Substructure searching

Written by Jiankun Lyu, 2017/09/13

The hierarchy of the directories:

substructure_searching----- working 
              |                |
              |                |------ ZINC-downloader-2D-smi.database_index
              |                | 
              |                |------ sub_pattern.smarts
              |                                                 
              |                                                 
              |
              ------- script ------ submit.csh
                              |
                              |------ submit_sub_search.csh
                              |
                              |------ run_sub_search.csh
                              |
                              |------ search_multi_substructures.py
                              |
                              |------ setup_substructure_searching_files.py

1) Make those directories above.

mkdir substructure_searching
cd substructure_searching
mkdir working
mkdir script

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

fig1

2.3) download the databases index file

fig2

3) Copy scripts from my path.

cd script
cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/setup_substructure_searching_files.py .
cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/submit.csh .
cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/run_sub_search.csh .
cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/submit_sub_search.csh .
cp /mnt/nfs/home/jklyu/zzz.script/analogs_searching/multi_sub_searching/search_multi_substructures.py .