Large-scale SMILES requesting: Difference between revisions
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cd working/db_zincid | cd working/db_zincid | ||
head -(number) ../extract_all.sort.uniq.txt | awk '{print $3" "$22}' > extract_all.top(number).sort.uniq.zincid.energy note: change number in the brackets | head -(number) ../extract_all.sort.uniq.txt | awk '{print $3" "$22}' > extract_all.top(number).sort.uniq.zincid.energy note: change number in the brackets | ||
split -d -l | split -d -a 3 -l 36000 extract_all.top(number).sort.uniq.zincid.energy top(number).zincid_ | ||
cd ../ | |||
3) Create a zincid.sdi file | |||
ls /full/path/to/db_zincid/top(number).zincid_* > zincid.sdi | |||
4) Set up | |||
Revision as of 22:39, 18 September 2017
Written by Jiankun Lyu, 20170918
The hierarchy of the directories:
smiles_requesting/----- working/
| |
| |------ extract_all.sort.uniq.txt file(soft link)
| |
| |------ db_zincid/
|
|
|
------- scripts/ ------ submit.csh
|
|------ setup_converting_fps_files.py
|
|------ combine_smi_and_fp.py
|
|------ check_outputs.csh
This tutorial is for requesting a large number of SMILES for docking results from ZINC server. Usually, the number is larger than 5M ZINC IDs.
1) make directories and copy scripts
mkdir smiles_requesting cd smiles_requesting mkdir working mkdir scripts cd working mkdir db_zincid ln -s /path/to/extract_all.sort.uniq.txt cd ../scripts cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/submit.csh . cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/setup_converting_fps_files.py . cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/combine_smi_and_fp.py cp /mnt/nfs/home/jklyu/zzz.script/large_scale_docking/cluster_analysis/best_first_clustering/converting_fps/check_outputs.csh cd ../
2) Get ZINC ID and energy columns from the extract_all.sort.uniq.txt file
cd working/db_zincid
head -(number) ../extract_all.sort.uniq.txt | awk '{print $3" "$22}' > extract_all.top(number).sort.uniq.zincid.energy note: change number in the brackets
split -d -a 3 -l 36000 extract_all.top(number).sort.uniq.zincid.energy top(number).zincid_
cd ../
3) Create a zincid.sdi file
ls /full/path/to/db_zincid/top(number).zincid_* > zincid.sdi
4) Set up