Re: [Rdkit-discuss] GetBestRMS and the carboxylic acid

Update, the explicit or not charge is not relevant. that just determines the behaviour of the AssignBondOrderstoTemplate. The behaviour is that GetBestRMS does not consider a carboxylate as symmetric. Can anyone suggest a workaround to treat as symmetric? *Kind Regards* Dr. Martin Watson VP

[Rdkit-discuss] GetBestRMS and the carboxylic acid

Hi I'm using GetBestRMS to score conformers in an sdf relative to a pdb extracted sdf ligand using the snippet below. I get odd behaviour when the molecule includes a carboxylic acid. depending on whether the charge is explicitly defined in the sdf or not I get a different RMS which seems to be

Re: [Rdkit-discuss] Interrogations about how N, H and charge are handled

The RDKit is fairly strict in checking that the charge + valence don't exceed reasonable values for the element, but it does not go so far as to catch these extreme cases. It's worth thinking about how to add this kind of sanity checking to the RDKit itself while still allowing "reasonable"

Re: [Rdkit-discuss] issue during parsing a smile

smiview is just so cool. Thanks (again) Andrew! On Mon, Apr 16, 2018 at 4:22 PM, Andrew Dalke wrote: > If you try this out with my smiview package, available from > https://bitbucket.org/dalke/smiview/downloads/ , it reports: > > > % smiview 'C\(C(C)C)=N/O' >

Re: [Rdkit-discuss] seg fault when importing Chem on OS-X 10.12

yeah, there are a ton of moving parts here and the RDKit builds on the Mac got caught between a couple of them.[1] The build of the beta that Brian mentions should work for everyone who's using python 3.6 and an up-to-date conda installation. If it doesn't, please, please let us know. -greg [1]