mattragoza/LiGAN

cannot run example, hung at GetBestRMS in rdkit

binzhougithub opened this issue · 3 comments

binzhougithub commented

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

Does the script run successfully after updating rdkit?

binzhougithub commented

thank you for your reply. the issue stays, actually I tested a couple of rdkit version. in other thread, #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

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.