Hi All,
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.
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:
Three-center one-electron valence bond graph (via CDK Depict)
[image: Inline images 2]
Using multicentre Sgroups (via CDK Depict)
[image: Inline images 3]
- John
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