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YYZ protocol

1. Acquire catalog, often as SDF

• This is often a manual step, by email, or download.
• pc2unix to remove \r

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
code to edit field table
code to load csv into synonyms

3. Deplete

previously was:  deplete.pl ibsbb < ibsbb.ism
now??

4. Desalt, filter out neverwants, stereochemical expansion, remove N stereochem, take 4 max

filter.py rules.txt ibsbb.ism ibsbbexp.ism > ibsbb.log
ignorenstereochem2.csh ibsbbexp.ism
sort -u ibsbbexp.ism | sort -k 2 | only4.pl > ibsbbexp4.ism 

5. protonation step with chemaxon!

cxcalc ... to generate a canonical form at pH 7.0

6. look up if exists in database (eventually load catalog_item, substance tables

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

7. generate protomers

cxcalc... dahlia procedure

8. create db, db2, mol2, sdf, pdbqt, solv

ryan's procedure 

UCSF protocol (OLD)

Acquire databases

• 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

pc2unix '*.sdf' 

• 3. make ism

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

• 4. Combine and move

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

• 5. There is no 5.

oh yeah?

• 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.