To everyone:
On Tuesday 23 January 2007 13:59, Stefan Kuhn wrote:
> jcp right now renders "any" bonds in mdl as single bonds. The mdl reader
> does not read the any type. The code of mdl reader is this:
> if (order == 4) {
> // aromatic bond
> bond = molecule.getBuilder().newBond(a1, a2,
> CDKConstants.BONDORDER_AROMATIC, stereo);
Mmm... I thought we got rid of all usage of that :(
> // mark both atoms and the bond as aromatic
> bond.setFlag(CDKConstants.ISAROMATIC, true);
> a1.setFlag(CDKConstants.ISAROMATIC, true);
> a2.setFlag(CDKConstants.ISAROMATIC, true);
Using flags, as is done here, it the agreed way of doing it.
> molecule.addBond(bond);
> } else {
> bond = molecule.getBuilder().newBond(a1, a2, (double)
> order, stereo);
> molecule.addBond(bond);
> }
Mmm....
> So we can see that order 8=any is not handled and that any is actually set
> to 8 (abstract renderer renders anything unknown to single) and that
> aromatic is still set to 1.5 (BONDORDER_AROAMTIC is 1.5). This is a bit
> nasty.
Agreed.
> My suggestion:
> Rename CDKConstants. BONDORDER_AROMATIC to BONDORDER_UNKNOWN (this is what
> it really is) and set flags for aromatic/any alongside.
I think that makes sense. I would suggest to still render UNKNOWN as a single
bond, to, at least, indicate the connectivity... possibly as grey or so? What
does the IUPAC suggest about this?
About the 8=any... I think we should use a flag for that too, and set the
order too to UNKNOWN.
Everyone: I think we need a community agreement here... what should the
behavior with respect with respect the 4=aromatic, 8=any, etc... ?
Egon
--
http://chem-bla-ics.blogspot.com/
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