Difference between revisions of "Zinc15 curators notes"

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create table target_class2 (like target_class);
  
 
[[Category:Curator]]
 
[[Category:Curator]]
 
[[Category:ZINC15]]
 
[[Category:ZINC15]]

Revision as of 17:40, 5 February 2015

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

cleaning up

create temporary table blah  (id integer);
\copy blah from 'ji4.txt'
begin;

\copy (select * from retired where replacement_fk in (select id from blah) ) to 'ji4.retired.save'
delete from substance where sub_id in (select id from blah) ; 
select * from catalog_item where sub_id_fk in (select id from blah);
commit;


create table target_class2 (like target_class);