Hello Greg, I continually placed your test molecule throughout my workflow and narrowed it down to two lines. The reaction product return value is a string that I then create a molecule from using the MolFromSmiles function. I then AddHs to this molecule and an exact copy of it (for use in other functions such as finding tertNitrogen atoms. It would appear that adding hydrogens explicitly and then passing this molecule on to other functions causes problems with future manipulations, like adding additional protons.
I am still curious about the weird smiles strings, but for now I don't AddH's to the copy of the molecule i send out for other functions. This seems to solve the issue. Thanks for the help. brian ________________________________ From: Greg Landrum [[email protected]] Sent: Wednesday, August 31, 2016 7:49 PM To: Bennion, Brian Cc: [email protected] Subject: Re: [Rdkit-discuss] protonating proper tertiary amines On Thu, Sep 1, 2016 at 1:01 AM, Bennion, Brian <[email protected]<redir.aspx?REF=2wkB4X-7JHuZ6o8-llu8NKocXG__iA8ff4hmjA2gdlH8mr91k9LTCAFtYWlsdG86YmVubmlvbjFAbGxubC5nb3Y.>> wrote: On one compute node with one thread, two reagents are combined in a synthesis function and then the tertNitrogenProt function is called and the current molecule is passed through to be searched for the tertiary nitrogen and protonated if found. What I am not clear on, is whether the properties are passed properly from the synthesis function to the tertNitrogenProt function. Yeah, given that the function works correctly when it's called on its own, I think the problem is likely to be in the way it's being called. Question, what are the outputs of UpdatePropertyCache()? When I test for output, only the word _none_ is printed. I don't know if that means there were no properties present, or they did not need to be updated. UpdatePropertyCache() doesn't return a value, that's why you're seeing None. The method just causes the implicit properties on each of the molecule's atoms to be re-computed, but it doesn't return anything. -greg
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