Revision as of 10:37, 28 April 2020 by Khtang (Talk | contribs)

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Load 2d

1. Extract smiles from sdf done on csh

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

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
sh /nfs/exa/work/khtang/ZINC21_load2d/loadenv_zinc21.sh
zinc-manage -e admin admin catalogs deplete -C 10000 <short_name> list2