>
> It's a chicken and egg problem... people don't use it, and even can't use
> it, because there are no good tools yet; not making good tools also ensures
> no one uses it.
I somewhat agree but MDL/ChemDraw support it and it's still not used.
> So, rather than trunking the CDK, I would suggest, let's make work of
> convincing the cheminformatics community of these advanced features, just
> like others are doing to the PTM-protein sequence mashups... let's be a
> leader, rather than a follower.
At the moment it makes the general case (with 99.999999% of uses) much
slower for a case that isn't used (yet). I think it should be possible to
do the exotic but not at the cost of the regular. As a library I would push
for getting the basics of the model right before moving on to extra bits, I
quote Jurassic park in jest :p:
*Your scientists were so preoccupied with whether or not they could, they
> didn’t stop to think if they should*
By argument
John
On 27 April 2017 at 09:36, Egon Willighagen <[email protected]>
wrote:
>
>
> On Thu, Apr 27, 2017 at 9:54 AM, John Mayfield <
> [email protected]> wrote:
>
>> I was wondering does anyone use n-way bonds in CDK (a bond with more than
>> two atoms)?
>>
>> IAtom atom1 = object.getBuilder().newInstance(IAtom.class, "C");
>>> IAtom atom2 = object.getBuilder().newInstance(IAtom.class, "O");
>>> IAtom atom3 = object.getBuilder().newInstance(IAtom.class, "C");
>>> IAtom atom4 = object.getBuilder().newInstance(IAtom.class, "C");
>>> IAtom atom5 = object.getBuilder().newInstance(IAtom.class, "C");
>>>
>>> IBond bond1 = new Bond(new IAtom[]{atom1, atom2, atom3, atom4, atom5});
>>>
>>> I don't deny they exists but not sure how useful they are as they don't
>> fit into traditional valence bond theory. Many useful algorithms break down
>> (e.g. simple traversals, substructure matching, and canonical labelling).
>> Rich Apodaca talks about it a little in FlexMol
>> <http://depth-first.com/articles/2006/12/20/a-molecular-language-for-modern-chemistry-getting-started-with-flexmol/>
>> and
>> shows it for doing Pi bonding - nice but again not really practical. I seem
>> to recall Egon saying CML can "store" them but I'm struggling to see if
>> it's anything more than nicety.
>>
>
> It's a chicken and egg problem... people don't use it, and even can't use
> it, because there are no good tools yet; not making good tools also ensures
> no one uses it.
>
> One of the reasons why we have incorrect data, is because at some point
> someone took a shortcut in some tool, because it covered most of the issues.
>
>
>> I believe a better way to handle (if you wanted to) would be with a
>> higher level description as sets/collections of atoms/bonds over a wrong
>> but acceptable valence bond graph:
>>
>
> We don't do much with transition states, but one of the key advantages of
> the CDK (over RDKit, OpenBabel) is that you actually can... Fairly, I did
> not track with literature citing the CDK actually uses these features...
>
> So, besides the obvious representation (and viz) use cases below (just
> think of what mess some PubChem/ChemSpider entries are), these kind of
> features are essential for reaction mechanisms, so the first place to check
> would be the MaCIE work and the metabolite identification cheminformatics
> work from Chris' lab in the past.
>
> Other use cases, one that I never found time for, is (also obvious from
> the below) cheminformatics for organometallics... there is a good bit of
> literature doing VS of such substances, typically severely limited in the
> cheminformatics they use...
>
>
>> Three-center one-electron valence bond graph (via CDK Depict)
>> [image: Inline images 2]
>> Using multicentre Sgroups (via CDK Depict)
>> [image: Inline images 3]
>>
>
> So, rather than trunking the CDK, I would suggest, let's make work of
> convincing the cheminformatics community of these advanced features, just
> like others are doing to the PTM-protein sequence mashups... let's be a
> leader, rather than a follower.
>
> 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/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
> ORCID: 0000-0001-7542-0286
> ImpactStory: https://impactstory.org/u/egonwillighagen
>
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