Generating extrema set

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Written by Jiankun Lyu, 2019/10/12

extrema_set_gen------- working 
                              |
                              |------ ZINC-downloader-3D-minu2.database_index
                              | 
                              |------ ZINC-downloader-3D-minu1.database_index
                              | 
                              |------ ZINC-downloader-3D-neutral.database_index
                              | 
                              |------ ZINC-downloader-3D-plus1.database_index
                              | 
                              |------ ZINC-downloader-3D-plus2.database_index

1) Make those directories above.

mkdir extrema_set_gen
cd extrema_set_gen
mkdir working

2) Download databases index from ZINC with different charge types

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

2.2) Choose the tranches you want to generate extrema set for testing the charge preference. The goldilocks set has been chosen here as an example.

Choose the -2 charged tranches for your extrema set
Choose the -1 charged tranches for your extrema set
Choose the neutral tranches for your extrema set
Choose the +1 charged tranches for your extrema set
Choose the +2 charged tranches for your extrema set

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