Dear Noel,
thanks for your fast and helpful answer. I still have an unanswered problem:
I'm looking for a method that e.g. for the following two molecules:
I: C(=O)3
II: O=C(OH)2
recognizes the first molecule with 6 bonds per carbon as "inconsistent" and
the second as "consistent".
So meanwhile I implemented a method getTypicalValence() below. This seems
to work, but do I understand from your answer that I'm looking for
something that I shouldnt be looking for ?
regards,
Rafel
unsigned int getTypicalValence(unsigned int atomNum) {
OpenBabel::OBMol mol;
mol.BeginModify();
mol.NewAtom(1) -> SetAtomicNum(atomNum);
mol.AddHydrogens();
mol.EndModify();
return mol.GetAtomById(1)->GetValence();
}
On Thu, Nov 7, 2013 at 10:43 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> AFAIK, all OBMol's are self-consistent.
>
> I'm guessing this is not the answer you are looking for. Perhaps the
> following is (taken from my notes at
> https://gist.github.com/baoilleach/4232459):
>
> """
> In the Open Babel world, the "valence" methods of an atom refer to the
> number of bonds, rather than the sum of BOs (which is actual valence).
>
> GetValence() -> Num explicit bonds
> GetImplicitValence() -> Num explicit bonds plus num implicit bonds
> (i.e. total number of bonds) (_impval property on OBAtom)
> GetHvyAtomValence() -> Num explicit bonds to non-H atoms
>
> To find the number of implicit Hs, GetImplicitValence() - GetValence()
>
> BOSum() -> The sum of the BOs of explicit bonds (otherwise known as
> ExplicitValence)
>
> To find the actual valence: BOSum() + GetImplicitHydrogenCount()
> """
>
> - Noel
>
> On 7 November 2013 09:23, Rafel Israels <rafelisra...@googlemail.com>
> wrote:
> > Hello,
> >
> > what would be the correct method to check the consistency of bonds in a
> > molecule ?
> >
> > My first try (below) is wrong: e.g. Aspirin fails this test and if I
> > understand correctly the reason seems that I compare total number of
> bonds
> > (i.e. counting double bonds twice) with maximum/expected number of
> > neighbors, which (for me unexpected but probably correct) considers
> > hybridization and equals 3 for SP2-carbons ?
> >
> > Is there something like atom->GetImplicitBOSum() and/or what would be the
> > correct implementation to check basic chemistry rules ?
> >
> > regards,
> >
> > Rafel
> >
> >
> > FOR_ATOMS_OF_MOL(atom, obMol)
> > if (atom->BOSum() > atom->GetImplicitValence())
> > return false;
> > return true;
> >
> >
> >
> >
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