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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
split on ; or ,  - parsing.

3. Deplete

previously was:  deplete.pl ibsbb < ibsbb.ism

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 

Load ChEMBL for ZINC, SEA export

get latest chembl

load into psql

export to files for SEA

create links between substance, annotation via note

target clustering

update SEA

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

(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

 updateit.pl < log
 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.