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mattragoza / LiGAN

Deep generative models of 3D grids for structure-based drug discovery
GNU General Public License v2.0
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cannot run example, hung at GetBestRMS in rdkit #42

Open binzhougithub opened 2 years ago

binzhougithub commented 2 years ago

Thank you for this great job on liGAN. I installed liGAN to run the examples, 'python3 generate.py config/generate.config', it hung at the 27th(28th?) example, i.e. 1 0 1.36521 PA2GA_HUMAN_21_144_0/5g3n_A_rec.pdb PA2GA_HUMAN_21_144_0/5g3n_A_rec_1poe_gel_lig_tt_docked_0.sdf.gz #-6.74282

I had to specify the maxMatches in GetBestRMS to avoid hanging up. I installed the latest rdkit('2022.03.2'), not sure if it matters.

Thanks

mattragoza commented 2 years ago

Does the script run successfully after updating rdkit?

binzhougithub commented 2 years ago

thank you for your reply. the issue stays, actually I tested a couple of rdkit version. in other thread, https://github.com/mattragoza/liGAN/issues/39, I was told to try rdkit=2020.09.5. I don't remember if I tried this version, and I do remember I was not able to use conda to install rdkit, just like what issue #39 states.

mattragoza commented 2 years ago

Ok, I have not yet nailed down the exact version(s) of rdkit that cause issues (I am using 2022.03.4), but I know that conda often fails to exactly resolve the dependencies which is why I recommend using mamba instead. Also make sure that you do not use pip/conda molgrid, but build molgrid from source.

I have just updated the README.md with detailed installation instructions.