Re: [Rdkit-discuss] Hypervalent halogen structures - chlorate etc.

On Wed, Nov 22, 2017 at 10:09 AM, Chris Earnshaw wrote: > Thanks Greg, I suspected that might be the case. I certainly don't > want to turn off all sanitization, but I could write a bit of code to > convert these salts back to my desired form as a separate step. > It's

Re: [Rdkit-discuss] Hypervalent halogen structures - chlorate etc.

Thanks Greg, I suspected that might be the case. I certainly don't want to turn off all sanitization, but I could write a bit of code to convert these salts back to my desired form as a separate step. Alternatively, I guess I could disable or rewrite halogenCleanup() in MolOps.cpp. Is this the

Re: [Rdkit-discuss] Hypervalent halogen structures - chlorate etc.

At the moment the only way to do this is to disable the "cleanup" functionality in SanitizeMol(). This can be done, but it will also have the consequence that things like the hypervalent N in nitro groups (i.e. "-N(=O)=O") is not cleaned up. In [2]: m =

Re: [Rdkit-discuss] Hypervalent halogen structures - chlorate etc.

Hi Oops - typo! The chlorate and perchlorate oxygens should all be [O-]. I was copying by hand from a different computer... Regards, Chris On 21 November 2017 at 09:19, Paolo Tosco wrote: > Hi Chris, > > if the behaviour with chlorate and perchlorate is the one you report

[Rdkit-discuss] Hypervalent halogen structures - chlorate etc.

Hi Sometime between 2014 and now there appears to have been a change in the way hypervalent halogen structures are handled. The old behaviour (involving some tweaking of atomic_data.cpp to allow the higher oxidation states) was to have a neutral halogen with double bonds to most of the oxygens,