Difference between revisions of "Generating extrema set"

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2.1) Go to ZINC http://zinc15.docking.org/tranches/home/#
 
2.1) Go to ZINC http://zinc15.docking.org/tranches/home/#
  
2.2) Choose the tranches you want to do substructure searching
+
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.
[[File:Minus2.png.png|thumb|center|500px|Choose the tranches you want to generate extrema set for testing the charge preference]]
+
[[File:Minus2.png|thumb|center|500px|Choose the -2 charged tranches for your extrema set]]
 +
[[File:Minus1.png|thumb|center|500px|Choose the -1 charged tranches for your extrema set]]
 +
[[File:0.png|thumb|center|500px|Choose the neutral tranches for your extrema set]]
  
 
2.3) download the databases index file
 
2.3) download the databases index file

Revision as of 13:12, 12 October 2019

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

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