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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