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

Choose the tranches you want to do substructure searching

2.3) download the databases index file

download the databases index file

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 .