On 09/08/2016 02:37 PM, Rocco Moretti wrote: > (2) There's special complications here that there are certain structures, > such as imidazole, which needs physical or explicit hydrogens on one of the > nitrogens in order to Kekulize properly. If you're implicit only, the RDKit > sanitizer will choke. Thus, there's special casing in various Add/RemoveHs > function to avoid implicit-izing these critical hydrogens.
So if I feed a mol file describing protonated histidine to rdkit, the rdmol I actually get by default is the one with NH2 and COOH? Ohkay... Great write-up, though, thank you. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
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