ZINC via curl: Difference between revisions
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(Created page with "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....") |
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= Download all the IDs in a file = | = Download all the IDs in a file = | ||
curl -s --data-urlencode zinc.ids=" | 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 (March 2020) = | |||
curl http://zinc15.docking.org/substances.txt -F zinc_id-in=@./zinc.txt -F output_fields="zinc_id mwt num_atoms num_rings" | |||
Output fields can be found at http://zinc15.docking.org/substances/help/ | |||
zinc.txt should look like: | |||
7 | |||
10 | |||
ZINC92349234 | |||
= Get all the information about an ID = | = Get all the information about an ID = | ||
| Line 12: | Line 31: | ||
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. | 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. | ||
[[Category: | [[Category:Tutorials]] | ||
[[Category:ZINC]] | [[Category:ZINC]] | ||
[[Category: | [[Category:API]] | ||
[[Category:NEED ATTENTION]] | |||
Latest revision as of 21:08, 11 March 2020
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 $i)" -d page.format=mol2 http://zinc.docking.org/results
end
Get all the information about an ID (March 2020)
curl http://zinc15.docking.org/substances.txt -F zinc_id-in=@./zinc.txt -F output_fields="zinc_id mwt num_atoms num_rings"
Output fields can be found at http://zinc15.docking.org/substances/help/ zinc.txt should look like:
7 10 ZINC92349234
Get all the information about an ID
This includes target annotations and such, using the "800-lb-gorilla" format
curl -s --data-urlencode zinc.ids="$( 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.