I've seen on the ZINC's wiki page that there are custom csh scripts to download (mol2, sdf and database format) from an ID, mostly ZINC ID. But I'd like to customize my queries using more advanced patterns like SMARTS and to integrate it into my shell scripts. From now, I'm still looking and haven't found lot of information. It would be greatly appreciated if somebody linked me some informative resources.
I do not know enough about ZINC to answer your question, but I know that Pubchem contains ZINC and provides a web interface http://pubchem.ncbi.nlm.nih.gov/search/search.cgi and a programmatic interface http://pubchem.ncbi.nlm.nih.gov/pug/pughelp.html to perform the type of queries you want to do. You can restrict the search to ZINC compounds by selecting ZINC as data source in Filters.
https://zinc.docking.org/search/structure This link may be helpful.
https://zinc.docking.org/search/structure
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