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[OpenBabel-scripting] Using CML with Open Babel Python - segfault

[richard a. <ric...@ya...>]

I get a segmentation fault on exiting interactive
python after using CML:

>>> import openbabel
>>> mol=openbabel.OBMol()
>>> c=openbabel.OBConversion()
>>> c.SetInAndOutFormats('smiles', 'cml')
True
>>> c.ReadString(mol, 'c1ccccc1')
True
>>> print c.WriteString(mol)
<molecule>
 <atomArray>
  <atom id="a1" elementType="C"/>
  <atom id="a2" elementType="C"/>
  <atom id="a3" elementType="C"/>
  <atom id="a4" elementType="C"/>
  <atom id="a5" elementType="C"/>
  <atom id="a6" elementType="C"/>
 </atomArray>
 <bondArray>
  <bond atomRefs2="a1 a2" order="1"/>
  <bond atomRefs2="a2 a3" order="2"/>
  <bond atomRefs2="a3 a4" order="1"/>
  <bond atomRefs2="a4 a5" order="2"/>
  <bond atomRefs2="a5 a6" order="1"/>
  <bond atomRefs2="a1 a6" order="2"/>
 </bondArray>
</molecule>

>>>#pressed [Ctrl-d]
Segmentation fault

My system is amd64 Linux (Mandriva 2007), Python 2.4.3
and Open Babel SVN trunk rev 1578.

Running the above code with input set to 'smi' and
output set to 'inchi' causes no segfault on exiting
interactive python.

I see a similar CML-releated problem when running
OBRuby. In that case, I also don't get the segfault
until interactive Ruby exits, or the Ruby interpreter
finished executing. And there, I only see the problem
when using CML, not with other format
interconversions.

Any ideas?

thanks,
Rich

____________________________
Richard Apodaca
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Re: [OpenBabel-scripting] Python bindings on amd64 Linux

[richard a. <ric...@ya...>]

Hi Marin,

Your suggestion worked perfectly. I changed the first
few lines of openbabel.py to the following:

import sys
if sys.platform.find("linux") != -1:
    #import dl
    sys.setdlopenflags(sys.getdlopenflags() | 0x100)

Doing this I can now import openbabel, create a
working OBConversion, and do a simple smiles->inchi
conversion.

Many thanks!
Rich

--- Martin Vogt <mar...@bi...> wrote:

> Hi,
> 
> there is indeed a simple workaround for this
> problem.
> Note that the dl module is only needed for the
> numerical constant
> 
> dl.RTLD_GLOBAL
> 
> This constant is defined from a system header
> 'dlfcn.h', if i recall 
> correctly. Searching through your system headers you
> might find that 
> this constant is equal to 0x100 (at least on my
> system: Suse 10.1 64bit).
> So you can replace the top lines with:
> 
> if sys.platform.find("linux") != -1:
> 	sys.setdlopenflags(sys.getdlopenflags() | 0x100)
> 
> avoiding the import of the dl module.
> 
> Hth, Martin
> 
> richard apodaca wrote:
> > Has anyone gotten the Python Open Babel interface
> to
> > work on amd64 Linux? I'm using rev 1578 of the svn
> > trunk
> > 
> > When I try to import openbabel, I get the
> following
> > error
> > 
> > 
> >>>>import openbabel
> > 
> > Traceback (most recent call last):
> >   File "<stdin>", line 1, in ?
> >   File
> > "/usr/lib64/python2.4/site-packages/openbabel.py",
> > line 3, in ?
> >     import dl
> > ImportError: No module named dl
> > 
> > I noticed a similar problem reported here, but no
> > solution:
> > 
> >
>
http://sourceforge.net/mailarchive/message.php?msg_id=37015184
> > 
> > I had no problems either compiling or installing
> > pyopenbabel - just loading it in python.
> > 
> > My system does lack the python dl module, which as
> far
> > as I can tell is supposed to be standard. In
> googling
> > around, I found several references to the python
> dl
> > module being unstable on amd64 - and therefore not
> > available.
> > 
> > So - has anyone found a workaround to this
> problem?
> > 
> > I tried one: comment out the code responsible for
> > loading dl in the first place (openbabel.py):
> > 
> > if sys.platform.find("linux") != -1:
> >     import dl
> >     sys.setdlopenflags(sys.getdlopenflags() |
> > dl.RTLD_GLOBAL)
> > 
> > I can in fact import openbabel after doing this.
> The
> > problem is that when using OBConversion, none of
> the
> > formats are loaded:
> > 
> > 
> >>>>import openbabel
> >>>>c=openbabel.OBConversion()
> > 
> > ==============================
> > *** Open Babel Error  in LoadFormatFiles
> >   /usr/local/lib/openbabel/cmlreactlformat.so did
> not
> > load properly
> > ==============================
> > 
> > ... and dozens more load errors after this one ...
> > 
> > thanks,
> > Rich
> > 
> > 
> > 
> > 
> > ____________________________
> > Richard Apodaca
> > Blog: http://depth-first.com
> > 
> > 
> >  
> >
>
____________________________________________________________________________________
> > Everyone is raving about the all-new Yahoo! Mail 
> > (http://advision.webevents.yahoo.com/mailbeta/)
> > 
> > 
> >
>
-------------------------------------------------------------------------
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> web services, security?
> > Get stuff done quickly with pre-integrated
> technology to make your job easier
> > Download IBM WebSphere Application Server v.1.0.1
> based on Apache Geronimo
> >
>
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> >
>
https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> 
> 
> -- 
> Martin Vogt
> Vorgebirgsstr. 14, D-53111 Bonn
> Email: mo...@t-...              Tel.: +49
> (0)228 634376
> 


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Re: [OpenBabel-scripting] Python bindings on amd64 Linux

[Martin V. <mar...@bi...>]

Hi,

there is indeed a simple workaround for this problem.
Note that the dl module is only needed for the numerical constant

dl.RTLD_GLOBAL

This constant is defined from a system header 'dlfcn.h', if i recall 
correctly. Searching through your system headers you might find that 
this constant is equal to 0x100 (at least on my system: Suse 10.1 64bit).
So you can replace the top lines with:

if sys.platform.find("linux") != -1:
	sys.setdlopenflags(sys.getdlopenflags() | 0x100)

avoiding the import of the dl module.

