Geoffrey Hutchison wrote:
>
> On Oct 29, 2009, at 2:40 PM, Craig A. James wrote:
>
>> This is a good topic for OpenBabel 3. There really is no such thing
>> as an "aromatic atom". Aromaticity is only a property of bonds and
>> ring systems. It might make sense to eliminate the "atom-is-aromatic"
>> property altogether.
>
> That's a tough call, though. What do you do with SMARTS "c" or atom
> typing for Sybyl Mol2, which wants "C.ar" or similar?
>
> I somewhat agree with your premise, but there's too much existing
> weight. A more accurate question would be "is this atom aromatic in this
> ring?"
I think the trick would be to keep the "aromatic atom" concept externally. As
you and others point out, it's useful. But it should be clearly defined as a
sort of conceptual shorthand for "an atom with aromatic bonds."
Internally, all algorithms that deal with aromaticity should do it at the bond
level. Take this function from ring.cpp:
bool OBRing::IsAromatic()
{
OBMol *mol = _parent;
vector<int>::iterator i;
for (i = _path.begin();i != _path.end();++i)
if (!(mol->GetAtom(*i))->IsAromatic())
return(false);
return(true);
}
This simply gives the wrong answer. The premise that, "A ring is aromatic if
its atoms are aromatic," is false.
Craig
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