Zinc15 curators notes: Difference between revisions
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(Created page with "Here are the curator's notes for ZINC 15. = protomer (re)build = as xyz: example 1. by catalog python ~/code/ZINC/contrib/fetch.py -t substance -f 'smiles,zinc_id' 'catalog...") |
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step3.csh | step3.csh | ||
= | = don't forget = | ||
psql> cluster each table by primary key (or whatever makes sense) | |||
psql > vacuum verbose analyze <table> for each fast moving table | |||
backups | |||
[[Category:Curator]] | [[Category:Curator]] | ||
[[Category:ZINC15]] | [[Category:ZINC15]] |
Revision as of 20:33, 10 November 2014
Here are the curator's notes for ZINC 15.
protomer (re)build
as xyz: example 1. by catalog
python ~/code/ZINC/contrib/fetch.py -t substance -f 'smiles,zinc_id' 'catalog.short_name = sial' | split -l 1000
example 2. by physical property tranche
python ~/code/ZINC/contrib/fetch.py -t substance -f 'smiles,zinc_id' 'structure.mwt < 200' 'protomer.prot_id is null' | split -a 4 -l 1000
- ls -l | wc -l (340)
qsub -t 1-340 ~ts/Code/DOCK/ligand/generate/example-protomer-wrapper.sh ~/work/protomer
delta incremental load of smiles from zinc8
as jji. based on exported smiles,sub_id from zinc8 since last update.
python ~/code/ZINC/zinc/load/create_substances.py xaa.ism --progress
database export by property tranche
as xyz per ~/zinc14/byproperty/
step1.csh step2.csh step3.csh
don't forget
psql> cluster each table by primary key (or whatever makes sense)
psql > vacuum verbose analyze
for each fast moving table backups