Loading ZINC12

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YYZ protocol

2. Parse SDF into ISM, harvesting data from SD tags into synonyms table

python parse_catalog.py ibsbb ibs2013oct_bb.sdf ibsbb.ism ibsbb.csv

3. Desalt, default representation, filter out neverwanteds

• formerly: filter.py
• now: ?

python find_new_substances.py ibsbb ibsbb.ism  catalog-item.csv

4. Load substance, catalog_item

Nothing here yet

5. Generate and load protomer

Nothing here yet.

Acquire

1. Get the catalog from the vendor, usually in SDF. NB. we need to automate this step as much as possible

2. on nfshead2 in ~xyz/raid3/stage3/ or /raid6/tmp/xyz/ gunzip SDF into a directory

3. pc2unix '*.sdf'

4. make ism

foreach i (*.sdf)
namesdf.pl '<TAG>' < $i > $i.sdf
convert.py --i=$i.sdf --o=$i.ism

end

5. combine and move

cat vendoris*.ism > all mv all ~xyz/raid8/catalog/vendorid.in ln -s !$ vendorid.ism

6. mark depleted

deplete.pl vendorid < vendorid.ism 

7. process on sgehead2 mas.csh vendorid vendorid.ism  ; # nb may run for a long time!

nb periodically delete output

8. update filter info, error info

9. export database on nfshead5

cd ~xyz/raid8/byvendor/.temp

mkdir vendorid
cd vendorid
callgr17.csh

(may take a long time)

10. export database on nfshead5

extractthis.csh vendorid nodb mol2   

NB db if annotated mol2 in all cases

11. if big, cluster on korn

kornit.csh vendorid `pwd`

12. finish off on wilco

./all.csh 
updateit.pl < log
./all.csh
cd vendorid
dosubset4.pl vendorid vendor

13. email vendor telling them their catalog has been updated in ZINC

14. write tweet, etc. announcing, if appropriate.