Hth, Martin

richard apodaca wrote:
> Has anyone gotten the Python Open Babel interface to
> work on amd64 Linux? I'm using rev 1578 of the svn
> trunk
> 
> When I try to import openbabel, I get the following
> error
> 
> 
>>>>import openbabel
> 
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File
> "/usr/lib64/python2.4/site-packages/openbabel.py",
> line 3, in ?
>     import dl
> ImportError: No module named dl
> 
> I noticed a similar problem reported here, but no
> solution:
> 
> http://sourceforge.net/mailarchive/message.php?msg_id=37015184
> 
> I had no problems either compiling or installing
> pyopenbabel - just loading it in python.
> 
> My system does lack the python dl module, which as far
> as I can tell is supposed to be standard. In googling
> around, I found several references to the python dl
> module being unstable on amd64 - and therefore not
> available.
> 
> So - has anyone found a workaround to this problem?
> 
> I tried one: comment out the code responsible for
> loading dl in the first place (openbabel.py):
> 
> if sys.platform.find("linux") != -1:
>     import dl
>     sys.setdlopenflags(sys.getdlopenflags() |
> dl.RTLD_GLOBAL)
> 
> I can in fact import openbabel after doing this. The
> problem is that when using OBConversion, none of the
> formats are loaded:
> 
> 
>>>>import openbabel
>>>>c=openbabel.OBConversion()
> 
> ==============================
> *** Open Babel Error  in LoadFormatFiles
>   /usr/local/lib/openbabel/cmlreactlformat.so did not
> load properly
> ==============================
> 
> ... and dozens more load errors after this one ...
> 
> thanks,
> Rich
> 
> 
> 
> 
> ____________________________
> Richard Apodaca
> Blog: http://depth-first.com
> 
> 
>  
> ____________________________________________________________________________________
> Everyone is raving about the all-new Yahoo! Mail 
> (http://advision.webevents.yahoo.com/mailbeta/)
> 
> 
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting


-- 
Martin Vogt
Vorgebirgsstr. 14, D-53111 Bonn
Email: mo...@t-...              Tel.: +49 (0)228 634376

[OpenBabel-scripting] Python bindings on amd64 Linux

[richard a. <ric...@ya...>]

Has anyone gotten the Python Open Babel interface to
work on amd64 Linux? I'm using rev 1578 of the svn
trunk

When I try to import openbabel, I get the following
error

>>> import openbabel
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File
"/usr/lib64/python2.4/site-packages/openbabel.py",
line 3, in ?
    import dl
ImportError: No module named dl

I noticed a similar problem reported here, but no
solution:

http://sourceforge.net/mailarchive/message.php?msg_id=37015184

I had no problems either compiling or installing
pyopenbabel - just loading it in python.

My system does lack the python dl module, which as far
as I can tell is supposed to be standard. In googling
around, I found several references to the python dl
module being unstable on amd64 - and therefore not
available.

So - has anyone found a workaround to this problem?

I tried one: comment out the code responsible for
loading dl in the first place (openbabel.py):

if sys.platform.find("linux") != -1:
    import dl
    sys.setdlopenflags(sys.getdlopenflags() |
dl.RTLD_GLOBAL)

I can in fact import openbabel after doing this. The
problem is that when using OBConversion, none of the
formats are loaded:

>>> import openbabel
>>> c=openbabel.OBConversion()
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/cmlreactlformat.so did not
load properly
==============================

... and dozens more load errors after this one ...

thanks,
Rich




____________________________
Richard Apodaca
Blog: http://depth-first.com


 
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Re: [OpenBabel-scripting] PyGTK widget completed

[Sam A. <ter...@ya...>]

Now everyone can check out the source code for the PyGTK project at http://code.google.com/p/pygtk-openbabel/ 

Re: [OpenBabel-scripting] PyGTK widget completed

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

On Oct 28, 2006, at 1:54 AM, Sam Aarons wrote:

> I have finished working on a PyGTK frontend to the always-great  
> program of OpenBabel.

Cool!

> Contributed Script Repository that Geoffrey has mentioned.

That would be great. My suggestion was a bit more humble (i.e., small  
snippets showing SMARTS matching, analysis of molecules, ...).

So I'm sure there would be a lot of interest in your project! If you  
send me a URL for a project page or download page, I'll get the rest  
started.

Thanks!
-Geoff

Re: [OpenBabel-scripting] Open Babel-Ruby - Success!

[richard a. <ric...@ya...>]

Open Babel conversions work in Ruby!

