -c and which/where/gcm command directly > after each other and paste in both the command you executed and its output. > >> >> > > >> >> > -greg > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > On Wed, Apr 14, 2021 at 4:46 PM Andrés Sánchez Ruiz < > andressanchezrui...@gmail.com> wrote: > >> >> >> > >> >> >> Dear Greg, > >> >> >> > >> >> >> This is what I see after activating my enviroment (foodpains) and > >> >> >> introducing your command: > >> >> >> > >> >> >> C:\Anaconda\envs\foodpains\lib\site-packages\IPython\__init__.py > >> >> >> C:\Anaconda\envs\foodpains\lib\site-packages\rdkit\__init__.py > >> >> >> > >> >> >> Best regards, > >> >> >> > >> >> >> Andrés > >> >> >> > >> >> >> El mié, 14 abr 2021 a las 15:42, Greg Landrum > >> >> >> (<greg.land...@gmail.com>) escribió: > >> >> >> > > >> >> >> > What do you see when you execute this quick test to ensure that > ipython and the rdkit are both really installed? > >> >> >> > > >> >> >> > python -c 'import IPython;import > rdkit;print(IPython.__file__,rdkit.__file__)' > >> >> >> > > >> >> >> > -greg > >> >> >> > > >> >> >> > On Wed, Apr 14, 2021 at 2:58 PM Andrés Sánchez Ruiz < > andressanchezrui...@gmail.com> wrote: > >> >> >> >> > >> >> >> >> Hello, > >> >> >> >> > >> >> >> >> I have not been able to solve the issue yet after installing > ipython > >> >> >> >> in the same enviroment in which I have RDKIT. > >> >> >> >> > >> >> >> >> ipython 7.22.0 py39hd4e2768_0 > >> >> >> >> ipython_genutils 0.2.0 pyhd3eb1b0_1 > >> >> >> >> . > >> >> >> >> . > >> >> >> >> . > >> >> >> >> rdkit 2021.03.1 py39hfadf033_0 > conda-forge > >> >> >> >> > >> >> >> >> From this enviroment I can call pandas (for example) but not > RDKIT. > >> >> >> >> What is still not working? > >> >> >> >> > >> >> >> >> Best regards, > >> >> >> >> > >> >> >> >> Andrés > >> >> >> >> > >> >> >> >> > >> >> >> >> _______________________________________________ > >> >> >> >> Rdkit-discuss mailing list > >> >> >> >> Rdkit-discuss@lists.sourceforge.net > >> >> >> >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >> > >> > >> _______________________________________________ > >> Rdkit-discuss mailing list > >> Rdkit-discuss@lists.sourceforge.net > >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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