[Joelib-help] aromaticity in SD files

[Wayne V. <vol...@re...>]

Hi Joerg,

A couple weeks ago I asked about the bond type "4" in the sd files
produced by JOELib.  You said

> ah, o.k., but that's not a bug that's a feature! These bonds are=20
> aromatic and you will find this also in the SD-FILE definition of MDL.
> That why you should use JOELib or OpenBabel, because they have a
really=20
> great chemical expert system behind 'simple' file conversion. Only if=20
> you know aromatic atoms/bonds you can create e.g. a MOL2 file !!!

I went and looked at the sd file definition on the mdl web site.  A bond
type of "4" is only permitted (required?) for structures intended for
use as queries (against, presumably, a database).  I'm sure you'll find
that particular distinction as odd as I do but at any rate, that's their
standard.

From what I've seen JOELib seems to be focused on representing specific,
rather than generic (i.e. query), molecules so it seems as though the sd
writer should put out alternating 1's and 2's.  Or perhaps it's sensible
to have behavior depend on a flag, so you can ask the sd writer to use
type "4" bonds if desired.

Here's a fragment of code that I think will do the trick.  Let me know
what you think.

Wayne

                    //check, if aromatic bond
                    if (atom.isAromatic() && nbr.isAromatic() ||
(bond.getBO() =3D=3D JOEBond.JOE_AROMATIC_BOND_ORDER))
                    {
                        //  Non-query structures must use Kekule
representation
                        if (bondPairs.containsKey(new
Integer(atom.getIdx())) || bondPairs.containsKey(new
Integer(nbr.getIdx())))=20
                        {
                            bondType =3D 1; // single bond
                        }
                        else
                        {
                            bondType =3D 2; // double bond
                            bondPairs.put(new Integer(atom.getIdx()),
new Integer(nbr.getIdx()));
                            bondPairs.put(new Integer(nbr.getIdx()), new
Integer(atom.getIdx()));
                        }
                    }
                    else
                    {
                        // 1 single
                        // 2 double
                        bondType =3D bond.getBO();
                    }

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