After studying the Python examples, I found that the
Open Babel-Ruby interface handles SMILES and Molfile
formats quite well (and presumably the others):

$ irb
irb(main):001:0> require 'openbabel_wrap'
=> true
irb(main):002:0> obc=Openbabel_wrap::OBConversion.new
=> #<Openbabel_wrap::OBConversion:0x2b5d3ca6bf98>
irb(main):003:0> mol=Openbabel_wrap::OBMol.new
=> #<Openbabel_wrap::OBMol:0x2b5d3ca670d8>
irb(main):004:0> obc.SetInAndOutFormats("smi", "mdl")
=> true
irb(main):005:0> obc.ReadString(mol, 'c1ccccc1')
=> true
irb(main):006:0> mol.NumAtoms
=> 6
irb(main):007:0> mol.AddHydrogens
=> true
irb(main):008:0> mol.NumAtoms
=> 12
irb(main):009:0> molfile=obc.WriteString mol
=> "\n OpenBabel10270622492D\n\n 12 12  0  0  0  0  0 
0  0  0999 V2000\n    0.0000    0.0000    0.0000 C   0
 0  0  0  0\n    0.0000    0.0000    0.0000 C   0  0 
0  0  0\n    0.0000    0.0000    0.0000 C   0  0  0  0
 0\n    0.0000    0.0000    0.0000 C   0  0  0  0  0\n
   0.0000    0.0000    0.0000 C   0  0  0  0  0\n   
0.0000    0.0000    0.0000 C   0  0  0  0  0\n   
0.0000    0.0000    0.0000 H   0  0  0  0  0\n   
0.0000    0.0000    0.0000 H   0  0  0  0  0\n   
0.0000    0.0000    0.0000 H   0  0  0  0  0\n   
0.0000    0.0000    0.0000 H   0  0  0  0  0\n   
0.0000    0.0000    0.0000 H   0  0  0  0  0\n   
0.0000    0.0000    0.0000 H   0  0  0  0  0\n  1  6 
2  0  0  0\n  1  2  1  0  0  0\n  1  7  1  0  0  0\n 
2  3  2  0  0  0\n  2  8  1  0  0  0\n  3  4  1  0  0 
0\n  3  9  1  0  0  0\n  4  5  2  0  0  0\n  4 10  1 
0  0  0\n  5  6  1  0  0  0\n  5 11  1  0  0  0\n  6
12  1  0  0  0\nM  END\n"
irb(main):010:0>    

I'm wondering about the best names for the library and
its modules. For example, this looks ideal to me:

require 'openbabel' # the name of the wrapper lib
                    # is openbabel - assuming no
                    # name clash w/ OB itself - I'll
                    # check this out.

mol = OpenBabel::OBMol.new
obc = OpenBabel::OBConversion.new

# etc.

This is easy to set up by editing the wrapper
generated by SWIG.

With some simple Ruby metaprogramming techniques, it's
even possible to give method names that follow Ruby
convention:

require 'openbabel'

mol = OpenBabel::OBMol.new

atom_count = mol.num_atoms
mw = mol.mol_wt

# ... etc.

And then it might be worth offering a RubyGem.
RMagick, which is the Ruby interface for ImageMagick
followed this route.

cheers,
Rich

--- richard apodaca <ric...@ya...> wrote:

> Success!
> 
> Geoff, I think this works now. I checked out OB-SVN.
> With a couple of minor modifications (for example,
> changing openbabel_ruby.cpp to openbabel_wrap.cpp,
> adding #include <math.h>) - I'll detail them
> shortly),
> I got the scripts/ruby wrapper compiled.
> 
> Behold:
> 
> $ irb
> irb(main):001:0> require 'openbabel_wrap'
> => true
> irb(main):002:0> m=Openbabel_wrap::OBMol.new
> => #<Openbabel_wrap::OBMol:0x2ba75b5563c8>
> irb(main):003:0> h=m.NewAtom
> => #<Openbabel_wrap::OBAtom:0x2ba75b552778>
> irb(main):004:0> h.SetAtomicNum(1)
> => nil
> irb(main):005:0> m.GetMolWt
> => 1.00794
> 
> It looks like all of the format interconversion
> utilities (smiles, mdl, etc) are missing, but we
> should be able to fix that. The important thing is
> now
> we've got a good place to start from.
> 
> It must have been the older version of OB that I was
> using (2.0.2) that was the source of the problems.
> 
> Could you verify that the above Ruby code works for
> you too?
> 
> BTW, I'll respond in more detail to you're
> suggestions
> below shortly.
> 
> cheers,
> Rich
> 
> --- Geoffrey Hutchison <ge...@ge...>
> wrote:
> 
> > 
> > On Oct 14, 2006, at 4:47 PM, richard apodaca
> wrote:
> > 
> > > (3) edit openbabel.i: comment out line 27 (Swig
> > can't
> > > find std_list.i for Ruby - it works for Python,
> > > though). Change line 5 to %module openbabel_wrap
> > > (don't want to risk a collision w/ installed
> > openbabel
> > > library)
> > 
> > Seems like it might soon be a good idea to have
> > different openbabel.i  
> > files for the different scripting modules. The SVN
> > version (for  
> > 2.1.0bX) has the std_list.i #ifdef'ed out
> > automatically.
> > 
> > > This generates lots of warnings that don't
> appear
> > when
> > > the argument is -python instead of -ruby (maybe
> > this
> > > is the problem):
> > 
> > Nah. I get these for Perl and Python too. The
> > problem is that C++ has  
> > different naming restrictions than scripting
> > languages. So some  
> > functions may not be available until remapped. Not
> a
> > problem for core  
> > functionality, as far as I've seen.
> > 
> > > (8) save the following as "extconf.rb":
> > > require 'mkmf'
> > >
> > > dir_config('openbabel')
> > > dir_config('openbabel-2.0')
> > > have_library('openbabel')
> > >
> > > create_makefile('openbabel_wrap')
> > 
> > One bit which might be good is to have a path to
> the
> > libopenbabel  
> > too. On my system it was looking in the normal
> > search path, which may  
> > or may not work for everyone (e.g., with a custom
> > --prefix call to  
> > the Open Babel configure script.)
> > 
> > > (9) create the makefile:
> > >
> > > ruby extconf.rb
> > >
> >
>
--with-openbabel-include='/usr/local/include/openbabel-2.0/openbabel'
> > >
> >
>
--with-openbabel-2.0-include='/usr/local/include/openbabel-2.0'
> > 
> > Ideally could this be something that could go into
> > the scripts/ 
> > Makefile.am as a shell script? The Makefiles
> should
> > have the correct  
> > paths already.
> > 
> > > (13) require 'openbabel_wrap'
> > > irb(main):001:0> require 'openbabel_wrap'
> > 
> > Here (on OS X, Ruby 1.8.4), I get:
> > 
> > irb(main):001:0> require 'openbabel_wrap'
> > => true
> > 
> > Not quite sure of enough ruby (or the binding) to
> > try anything else  
> > yet... Maybe you should try this on the SVN
> version?
> > I'd obviously  
> > like to get a ruby module into 2.1.0 anyway.
> > 
> > Cheers,
> > -Geoff
> > 
> 
> 
> 
>  
>
____________________________________________________________________________________
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>
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> 



