pdbfixer
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openmm
pypi version
Will there ever be a pypi package for the module ? If you are planning for that i can offer some help! Thanks!
I hope so! We first need PyPI packages for OpenMM, which PDBFixer depends on. We're investigating that right now: https://github.com/openmm/openmm/issues/3796. If you want to help, that would be fantastic.
Hi, I want to do a quick follow up on this issue.
Why don't we make PDBFixer a PyPI package alone? The main OpenMM module seems tricky because of the cuda stuff, but you could assume people have already installed the OpenMM before they need PDBFixer? Just save people from downloading the whole repo before installation.
What would be the use case for that? If you've already installed OpenMM with conda, what's the benefit of installing PDBFixer with pip instead of conda?
I am not sure if I take it correctly. Do you mean PDBFixer itself can be installed by conda? I didn't see that in the installation tutorials
One common case for me is that, I have installed OpenMM according to the official document:
conda install -c conda-forge openmm cudatoolkit=xx.x
Then I realize that I also need PDBfixer to preprocess PDB files.
It would be great if I could simply do pip install PDBFixer instead of git clone the whole repo and run pip install .
Correct. This will install it, including all dependencies.
conda install -c conda-forge pdbfixer
We should add that to the README.
Got it! That makes much more sense now. Yes, should add this to the README. Thank you for the clarification.
If pdbfixer were on pypi it would be convenient to install it along with dependencies via poetry. Poetry can also handle dependencies like conda, but unlike it it shows better performance
