Hello Dimitri,

Yes, I do have explicit hydrogen throughout entire process.
Thank you for the tip. I will check out the link.

Bin









-------- Original Message --------
Subject: Re: [Rdkit-discuss] How to find the idx of hydrogens bonded to a 
specific atom
Local Time: October 14, 2016 2:26 AM
UTC Time: October 13, 2016 6:26 PM
From: dmaz...@bmrb.wisc.edu
To: rdkit-discuss@lists.sourceforge.net

On 10/13/2016 12:12 PM, Paul Emsley wrote:

> Are you sure? I use HasSubstrMatch to match hydrogens.

Perhaps this
http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg05897.html
may be useful?

If OP's looking at crystal structures, they're likely dealing with pdb
data model where all hydrogens are explicitly present and indexed. I
wonder if they stay that way throughout the steps leading to (and past)
the smarts match.

--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu

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