 
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[OpenBabel-scripting] PyGTK widget completed

[Sam A. <ter...@ya...>]

I have finished working on a PyGTK frontend to the always-great program of OpenBabel.  Anyways, it's totally written using the python bindings and if anyone would like to see the code just e-mail me.  Basic conversion between all formats and a frontend to the PubChem database (which has 8 million compounds).  Also, this app could be the first program to be in the Contributed Script Repository that Geoffrey has mentioned.

[OpenBabel-scripting] Open Babel-Ruby - Success!

[richard a. <ric...@ya...>]

Success!

Geoff, I think this works now. I checked out OB-SVN.
With a couple of minor modifications (for example,
changing openbabel_ruby.cpp to openbabel_wrap.cpp,
adding #include <math.h>) - I'll detail them shortly),
I got the scripts/ruby wrapper compiled.

Behold:

$ irb
irb(main):001:0> require 'openbabel_wrap'
=> true
irb(main):002:0> m=Openbabel_wrap::OBMol.new
=> #<Openbabel_wrap::OBMol:0x2ba75b5563c8>
irb(main):003:0> h=m.NewAtom
=> #<Openbabel_wrap::OBAtom:0x2ba75b552778>
irb(main):004:0> h.SetAtomicNum(1)
=> nil
irb(main):005:0> m.GetMolWt
=> 1.00794

It looks like all of the format interconversion
utilities (smiles, mdl, etc) are missing, but we
should be able to fix that. The important thing is now
we've got a good place to start from.

It must have been the older version of OB that I was
using (2.0.2) that was the source of the problems.

Could you verify that the above Ruby code works for
you too?

BTW, I'll respond in more detail to you're suggestions
below shortly.

cheers,
Rich

--- Geoffrey Hutchison <ge...@ge...>
wrote:

> 
> On Oct 14, 2006, at 4:47 PM, richard apodaca wrote:
> 
> > (3) edit openbabel.i: comment out line 27 (Swig
> can't
> > find std_list.i for Ruby - it works for Python,
> > though). Change line 5 to %module openbabel_wrap
> > (don't want to risk a collision w/ installed
> openbabel
> > library)
> 
> Seems like it might soon be a good idea to have
> different openbabel.i  
> files for the different scripting modules. The SVN
> version (for  
> 2.1.0bX) has the std_list.i #ifdef'ed out
> automatically.
> 
> > This generates lots of warnings that don't appear
> when
> > the argument is -python instead of -ruby (maybe
> this
> > is the problem):
> 
> Nah. I get these for Perl and Python too. The
> problem is that C++ has  
> different naming restrictions than scripting
> languages. So some  
> functions may not be available until remapped. Not a
> problem for core  
> functionality, as far as I've seen.
> 
> > (8) save the following as "extconf.rb":
> > require 'mkmf'
> >
> > dir_config('openbabel')
> > dir_config('openbabel-2.0')
> > have_library('openbabel')
> >
> > create_makefile('openbabel_wrap')
> 
> One bit which might be good is to have a path to the
> libopenbabel  
> too. On my system it was looking in the normal
> search path, which may  
> or may not work for everyone (e.g., with a custom
> --prefix call to  
> the Open Babel configure script.)
> 
> > (9) create the makefile:
> >
> > ruby extconf.rb
> >
>
--with-openbabel-include='/usr/local/include/openbabel-2.0/openbabel'
> >
>
--with-openbabel-2.0-include='/usr/local/include/openbabel-2.0'
> 
> Ideally could this be something that could go into
> the scripts/ 
> Makefile.am as a shell script? The Makefiles should
> have the correct  
> paths already.
> 
> > (13) require 'openbabel_wrap'
> > irb(main):001:0> require 'openbabel_wrap'
> 
> Here (on OS X, Ruby 1.8.4), I get:
> 
> irb(main):001:0> require 'openbabel_wrap'
> => true
> 
> Not quite sure of enough ruby (or the binding) to
> try anything else  
> yet... Maybe you should try this on the SVN version?
> I'd obviously  
> like to get a ruby module into 2.1.0 anyway.
> 
> Cheers,
> -Geoff
> 



 
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Re: [OpenBabel-scripting] Ruby-Open Babel not Still Not Working (detailed)

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

On Oct 14, 2006, at 4:47 PM, richard apodaca wrote:

> (3) edit openbabel.i: comment out line 27 (Swig can't
> find std_list.i for Ruby - it works for Python,
> though). Change line 5 to %module openbabel_wrap
> (don't want to risk a collision w/ installed openbabel
> library)

Seems like it might soon be a good idea to have different openbabel.i  
files for the different scripting modules. The SVN version (for  
2.1.0bX) has the std_list.i #ifdef'ed out automatically.

