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How to add RDKit to project in PyCharm?

So, I am trying to add RDKit to my project in PyCharm. I have found that if you are using interpreter /usr/bin/python2.7 PyCharm will try to install stuff using the pip. While, RDKit requires conda. I have tried to change the interpreter to conda, but RDKit is either not on the list or it can't open the URL with the repo. Does anyone know how to fix that?

By the way, is it possible while keeping the interpreter /usr/bin/python2.7 to make it use anything else (not pip), while installing stuff?

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Anna-Lischen Avatar asked Jan 20 '16 11:01

Anna-Lischen


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How do I get an RDKit in Python?

Linux, Windows, and macOS RDKit platform wheels are available at the rdkit PyPi repository for all major Python versions. You can install RDKit using pip. Build information and details can be found at the https://github.com/kuelumbus/rdkit-pypi GitHub page.

What is RDKit package?

RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. BSD license - a business friendly license for open source. Core data structures and algorithms in C++


1 Answers

I have finally found how to do that and it's not difficult at all:

  1. Install conda;
  2. Install RDKit, following these instructions
  3. Go to the preferences in PyCharm either like this:

enter image description here

or like this (you need a wrench):

enter image description here

  1. In the project interpreter select: ~/anaconda/envs/my-rdkit-env/bin/python

  2. Make sure you add or update the corresponding python paths to PATH, otherwise it wouldn't work.

TESTS:

  1. Tried to install fiona - success, so there's no impact on the installation;
  2. Tried the simple code: print('HELLO WORLD!') - worked
  3. Tried rdkit code

        from rdkit import Chem
    
    
        m = Chem.MolFromSmiles('Cc1ccccc1')
    
        print(m)
    

worked, the log: <rdkit.Chem.rdchem.Mol object at 0x101125080>

like image 87
Anna-Lischen Avatar answered Sep 21 '22 17:09

Anna-Lischen