On 2014-03-08 22:21, Paul van Maaren wrote:
> I had a look at it too, the following hack seems to work for all types
> of imidazolium ions.
>
> In gaussformat.cpp I moved mol.SetTotalCharge(charge) close to the
> location where the charge is extracted from the Gaussian file and in
> kekulize.cpp I added the following:
>
> diff --git a/src/kekulize.cpp b/src/kekulize.cpp
> index dedf371..e5f7841 100644
> --- a/src/kekulize.cpp
> +++ b/src/kekulize.cpp
> @@ -515,6 +515,9 @@ namespace OpenBabel
> int idx;
> OBAtom *atom;
> OBBond *bond;
> + int charge;
> +
> + charge = _totalCharge;
>
> // Figure out which atoms are in this ring system and whether or not
> each
> // atom can donate an electron.
> @@ -532,6 +535,13 @@ namespace OpenBabel
> atomState[idx] = DOUBLE_PROHIBITED;
> if (DEBUG) { cout << "atom " << idx << " rejected NR3 double bonds
> " << endl; }
> }
> +
> + if (atom->IsNitrogen() && atom->GetFormalCharge() == 0 &&
> atom->GetValence() == 3 && charge > 0) {
> + atomState[idx] = DOUBLE_ALLOWED; // It has an electron it can
> donate, because of the total charge
> + charge--;
> + if (DEBUG) { cout << "atom " << idx << " rejected NR3 double bonds
> overruled by totalcharge " << endl; }
> + }
> +
>
> And I get:
>
> babel -ig03 1-ethyl-3-methylimidazolium3-esp.log.gz -osmi
> c1n(ccn1C)CC
>
Any further insights?
Are we on the right track here or should this be handled differently?
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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