> This generates lots of warnings that don't appear when
> the argument is -python instead of -ruby (maybe this
> is the problem):

Nah. I get these for Perl and Python too. The problem is that C++ has  
different naming restrictions than scripting languages. So some  
functions may not be available until remapped. Not a problem for core  
functionality, as far as I've seen.

> (8) save the following as "extconf.rb":
> require 'mkmf'
>
> dir_config('openbabel')
> dir_config('openbabel-2.0')
> have_library('openbabel')
>
> create_makefile('openbabel_wrap')

One bit which might be good is to have a path to the libopenbabel  
too. On my system it was looking in the normal search path, which may  
or may not work for everyone (e.g., with a custom --prefix call to  
the Open Babel configure script.)

> (9) create the makefile:
>
> ruby extconf.rb
> --with-openbabel-include='/usr/local/include/openbabel-2.0/openbabel'
> --with-openbabel-2.0-include='/usr/local/include/openbabel-2.0'

Ideally could this be something that could go into the scripts/ 
Makefile.am as a shell script? The Makefiles should have the correct  
paths already.

> (13) require 'openbabel_wrap'
> irb(main):001:0> require 'openbabel_wrap'

Here (on OS X, Ruby 1.8.4), I get:

irb(main):001:0> require 'openbabel_wrap'
=> true

Not quite sure of enough ruby (or the binding) to try anything else  
yet... Maybe you should try this on the SVN version? I'd obviously  
like to get a ruby module into 2.1.0 anyway.

Cheers,
-Geoff

Re: [OpenBabel-scripting] Contributed Script repository?

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

I've gotten a few requests for more examples of Open Babel scripting  
access.

Judging from the recent (valid) complaints that I managed to break  
the Python module in the Subversion trunk, do I have a few volunteers  
to contribute some snippets for a "repository" on the wiki?

These examples would become part of the Python developer tutorial,  
and would include attribution and immortal fame. :-)

Thanks!
-Geoff

Re: [OpenBabel-scripting] Python Bindings

[Martin V. <mar...@bi...>]

I suppose you should try the attached openbabel.i. which includes the
headers 'residue.h', 'mol.h' and 'atom.h'.

You need to rebuild openbabel_python.cpp of course.

I suppose the bindings broke when the declarations of OBResidue, OBMol
and OBAtom were moved out of 'mol.h'

- Martin

Pascoe, S (Stephen) wrote:
> I can confirm that I get a similar error when trying to build the python
> bindings with r1574 of the SVN source.  I have set OPENBABEL_INSTALL
> such that $OPENBABEL_INSTALL/include/openbabel-2.0 exists.  I have even
> tried recreating openbabel_python.cpp with the latest swig.  This is the
> truncated error:
> ...

-- 
Martin Vogt
B-IT Life Science Informatics, <http://www.bit.uni-bonn.de>
Dahlmannstrasse 2, D-53113 Bonn
phone: +49 228 2699 310, <mailto:mar...@bi...>

Re: [OpenBabel-scripting] Python Bindings

[Pascoe, S \(Stephen\) <S.P...@rl...>]

Thanks Martin that works a treat!

Stephen.

---
Stephen Pascoe  01235 445980
British Atmospheric Data Centre
Rutherford Appleton Laboratory, CCLRC

-----Original Message-----
From: Martin Vogt [mailto:mar...@bi...]=20
Sent: 25 October 2006 11:34
To: Pascoe, S (Stephen)
Cc: ope...@li...
Subject: Re: [OpenBabel-scripting] Python Bindings

I suppose you should try the attached openbabel.i. which includes the
headers 'residue.h', 'mol.h' and 'atom.h'.

You need to rebuild openbabel_python.cpp of course.

I suppose the bindings broke when the declarations of OBResidue, OBMol
and OBAtom were moved out of 'mol.h'

- Martin

Pascoe, S (Stephen) wrote:
> I can confirm that I get a similar error when trying to build the=20
> python bindings with r1574 of the SVN source.  I have set=20
> OPENBABEL_INSTALL such that $OPENBABEL_INSTALL/include/openbabel-2.0=20
> exists.  I have even tried recreating openbabel_python.cpp with the=20
> latest swig.  This is the truncated error:
> ...

--
Martin Vogt
B-IT Life Science Informatics, <http://www.bit.uni-bonn.de>
Dahlmannstrasse 2, D-53113 Bonn
phone: +49 228 2699 310, <mailto:mar...@bi...>

Re: [OpenBabel-scripting] Python Bindings

[Noel O'B. <bao...@gm...>]

As Geoff pointed out in a previous email, your LD_LIBRARY_PATH may be
the key. What is its value?

