Re: [OpenBabel-Devel] Smarts & GAFF blues / Kekulization

[David O. <dav...@gm...>]

> Any pointers to where to start fixing this?
> 
> I'm happy to do some programming, but it seems the problems lie deeper 
> in the code than in forcefieldgaff.cpp.
> 
> 

Ive had a look at this - I think the problem is in the gaussian input parsing

the primary issue is that the SMILES from gaussian is

[CH]1N(C=CN1C)CC

rather than

[CH]=1N(C=CN1C)CC

(taken from pubchem for the molecule)

note same is true for mol format - the real molecule has 2 double bonds assigned
in the ring - the output from gaussian parsing  only 1
charge does not seem to matter

with [CH]=1N(C=CN1C)CC it seems to assign ca/na to the 5 membered ring

I have a dirty python script which I was using to play with parameterization 
as per the function in forcefieldgaff.cpp (it simply emulates what the typing
function was doing in c++ in python) - it is a playing script but I can send it to you
if you want - my analysis is from the output of this script not running anything
else in openbabel

I suspect the issue in the guassian parsing is the difficulty of assigning
integral bond orders from a partial double bond geometry

David