Generating extrema set

Written by Jiankun Lyu, 2019/10/12

extrema_set_gen------- working 
                               |
                               |------ ZINC-downloader-3D-smi.database_index
                               | 
                               |------ sub_pattern.smarts

1) Make those directories above.

mkdir extrema_set_gen
cd extrema_set_gen
mkdir working

2) Download databases index from ZINC

2.1) Go to ZINC http://zinc15.docking.org/tranches/home/#

2.2) Choose the tranches you want to do substructure searching

Choose the tranches you want to do substructure searching

2.3) download the databases index file

download the databases index file

2.4) download the file above and save it as ZINC-downloader-2D-smi.database_index, then upload the file to the working directory

3) Run extrema set generation on 5 different charge types