On 25/10/06, Pascoe, S (Stephen) <S.P...@rl...> wrote:
>
>
> I can confirm that I get a similar error when trying to build the python
> bindings with r1574 of the SVN source.  I have set OPENBABEL_INSTALL such
> that $OPENBABEL_INSTALL/include/openbabel-2.0 exists.  I
> have even tried recreating openbabel_python.cpp with the latest swig.  This
> is the truncated error:
>
> > python setup.py build 2>&1 | less
> INFO: Using the value of $OPENBABEL_INSTALL
> (/research/home/spascoe/host/saturn/
> opt/openbabel)
> running build
> running build_py
> copying openbabel.py -> build/lib.linux-i686-2.4
> running build_ext
> building '_openbabel' extension
> gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -march=i586 -mtune=i686
> -fmessage
> -length=0 -Wall -D_FORTIFY_SOURCE=2 -g -fPIC
> -I/research/home/spascoe/host/satur
> n/opt/openbabel/include/openbabel-2.0
> -I/research/home/spascoe/host/saturn/opt/o
> penbabel/include/openbabel-2.0/openbabel -I/usr/include/python2.4 -c
> openbabel_p
> ython.cpp -o build/temp.linux-i686-2.4/openbabel_python.o
> openbabel_python.cpp: In function 'PyObject*
> _wrap_OBMol_CreateResidue(PyObject*
> , PyObject*)':
> openbabel_python.cpp:38606: error: 'OBResidue' was not declared in this
> scope
> openbabel_python.cpp:38606: error: 'result' was not declared in this scope
> openbabel_python.cpp:38617: error: expected primary-expression before ')'
> token
> openbabel_python.cpp: In function 'PyObject*
> _wrap_OBMol_DestroyResidue(PyObject
> *, PyObject*)':
> openbabel_python.cpp:38688: error: 'OBResidue' was not declared in this
> scope
> openbabel_python.cpp:38688: error: 'arg2' was not declared in this scope
> openbabel_python.cpp:38688: error: expected primary-expression before ')'
> token
> openbabel_python.cpp:38688: error: expected `;' before numeric constant
> openbabel_python.cpp:38706: error: expected type-specifier before
> 'OBResidue'
> openbabel_python.cpp:38706: error: expected `>' before 'OBResidue'
> openbabel_python.cpp:38706: error: expected `(' before 'OBResidue'
> openbabel_python.cpp:38706: error: expected primary-expression before '>'
> token
> openbabel_python.cpp:38706: error: expected `)' before ';' token
> openbabel_python.cpp:38707: error: no matching function for call to
> 'OpenBabel::
> OBMol::DestroyResidue(<type error>)'
>  ...
>
> A summary of my system:
>
> > uname -a; cat /etc/issue; gcc -v
> Linux saturn 2.6.13-15.8-smp #1 SMP Tue Feb 7 11:07:24 UTC 2006 i686 i686
> i386 GNU/Linux
>
> Welcome to SUSE LINUX 10.0 (i586) - Kernel \r (\l).
>
>
> Using built-in specs.
> Target: i586-suse-linux
> Configured with: ../configure --enable-threads=posix --prefix=/usr
> --with-local-prefix=/usr/local --infodir=/usr/share/info
> --mandir=/usr/share/man --libdir=/usr/lib --libexecdir=/usr/lib
> --enable-languages=c,c++,objc,f95,java,ada
> --disable-checking
> --with-gxx-include-dir=/usr/include/c++/4.0.2
> --enable-java-awt=gtk --disable-libjava-multilib --with-slibdir=/lib
> --with-system-zlib --enable-shared --enable-__cxa_atexit
> --without-system-libunwind --host=i586-suse-linux
> Thread model: posix
> gcc version 4.0.2 20050901 (prerelease) (SUSE Linux)
>
> Stephen.
>
> ---
> Stephen Pascoe
> British Atmospheric Data Centre
> Rutherford Appleton Laboratory, CCLRC
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job
> easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>
>

Re: [OpenBabel-scripting] Python Bindings

[Pascoe, S \(Stephen\) <S.P...@rl...>]

I can confirm that I get a similar error when trying to build the python
bindings with r1574 of the SVN source.  I have set OPENBABEL_INSTALL
such that $OPENBABEL_INSTALL/include/openbabel-2.0 exists.  I have even
tried recreating openbabel_python.cpp with the latest swig.  This is the
truncated error:
=20
> python setup.py build 2>&1 | less
INFO: Using the value of $OPENBABEL_INSTALL
(/research/home/spascoe/host/saturn/
opt/openbabel)
running build
running build_py
copying openbabel.py -> build/lib.linux-i686-2.4
running build_ext
building '_openbabel' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -march=3Di586 =
-mtune=3Di686
-fmessage
-length=3D0 -Wall -D_FORTIFY_SOURCE=3D2 -g -fPIC
-I/research/home/spascoe/host/satur
n/opt/openbabel/include/openbabel-2.0
-I/research/home/spascoe/host/saturn/opt/o
penbabel/include/openbabel-2.0/openbabel -I/usr/include/python2.4 -c
openbabel_p
ython.cpp -o build/temp.linux-i686-2.4/openbabel_python.o
openbabel_python.cpp: In function 'PyObject*
_wrap_OBMol_CreateResidue(PyObject*
, PyObject*)':
openbabel_python.cpp:38606: error: 'OBResidue' was not declared in this
scope
openbabel_python.cpp:38606: error: 'result' was not declared in this
scope
openbabel_python.cpp:38617: error: expected primary-expression before
')' token
openbabel_python.cpp: In function 'PyObject*
_wrap_OBMol_DestroyResidue(PyObject
*, PyObject*)':
openbabel_python.cpp:38688: error: 'OBResidue' was not declared in this
scope
openbabel_python.cpp:38688: error: 'arg2' was not declared in this scope
openbabel_python.cpp:38688: error: expected primary-expression before
')' token
openbabel_python.cpp:38688: error: expected `;' before numeric constant
openbabel_python.cpp:38706: error: expected type-specifier before
'OBResidue'
openbabel_python.cpp:38706: error: expected `>' before 'OBResidue'
openbabel_python.cpp:38706: error: expected `(' before 'OBResidue'
openbabel_python.cpp:38706: error: expected primary-expression before
'>' token
openbabel_python.cpp:38706: error: expected `)' before ';' token
openbabel_python.cpp:38707: error: no matching function for call to
'OpenBabel::
OBMol::DestroyResidue(<type error>)'
 ...
=20
A summary of my system:
=20
> uname -a; cat /etc/issue; gcc -v
Linux saturn 2.6.13-15.8-smp #1 SMP Tue Feb 7 11:07:24 UTC 2006 i686
i686 i386 GNU/Linux
=20
Welcome to SUSE LINUX 10.0 (i586) - Kernel \r (\l).
=20

