LoadingZINC21: Difference between revisions
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ZINC20 loading procedure | |||
TBD | |||
=== Load 2d === | === Load 2d === | ||
''' Scripts mentioned below are saved in /nfs/home/khtang/exa/ZINC21_load2d/zinc21_load_scripts ''' | |||
export SCRIPT='/nfs/home/khtang/exa/ZINC21_load2d/zinc21_load_scripts' | |||
source $SCRIPT/loadenv_zinc21.sh | |||
1a. Extract smiles from sdf | |||
csh $SCRIPT/1a_smiles_extraction.csh <sdf> <id_field_name> | |||
(Optional) 1b. Price filter | |||
csh $SCRIPT/1b_filter.csh <csv> <smallest pack size price field name> <shortname> #shortname shouldn't be contain any price suffix ie chbr, chbr-v | |||
2. Submit job | |||
mkdir <short_name> | |||
mv <smiles file> <short_name>/<short_name>.ism | |||
cd <short_name> | |||
sh /nfs/exa/work/khtang/ZINC21_load2d/zinc21_load_scripts/batch_zinc21 <short_name>.ism | |||
3. Process outputs | |||
csh $SCRIPT/3_process_outputs.csh | |||
4. Depletion | |||
source $SCRIPT/loadenv_zinc21.sh | |||
csh $SCRIPT/4_depletion.csh <full/increment> | |||
=== Load 2d (OLD) === | |||
1. Extract smiles from sdf done on csh | 1. Extract smiles from sdf done on csh | ||
source /nfs/exa/work/khtang/ZINC21_load2d/loadenv_zinc21.sh | |||
source ~jji/cshrc.save | source ~jji/cshrc.save | ||
pc2unix <sdf> | pc2unix <sdf> | ||
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2. Submit job | 2. Submit job | ||
source /nfs/exa/work/khtang/ZINC21_load2d/loadenv_zinc21.sh | |||
mkdir <short_name> | mkdir <short_name> | ||
mv <smiles file> <short_name>/<short_name>.ism | mv <smiles file> <short_name>/<short_name>.ism | ||
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#source ZINC21 envs **must run on bash shell** | #source ZINC21 envs **must run on bash shell** | ||
source /nfs/exa/work/khtang/ZINC21_load2d/loadenv_zinc21.sh | |||
zinc-manage -e admin admin catalogs deplete -C 10000 <short_name> list2 | zinc-manage -e admin admin catalogs deplete -C 10000 <short_name> list2 | ||
csh /nfs/ex9/work/khtang/move.csh | csh /nfs/ex9/work/khtang/move.csh |
Latest revision as of 19:10, 22 March 2024
ZINC20 loading procedure
TBD
Load 2d
Scripts mentioned below are saved in /nfs/home/khtang/exa/ZINC21_load2d/zinc21_load_scripts
export SCRIPT='/nfs/home/khtang/exa/ZINC21_load2d/zinc21_load_scripts' source $SCRIPT/loadenv_zinc21.sh
1a. Extract smiles from sdf
csh $SCRIPT/1a_smiles_extraction.csh <sdf> <id_field_name>
(Optional) 1b. Price filter
csh $SCRIPT/1b_filter.csh <csv> <smallest pack size price field name> <shortname> #shortname shouldn't be contain any price suffix ie chbr, chbr-v
2. Submit job
mkdir <short_name> mv <smiles file> <short_name>/<short_name>.ism cd <short_name> sh /nfs/exa/work/khtang/ZINC21_load2d/zinc21_load_scripts/batch_zinc21 <short_name>.ism
3. Process outputs
csh $SCRIPT/3_process_outputs.csh
4. Depletion
source $SCRIPT/loadenv_zinc21.sh csh $SCRIPT/4_depletion.csh <full/increment>
Load 2d (OLD)
1. Extract smiles from sdf done on csh
source /nfs/exa/work/khtang/ZINC21_load2d/loadenv_zinc21.sh source ~jji/cshrc.save pc2unix <sdf> source ~teague/virtualenvs/zinc/env.csh zincload-sdf --id-field <id_field> --name <catalog_name> <sdf>
2. Submit job
source /nfs/exa/work/khtang/ZINC21_load2d/loadenv_zinc21.sh mkdir <short_name> mv <smiles file> <short_name>/<short_name>.ism cd <short_name> sh /nfs/exa/work/khtang/ZINC21_load2d <short_name>.ism
3. Depletion
find outputs -name '51-*-ids.tsv' | xargs sort -n -u > list find outputs -name '*.filtered' | xargs cat > filtered find outputs -name '14-neutralize.log' |xargs cat | grep -v processed > errors sort -n list > list2 wc -l list filtered errors list2 //check if most of molecules are successfully loaded on ZINC
#source ZINC21 envs **must run on bash shell** source /nfs/exa/work/khtang/ZINC21_load2d/loadenv_zinc21.sh zinc-manage -e admin admin catalogs deplete -C 10000 <short_name> list2 csh /nfs/ex9/work/khtang/move.csh