Zinc15 curators notes: Difference between revisions
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create table target_class2 (like target_class); | |||
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[[Category:ZINC15]] | [[Category:ZINC15]] |
Revision as of 00:40, 6 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
- 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 backupscleaning 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);