Using built-in specs.
Target: i586-suse-linux
Configured with: ../configure --enable-threads=3Dposix --prefix=3D/usr
--with-local-prefix=3D/usr/local --infodir=3D/usr/share/info
--mandir=3D/usr/share/man --libdir=3D/usr/lib --libexecdir=3D/usr/lib
--enable-languages=3Dc,c++,objc,f95,java,ada --disable-checking
--with-gxx-include-dir=3D/usr/include/c++/4.0.2 --enable-java-awt=3Dgtk
--disable-libjava-multilib --with-slibdir=3D/lib --with-system-zlib
--enable-shared --enable-__cxa_atexit --without-system-libunwind
--host=3Di586-suse-linux
Thread model: posix
gcc version 4.0.2 20050901 (prerelease) (SUSE Linux)

Stephen.
=20
---
Stephen Pascoe=20
British Atmospheric Data Centre
Rutherford Appleton Laboratory, CCLRC
=20

Re: [OpenBabel-scripting] Python shared object file error

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

On Oct 22, 2006, at 8:21 PM, Sam Aarons wrote:

> I finally got everything in the bindings to work
> correctly, but when i'm running my python application
> (which uses openbabel bindings) i get this error
> message.
...
> ImportError: libopenbabel.so.1: cannot open shared
> object file: No such file or directory

By default, Open Babel compiles and installs into /usr/local (i.e., / 
usr/local/libopenbabel.so)

Depending on your machine, this may not be in a normal library search  
path. If you're running Linux (looks like it), you'll need to edit / 
etc/ld.so.conf or the LD_LIBRARY_PATH:

http://tldp.org/HOWTO/Program-Library-HOWTO/shared-libraries.html

Cheers,
-Geoff

[OpenBabel-scripting] Python shared object file error

[Sam A. <ter...@ya...>]

I finally got everything in the bindings to work
correctly, but when i'm running my python application
(which uses openbabel bindings) i get this error
message.

dlopen("/usr/lib/python2.4/site-packages/_openbabel.so",
2);
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
ImportError: libopenbabel.so.1: cannot open shared
object file: No such file or directory

Can anyone help me on this?

[OpenBabel-scripting] Python BIndings

[Sam A. <ter...@ya...>]

I have the latest version of Openbabel (SVN)
installed.  Then i proceeded to install the Python
bindings and everything went berzerk.

