Zinc15 curators notes - Revision history

Frodo: asdf

2016-09-06T18:40:14Z

asdf

← Older revision		Revision as of 18:40, 6 September 2016
Line 40:		Line 40:

	create table target_class2 (like target_class);		create table target_class2 (like target_class);


			= on postgres vacuuming =
			I am noticing that, when I am doing major revisions of the protomer, substance and chembl21a.sea tables, where "major revisions" means adding, modifying or deleting multiple millions of rows per week and sometimes even per day, that when these massive changes are being done, I need to vacuum analyze the table at least once a week to prevent autovacuum from kicking in. Autovacuum is slower than a manually executed vacuum verbose analyze, and does not do as good a job. For those tables that are changing less than one million rows a week, vacuuming once a month is probably good enough.


	[[Category:Curator]]		[[Category:Curator]]
	[[Category:ZINC15]]		[[Category:ZINC15]]

Frodo: blah

2015-02-06T00:40:12Z

blah

← Older revision		Revision as of 00:40, 6 February 2015
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			create table target_class2 (like target_class);

	[[Category:Curator]]		[[Category:Curator]]
	[[Category:ZINC15]]		[[Category:ZINC15]]

Frodo: b;lah

2015-02-05T23:41:26Z

b;lah

← Older revision	Revision as of 23:41, 5 February 2015
Line 27:	Line 27:



		= 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;

Frodo: blah

2014-11-10T20:33:24Z

blah

← Older revision		Revision as of 20:33, 10 November 2014
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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]]

Frodo: 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..."

2014-11-10T20:32:04Z

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..."

New page

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

=

[[Category:Curator]]
[[Category:ZINC15]]