RDKit installation problem on macOS Big Sur about homebrew-rdkit HOT 7 CLOSED

I guess you are not using the python interpreter for which rdkit was installed.
Now comes the next question: how to find out which one it is...
Brute force answer: find all the python3 executables on your computer, try import rdkit in them one by one...

from homebrew-rdkit.

The script roundtrip_test.py uses /usr/local/bin/python3.9. You can try this one first.

from homebrew-rdkit.

Short update: FYI, I installed anaconda3 (python 3.7, download of actual version) and was able to run rdkit including additional tools (like Mol2Vec) succesfully. Due to the limitations I do not like (and normally do not use) conda, I will try to figure out which python version is working with rdkit as recommended. However, the setting of DYLD_LIBRARY_PATH is obviously wrong, could you please give an update here which directory should be referred to? Or is the installation description not longer valid? (Normally I do not use also PYTHONHOME and PYTHONPATH, I only set those variables due to the installation guidance). Thanks in advance!

from homebrew-rdkit.

On the Mac where I have rdkit installed and working via brew:
DYLD_LIBRARY_PATH is empty.
PYTHONHOME and PYTHONPATH are also empty.
The python interpreter is this one: /usr/local/bin/python3.9

PS: I really do not like conda (too slow, too stpuid at updating an existing environment, only
working when creating a new environment from scratch, polluting many environment variables)

from homebrew-rdkit.

You can try this to force brew installing rdkit (brew is also a rather dumb package manager, with bad reproducibility of installs):

# backup you installed packages list
brew list --formula > my_brew_packages.txt
# uninstall all of them
brew uninstall --force $(brew list --formula)
# try installing rdkit from fresh
brew install rdkit --with-python3 --with-inchi

from homebrew-rdkit.

FTR on a recent Ubuntu:

sudo apt install python3-rdkit

And the job would be done, system-wide, for a fraction of the time... :)

from homebrew-rdkit.

Ok thanks I followed your brew deinstallation suggestion and afterwards I reinstalled Python 3.9.1 and now it works. I need to get rid of conda and clean the environment variables (I assume the problem occurs when pyenv is installed?). Again thanks for your great support )

from homebrew-rdkit.