Re: [Rdkit-discuss] nitrogen valence issues

2017-10-07 Thread Chris Earnshaw
gearns...@gmail.com] > Sent: Thursday, October 05, 2017 08:46 > To: Bennion, Brian <benni...@llnl.gov> > Cc: RDKit Discuss (rdkit-discuss@lists.sourceforge.net) < > rdkit-discuss@lists.sourceforge.net> > Subject: Re: [Rdkit-discuss] nitrogen valence issues &g

Re: [Rdkit-discuss] nitrogen valence issues

2017-10-06 Thread Bennion, Brian
continue to have problems. > > Brian > > > > From: Chris Earnshaw <cgearns...@gmail.com> > Sent: Thursday, October 5, 2017 12:04:02 AM > To: Bennion, Brian; RDKit Discuss > (rdkit-discuss@lists.sourceforge.net) >

Re: [Rdkit-discuss] nitrogen valence issues

2017-10-05 Thread Chris Earnshaw
> From: Chris Earnshaw <cgearns...@gmail.com> > Sent: Thursday, October 5, 2017 12:04:02 AM > To: Bennion, Brian; RDKit Discuss (rdkit-discuss@lists.sourceforge.net) > Subject: Re: [Rdkit-discuss] nitrogen valence issues > > Hi > > Be aware t

Re: [Rdkit-discuss] nitrogen valence issues

2017-10-05 Thread Chris Earnshaw
Hi Be aware that there is a problem with one of the azide groups in CHEMBL592333 - in SMILES it's '-N=[NH+]-[NH-]' rather than '-N=[N+]=[N-]. This doesn't render the structure chemically invalid but it's probably wrong. What's the provenance of your SD file? It isn't the same as as a fresh

Re: [Rdkit-discuss] nitrogen valence issues

2017-10-04 Thread Greg Landrum
Hi Brian, When you pasted that into the email the formatting of the mol block did end up screwed up, which makes this hard to reproduce. Could you please attach the mol block to the message as a file? -greg On Thu, Oct 5, 2017 at 2:21 AM, Bennion, Brian wrote: > Hello, > >