Difference between revisions of "Generating extrema set"

From DISI
Jump to: navigation, search
(Created page with "Written by Jiankun Lyu, 2019/10/12 extrema_set_gen------- working | |------ ZINC-downloader-3D-smi.database_...")
 
Line 2: Line 2:
  
 
  extrema_set_gen------- working  
 
  extrema_set_gen------- working  
                                |
+
                              |
                                |------ ZINC-downloader-3D-smi.database_index
+
                              |------ ZINC-downloader-3D-minu2.database_index
                                |  
+
                              |  
                                |------ sub_pattern.smarts
+
                              |------ 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.
 
1) Make those directories above.
Line 12: Line 18:
 
  mkdir working
 
  mkdir working
  
2) Download databases index from ZINC
+
2) Download databases index from ZINC with different charge types
  
 
2.1) Go to ZINC http://zinc15.docking.org/tranches/home/#
 
2.1) Go to ZINC http://zinc15.docking.org/tranches/home/#

Revision as of 14:02, 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 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