[Zinc-fans] Explicit hydrogens

John Irwin jji at cgl.ucsf.edu
Wed Sep 14 23:50:39 PDT 2005

Hi Agnes
With SMARTS there are a couple of ways to match hydrogens, for which I refer
you to the Daylight SMARTS manual, or the corresponding section in other
documentation like Cactvs. The problem is that hydrogens are often stored
implicitly. I am not an expert on this topic, but I usually try to use [#1]
to match a proton. The search engine in ZINC currently uses Cactvs. 
If you are going to do a lot of searching, you may prefer to download the
entire ZINC database in SMILES and do the searches locally on your own
hardware - it will be faster, and you'll have a lot more control.
Hope this helps. Good luck!


From: zinc-fans-bounces at docking.org [mailto:zinc-fans-bounces at docking.org]
On Behalf Of Tan Lay Choo Agnes
Sent: Monday, September 12, 2005 2:52 AM
To: zinc-fans at docking.org
Subject: [Zinc-fans] Explicit hydrogens

How do I include explicit hydrogens in substructure searches? It will be a
real handicap if I can't.
Agnes Tan
Institute of Molecular and Cell Biology

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