cannot run example, hung at GetBestRMS in rdkit

[binzhougithub]

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]

Does the script run successfully after updating rdkit?

[binzhougithub]

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]

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.