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 for each charge type

download the databases index file for each charge type

2.4) download the files above and save it as ZINC-downloader-3D-(charge-type).database_index, then upload the file to the working directory. In the working directory, you are supposed to have 5 files with names: ZINC-downloader-3D-minu2.database_index, ZINC-downloader-3D-minu1.database_index, ZINC-downloader-3D-neutral.database_index, ZINC-downloader-3D-plus1.database_index and ZINC-downloader-3D-plus2.database_index.

3) Run extrema set generation on 5 different charge types