openbabel-scripting

[openbabel-scripting] using the perl wrapper

[Bruce R. <br...@an...>]

Hi,

I stumbled across OpenBabel the other day.  It was really one of those things
that came along at just the right moment.  I am the author of a largish
package written in perl use for the analysis of x-ray absorption spectroscopy
data with a user base of many hundreds.  One component of the package requires
lists of atomic coordinates.  I am interested in making it easy for people
armed with, say, a PDB file to use the software.  OpenBabel looks like the
cat's pyjamas -- especially since there is a perl/SWIG wrapper.  Cool!

I just read through all the discussion on the scripting mailing list.  It
seems as though there was a solution for the problem characterized by 
 
   /usr/local/lib/openbabel/<whatever>.so did not load properly

but I am not clear what the solution is.

I guess I should say also that, if the perl interface works well for me, this
will become an important part of the software for many of my users.  I'll be
happy to help test (and might even contribute to) the perl wrapper.

Thanks,
B

-- 
 Bruce Ravel  ---------------------------------------------- br...@an...

 Molecular Environmental Science Group, Building 203, Room E-165
 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007

 Argonne National Laboratory         phone and voice mail: (1) 630 252 5033
 Argonne IL 60439, USA                                fax: (1) 630 252 9793

 My homepage:    http://cars9.uchicago.edu/~ravel 
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/

Re: [openbabel-scripting] using the perl wrapper

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

Hi Bruce,

> seems as though there was a solution for the problem characterized by
>
>    /usr/local/lib/openbabel/<whatever>.so did not load properly
>
> but I am not clear what the solution is.

Find the line "@EXPORT = qw( );" near the top of OpenBabel.pm.
Add this to the next line:

  sub dl_load_flags { 0x01 }

That should do it. An updated Perl wrapper will probably hit CPAN  
soon, and will also be in 2.0.1.

> I guess I should say also that, if the perl interface works well  
> for me, this
> will become an important part of the software for many of my  
> users.  I'll be
> happy to help test (and might even contribute to) the perl wrapper.

Great! Glad to hear Open Babel and the perl wrapper help you out.

Cheers,
-Geoff

Re: [openbabel-scripting] using the perl wrapper

[Bruce R. <br...@an...>]

On Tuesday 07 February 2006 18:09, you wrote:
> Find the line "@EXPORT =3D qw( );" near the top of OpenBabel.pm.
> Add this to the next line:
>
> =A0 sub dl_load_flags { 0x01 }
>
> That should do it. An updated Perl wrapper will probably hit CPAN =A0
> soon, and will also be in 2.0.1.

It does, indeed.  Thanks!  I look forward to playing around in earnest with
OB.

B

=2D-=20
 Bruce Ravel  ---------------------------------------------- br...@an...

 Molecular Environmental Science Group, Building 203, Room E-165
 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007

 Argonne National Laboratory         phone and voice mail: (1) 630 252 5033
 Argonne IL 60439, USA                                fax: (1) 630 252 9793

 My homepage:    http://cars9.uchicago.edu/~ravel=20
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/