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I want to use RDKit with a python script in PyMOL. RDKit requires a conda environment, so I think I need to be able to specify that the instance of python that I want to use would be in that environment, instead of the default for PyMOL, so that I can run it through PyMOL. The script I made is working for me through PyCharm when I test it, by using the RDkit environment "rdkit-env" as my python interpreter, with all of the additional modules I need installed there as well.

I would like to run it through PyMOL so I can add some PyMOL specific functionality as well. I've tried using shebang to specify the RDkit environment that I made, but that does not seem to be working for me with Windows.

Could someone please help me figure out what other approach might work for this? I'm new to this area, so I would appreciate any insights. Thank you!

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So it is really hard to make a given python instance run a library from a different instance. It is not just one dist-packages library folder, but multiple that you would need to link, and all that assuming they use the same version of python. So the best bet is to install a new instance of pymol the python module.

The module can be installed in a python that uses conda with

conda install -c schrodinger pymol

This is the incentive version of PyMOL 2 and does not require a licence. You installed rdkit, so I am assuming you used conda as conda install -c rdkit rdkit. But just in case you went through the pain of compiling rdkit for a given python instance without conda and want the same for PyMOL. There are guides of instructions required to compile open source. Such as https://pymolwiki.org/index.php/Windows_Install. On a barebone OS like a Pi's Raspsian, I had to do a lot more than claimed say sudo apt-get install python3-dev libglm-dev freeglut3-dev libglew-dev libpng12-dev libfreetype6-dev build-essential libxml++3.6-dev and link a few things manually. So just like for rdkit, conda make life a breeze.

PS. RDKit and PyMOL? Add PyRosetta and you just my favourite modules!

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