Difference between revisions of "Zinc15 curators notes"

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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  
  
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= don't forget =
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psql> cluster each table by primary key (or whatever makes sense)
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psql > vacuum verbose analyze <table> for each fast moving table
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backups
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[[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


  1. 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