[ghemical-devel] Re: OB-2.0 changes for ghemical

[Jean Bréfort]

Le mercredi 28 septembre 2005 à 15:21 +0300, Tommi Hassinen a écrit :
> On Tue, 27 Sep 2005, Geoffrey Hutchison wrote:
> 
> > Hi Tommi,
> >
> > I've made some initial changes to integrate Open Babel 2.0 into ghemical (CVS 
> > HEAD). Before I contribute any sort of patch, I'd like to ask a few 
> > questions.
> >
> > * There are significant changes in how files are read under OB 2.0. Do you 
> > want ghemical to support OB 1.x versions and try to detect them via 
> > configure? Or should Ghemical 2.0 rely on OB 2.0? (Seems like a nice set of 
> > version numbers. :-)
> 
> Hi,
> 
> I'm not really an expert myself what comes into configure scripts and such 
> things. I think supporting both versions is an OK option, the hardest part 
> is the configure script.
> 
> Now the configure script defines a macro ENABLE_OPENBABEL if we had 
> --enable-openbabel at the command line. Perhaps this could be changed so 
> that it would (additionally?) define either ENABLE_OPENBABEL_V1 or 
> ENABLE_OPENBABEL_V2 (or whatever the macro names are) depending on what 
> configuration was found on the system. The V1 option would be for the 
> current version and V2 for the updated version.

It is not difficult to detect which openbabel version is available (I do
it in the current gchemutils/gchempaint stable branches). But, IMHO, it
would be much better to use only openbabel-2 in ghemical-2.

> > * Is the ghemical file format somewhat stable again? It seems like the 
> > current CVS version will read OB output, and vice versa. Granted, the new 
> > file format isn't compatible with OB 1.x code, but seems completely 
> > compatible with OB-2.0.
> >
> > * Are there more changes needed to the OB-2.0 ghemical format support?
> 
> I might need to add a new !Section for saving secondary structure 
> constraints and related information. But in OpenBabel I think this have to 
> be handled so that these new and unknown keywords are just ignored and 
> skipped.
> 
> So in this sense I expect the file format to be stable.
> 
> Please note that in ghemical-1.90 you might get a different file if you do 
> a "save as" or an "export .gpr" operation. Also, at src/project.cpp 
> starting from line 292 there is the function
> 
> bool project::ExportFile(const char * filename, int index)
> 
> where the file export is done ; there is a call
> 
>  	WriteGPR_v100((* this), intermed);
> 
> that should be changed into
> 
>  	WriteGPR((* this), intermed);
> 
> for most rigorous testing.
> 
> > Cheers,
> > -Geoff
> >
> > P.S. On an unrelated note, do you want me to go and fix all the "backwards" 
> > header warnings? I'm assuming that most people are using GCC-3.0 or an 
> > otherwise recent ISO C++ compiler. It's pretty easy to run a sed script and 
> > clean up the warnings.
> 
> I once started to convert these manually, but the job never finished... :(
> 
> It's OK if you fix the warnings. Also if you could you send me such a 
> script, I would be glad to try it.
> 
> Regards,
> 
>  	Tommi
> 
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