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Re: [openbabel-scripting] openbabel and swig

[S J. S. <swa...@gm...>]

Let me point out I'm only familiar wiht python, not perl at all. So
everything i say here has that slant.

One sticky issue in particular is the '>>' and '<<' methods of
molecules. Swig/python don't really know what to do with these and
drops them. Molecule input/output in openbable relies heavily on this
feaure.

I know there are some lesser known ways of molecule input/output which
can use stringio and file pointers to input molecules which could
resolve this. In my opinion, we need to come up with a structure that
will allow open bable to read a molecule from any
file-emulating-object of the scripting target language, not just real
files (very important for python).

One solution could be to make a wrapper iterator to include in the
swig file which provides the described functionallity to python.

The other major problem i was stuck on was compiling the wrapper swig
produced. I never got to the bottom of which i couldn't. I can go back
and look again. In my (limited) experience, this is a sign swig
misunderstood some more complex uses of c++ syntax.

It has been a while since I tried to wrap openbabel. Since then their
has been a new version of swig developed (with a lot of great
enhancements). So some of what I recall might have been resolved.

Let me know how you want to go about this from here:

Josh

On 6/13/05, Geoff Hutchison <ge...@ge...> wrote:
> > wrapping software out there. I do think we need to discuss the best
> > pardigm for doing this, the mol.h header file is to complex for swig
> > to digest.
>=20
> I'll bite. Using the development openbabel-new-framework line, I can
> certainly get SWIG to output a wrapper that looks fine to me. I
> haven't had much time to figure out why the modules won't load into
> Perl or Python, but SWIG certainly seems to be doing the right thing.
>=20
> If you think mol.h is too complex, I'm certainly open to hearing
> proposals to improve it. Anything in particular?
>=20
> Thanks,
> -Geoff
>=20
>=20
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Re: [openbabel-scripting] openbabel and swig

[Geoff H. <ge...@ge...>]

> wrapping software out there. I do think we need to discuss the best
> pardigm for doing this, the mol.h header file is to complex for swig
> to digest.

I'll bite. Using the development openbabel-new-framework line, I can  
certainly get SWIG to output a wrapper that looks fine to me. I  
haven't had much time to figure out why the modules won't load into  
Perl or Python, but SWIG certainly seems to be doing the right thing.

If you think mol.h is too complex, I'm certainly open to hearing  
proposals to improve it. Anything in particular?

Thanks,
-Geoff

[openbabel-scripting] openbabel and swig

[S J. S. <swa...@gm...>]

Hey All,

I highly reccomend sticking with swig. It is the most flexible
wrapping software out there. I do think we need to discuss the best
pardigm for doing this, the mol.h header file is to complex for swig
to digest.

S Joshua Swamidass