Re: [OpenBabel-Devel] Change to SMILES writer for hypervalent atoms

The discussion over at opensmiles was that both forms are reasonable and Geoff prefers the current behavior, so I'll stick to that. On Thursday, 2 March 2017, Andrew Dalke wrote: > On Mar 2, 2017, at 21:31, Andrew Dalke >

Re: [OpenBabel-Devel] Change to SMILES writer for hypervalent atoms

To avoid multiple threads, let's move this over to the opensmiles list. On 2 March 2017 at 20:31, Andrew Dalke wrote: > On Mar 2, 2017, at 20:34, Craig James wrote: >> Well, "FIF" violates the OpenSMILES spec in section 3.1.5, which states that

Re: [OpenBabel-Devel] Change to SMILES writer for hypervalent atoms

On Mar 2, 2017, at 20:34, Craig James wrote: > Well, "FIF" violates the OpenSMILES spec in section 3.1.5, which states that > the "organic subset" are only allowed outside of brackets if they're in their > normal lowest-valence state. Actually, now that I read it, it's

Re: [OpenBabel-Devel] Change to SMILES writer for hypervalent atoms

Hi Craig, >From what you say, it sounds like this is a better discussion for the OpenSMILES list. My intention is to match existing usage and what I believe to be Daylight usage. Let's have this discussion over there, and can clarify the spec either way depending on the outcome. - Noel On 2

Re: [OpenBabel-Devel] Change to SMILES writer for hypervalent atoms

Hi Noel, On Thu, Mar 2, 2017 at 10:11 AM, Noel O'Boyle wrote: > In the course of sorting out the handling of implicit Hs, I've found > that the current SMILES writer writes hypervalent atoms from the > organic subset in square brackets. E.g. Texas carbons: > > >obabel

[OpenBabel-Devel] Change to SMILES writer for hypervalent atoms

Hi there, In the course of sorting out the handling of implicit Hs, I've found that the current SMILES writer writes hypervalent atoms from the organic subset in square brackets. E.g. Texas carbons: >obabel -:C(C)(C)(C)(C)C -osmi [C](C)(C)(C)(C)C or "FIF" as "F[I]F". This is unusual behaviour