ImportError: (SOLVED)

Computer-Aided Drug Design at the Durrant Lab Forums Gypsum-DL ImportError: (SOLVED)

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    • #16310
      Iñigo Marcos-Alcalde


      I’ve just downloaded Gypsum-DL to check it out, but following the environment setup provided in the file (conda install -c rdkit rdkit numpy scipy mpi4py) failed to work in this particular machine environment (Linux Mint 20 Ulyana without libboost-dev installed) with:

      ImportError: cannot open shared object file: No such file or directory

      Exception: You need to install rdkit and its dependencies.

      I am guessing that rdkit might dependency on the boost libraries cannot be solved in conda using the rdkit channel. I suppose that this could be solved by installing the libboost-dev package with apt-get, but that would defeat the purpose of creating an "standalone" conda environment capable of running Gypsum-DL regardless of Linux distro.

      As indicated in the rdkit documentation, it turns out that rdkit can be installed using the conda-forge channel as well. Doing so, allows conda to satisfy the boost library dependency internally and creates an environment that is capable of running Gypsum-DL out of the box.

      In case this is useful to anyone, the "recipe" to create and test such environment would be:

      conda create -c conda-forge –name gypsum_dl_env rdkit numpy scipy mpi4py -y
      conda activate gypsum_dl_env

      python ./ –test

      Thank you very much for all the hard work dedicated to create such a useful tool!

    • #16375
      Iñigo Marcos-Alcalde

      Sorry for the double post. I’ve just seen that the format of my previous post has some weird formatting with varying font sizes, bold letters and pairs of short hyphens converted to long dashes. To be honest, I am not entirely sure about how I did this, it was supposed to be just plain text.

      Anyway, I am pointing this out just because long dashes in the commands really are just two hyphens. Otherwise, those lines won’t work.

    • #20388
      Jacob Durrant

      Hi Iñigo! I meant to thank you for your very helpful tip. I updated the Gypsum-DL file to mention your suggestion:

      Take care.

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