Re: [Cdk-devel] Kekulisation naming

[Syed A. R. <s9...@gm...>]

My vote is for “Kekulize" as a method name.


On 28 Apr 2014, at 09:06, John May <joh...@gm...> wrote:

>> And "fix" has the double meaning of correcting and positioning…
> 
> Yep - that really puts me off. The method doesn’t remove aromatic flags so dearomatize isn’t really right. 
> 
> I really am leaning kekulize as a good method name. It is what I searched for when I first needed the functionality and seems to coincide with 3/5 major toolkits. I’m struggling with the class name though.
> 
> From some other toolkits
> 
> mol.Kekulize() (OpenBabel)
> m.dearomatize() (Indigo)
> m.dearomatize() (JChem)
> 
> MolOps::Kekulize(mol) (RDKit)
> OEKekulize(mol) (OEChem)
> 
> J
> 
> On 28 Apr 2014, at 08:00, Egon Willighagen <ego...@gm...> wrote:
> 
>> On Sun, Apr 27, 2014 at 9:11 PM, John May <joh...@gm...> wrote:
>>> Possibly, might be worth keeping saturation checker as that seems to be solving a slightly different but related problem.
>> 
>> Yeah, it did a few things indeed, but not sure we really want to keep
>> those in one class...
>> 
>> Anyways... what about calling the method fixDoubleBondPositions() ?
>> 
>> That is more clear than .saturate() (could also be fixing hydrogen
>> counts (which happens to be another purpose)), .deAromatize() (because
>> if the molecule was aromatic, it still is), though perhaps
>> .decideBondOrder() comes close and is a bit shorter...
>> 
>> And "fix" has the double meaning of correcting and positioning...
>> 
>> Egon
>> 
>> -- 
>> E.L. Willighagen
>> Department of Bioinformatics - BiGCaT
>> Maastricht University (http://www.bigcat.unimaas.nl/)
>> Homepage: http://egonw.github.com/
>> LinkedIn: http://se.linkedin.com/in/egonw
>> Blog: http://chem-bla-ics.blogspot.com/
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>> ORCID: 0000-0001-7542-0286
>> 
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