ZINC via curl

You can query ZINC using curl as follows:

Download all the IDs in a file

curl -s --data-urlencode zinc.ids="( cat test.list )" -d page.format=properties http://zinc.docking.org/results

Suppose your file is big, then use the following script to chunk it up by 1000 molecules at a time:

split -l 1000 test.list
foreach i (x??)
       curl -o $i.mol2 --data-urlencode zinc.ids="(cat $i)" -d page.format=mol2 http://zinc.docking.org/results
end

Get all the information about an ID

This includes target annotations and such, using the "800-lb-gorilla" format

curl -s --data-urlencode zinc.ids="$( cat test.list )" -d page.format=800-lb-gorilla http://zinc.docking.org/results

This format is basically tab-delimited, with a few columns that are semi-colon sub-delimited (and column sub-sub-delimited). It's meant to be used with awk. I can give you json output if you'd like to format it yourself.