Difference between revisions of "ZINC:FAQ"

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  sed -e 's/^/fget2.pl?f=m\&l=0\&z=/' codes  > codes2
 
  sed -e 's/^/fget2.pl?f=m\&l=0\&z=/' codes  > codes2
 
  wget -O all.mol2 -a listing  -B http://zinc8.docking.org/ -i codes2
 
  wget -O all.mol2 -a listing  -B http://zinc8.docking.org/ -i codes2
 +
 +
 +
Note this currently only gets a single (pH 7) representation of each molecule.
  
  
 
[[Category:FAQ]]
 
[[Category:FAQ]]
 
[[Category:ZINC]]
 
[[Category:ZINC]]

Revision as of 22:27, 6 December 2007

Here are frequently asked questions about ZINC.


Q1. I am trying to generate a subset of your "drug-like" molecule subset for virtual screening. I was thinking your 60% diversity group (about 12,000 molecules) would be a place to start, and I downloaded the .smi file. I relatively new to chemoinformatics and I was wondering if there is an elegant way to separate the compounds listed in the .smi file from the larger library containing the mol2 files from the 2,000,000 "usual" set that I have downloaded from ZINC?

A1.

wget http://zinc8.docking.org/subset1/3/3_t60.smi
awk '{print $2}' 3_t60.smi >! codes
sed -e 's/^/fget2.pl?f=m\&l=0\&z=/' codes  > codes2
wget -O all.mol2 -a listing  -B http://zinc8.docking.org/ -i codes2


Note this currently only gets a single (pH 7) representation of each molecule.