On Wed, Jan 17, 2018 at 10:12 AM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
wrote:
> On 2018-01-16 22:46, Greg Landrum wrote:
>
> It might be worth thinking about adding an option to the aromaticity
>> perception code to maintain the original bond types and just set the
>> "isAromatic" flag on the bonds.
>>
>
> This is how it's modeled in mmCIF chem. comp. It may or may not come from
> openeye they were using originally to process their ligands/chem comps.
>
> From programming perspective it's pretty annoying since you have to
> remember to add an extra if stanza to all your code, queries, etc.
>
> What's wrong with keeping a copy of the original molecule around? -- I'm
> not sure I get the "I want to sanitize and keep the original bonds too", it
> sounds too much like the proverbial cake.
>
To the extent possible, I do want to allow users to have and eat the cake
:-).
For the case in question, I find that if I read in a mol file containing 2D
coordinates, and I skip the sanitization step altogether, then the 3D
embedding algorithms fail.
>
> Dima
>
>
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