WARNING: Environment variable OPENBABEL_INSTALL is not
set
INFO: Looking for library and include files in
../../src
running build
running build_py
creating build
creating build/lib.linux-i686-2.4
copying openbabel.py -> build/lib.linux-i686-2.4
copying pyopenbabel.py -> build/lib.linux-i686-2.4
running build_ext
building '_openbabel' extension
creating build/temp.linux-i686-2.4
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O3
-Wall -Wstrict-prototypes -fPIC -I../../src
-I/usr/include/python2.4 -c openbabel_python.cpp -o
build/temp.linux-i686-2.4/openbabel_python.o
cc1plus: warning: command line option
"-Wstrict-prototypes" is valid for Ada/C/ObjC but not
for C++
openbabel_python.cpp: In function ‘PyObject*
_wrap_OBMol_CreateResidue(PyObject*, PyObject*)’:
openbabel_python.cpp:38606: error: ‘OBResidue’ was not
declared in this scope
openbabel_python.cpp:38606: error: ‘result’ was not
declared in this scope
openbabel_python.cpp:38617: error: expected
primary-expression before ‘)’ token
openbabel_python.cpp: In function ‘PyObject*
_wrap_OBMol_DestroyResidue(PyObject*, PyObject*)’:
openbabel_python.cpp:38688: error: ‘OBResidue’ was not
declared in this scope
openbabel_python.cpp:38688: error: ‘arg2’ was not
declared in this scope
openbabel_python.cpp:38688: error: expected
primary-expression before ‘)’ token
openbabel_python.cpp:38688: error: expected `;' before
numeric constant
openbabel_python.cpp:38706: error: expected
type-specifier before ‘OBResidue’
openbabel_python.cpp:38706: error: expected `>' before
‘OBResidue’
openbabel_python.cpp:38706: error: expected `(' before
‘OBResidue’
openbabel_python.cpp:38706: error: expected
primary-expression before ‘>’ token
openbabel_python.cpp:38706: error: expected `)' before
‘;’ token
openbabel_python.cpp: In function ‘PyObject*
_wrap_OBMol_AddResidue(PyObject*, PyObject*)’:
openbabel_python.cpp:39090: error: ‘OBResidue’ was not
declared in this scope
openbabel_python.cpp:39090: error: ‘arg2’ was not
declared in this scope
openbabel_python.cpp:39112: error: expected
type-specifier before ‘OBResidue’
openbabel_python.cpp:39112: error: expected `>' before
‘OBResidue’
openbabel_python.cpp:39112: error: expected `(' before
‘OBResidue’
openbabel_python.cpp:39112: error: expected
primary-expression before ‘>’ token
openbabel_python.cpp:39112: error: expected `)' before
‘;’ token
openbabel_python.cpp: In function ‘PyObject*
_wrap_OBMol_DeleteResidue(PyObject*, PyObject*)’:
openbabel_python.cpp:39220: error: ‘OBResidue’ was not
declared in this scope
openbabel_python.cpp:39220: error: ‘arg2’ was not
declared in this scope
openbabel_python.cpp:39220: error: expected
primary-expression before ‘)’ token
openbabel_python.cpp:39220: error: expected `;' before
numeric constant
openbabel_python.cpp:39239: error: expected
type-specifier before ‘OBResidue’
openbabel_python.cpp:39239: error: expected `>' before
‘OBResidue’
openbabel_python.cpp:39239: error: expected `(' before
‘OBResidue’
openbabel_python.cpp:39239: error: expected
primary-expression before ‘>’ token
openbabel_python.cpp:39239: error: expected `)' before
‘;’ token
openbabel_python.cpp: In function ‘PyObject*
_wrap_OBMol_NewResidue(PyObject*, PyObject*)’:
openbabel_python.cpp:39273: error: ‘OBResidue’ was not
declared in this scope
openbabel_python.cpp:39273: error: ‘result’ was not
declared in this scope
openbabel_python.cpp:39284: error: expected
primary-expression before ‘)’ token
openbabel_python.cpp: In function ‘PyObject*
_wrap_OBMol_GetResidue(PyObject*, PyObject*)’:
openbabel_python.cpp:39863: error: ‘OBResidue’ was not
declared in this scope
openbabel_python.cpp:39863: error: ‘result’ was not
declared in this scope
openbabel_python.cpp:39882: error: expected
primary-expression before ‘)’ token
openbabel_python.cpp: In function ‘PyObject*
_wrap_OBMol_BeginResidue(PyObject*, PyObject*)’:
openbabel_python.cpp:43939: error: ‘OBResidue’ was not
declared in this scope
openbabel_python.cpp:43939: error: ‘OBResidue’ cannot
appear in a constant-expression
openbabel_python.cpp:43939: error: template argument 1
is invalid
openbabel_python.cpp:43939: error: template argument 1
is invalid
openbabel_python.cpp:43939: error: template argument 2
is invalid
openbabel_python.cpp:43939: error: expected
initializer before ‘*’ token
openbabel_python.cpp:43940: error: ‘result’ was not
declared in this scope
openbabel_python.cpp:43961: error: ‘arg2’ was not
declared in this scope
openbabel_python.cpp:43961: error: ‘OBResidue’ cannot
appear in a constant-expression
openbabel_python.cpp:43961: error: ‘OBResidue’ cannot
appear in a constant-expression
openbabel_python.cpp:43961: error: template argument 1
is invalid
openbabel_python.cpp:43961: error: template argument 1
is invalid
openbabel_python.cpp:43961: error: template argument 2
is invalid
openbabel_python.cpp:43961: error: expected `>' before
‘::’ token
openbabel_python.cpp:43961: error: expected `(' before
‘::’ token
openbabel_python.cpp:43961: error: ‘::iterator’ has
not been declared
openbabel_python.cpp:43961: error: expected
primary-expression before ‘>’ token
openbabel_python.cpp:43961: error: expected `)' before
‘;’ token
openbabel_python.cpp:43962: error: expected
primary-expression before ‘)’ token
openbabel_python.cpp: In function ‘PyObject*
_wrap_OBMol_NextResidue(PyObject*, PyObject*)’:
openbabel_python.cpp:43973: error: ‘OBResidue’ was not
declared in this scope
openbabel_python.cpp:43973: error: ‘OBResidue’ cannot
appear in a constant-expression
openbabel_python.cpp:43973: error: template argument 1
is invalid
openbabel_python.cpp:43973: error: template argument 1
is invalid
openbabel_python.cpp:43973: error: template argument 2
is invalid
openbabel_python.cpp:43973: error: expected
initializer before ‘*’ token
openbabel_python.cpp:43974: error: ‘result’ was not
declared in this scope
openbabel_python.cpp:43995: error: ‘arg2’ was not
declared in this scope
openbabel_python.cpp:43995: error: ‘OBResidue’ cannot
appear in a constant-expression
openbabel_python.cpp:43995: error: ‘OBResidue’ cannot
appear in a constant-expression
openbabel_python.cpp:43995: error: template argument 1
is invalid
openbabel_python.cpp:43995: error: template argument 1
is invalid
openbabel_python.cpp:43995: error: template argument 2
is invalid
openbabel_python.cpp:43995: error: expected `>' before
‘::’ token
openbabel_python.cpp:43995: error: expected `(' before
‘::’ token
openbabel_python.cpp:43995: error: ‘::iterator’ has
not been declared
openbabel_python.cpp:43995: error: expected
primary-expression before ‘>’ token
openbabel_python.cpp:43995: error: expected `)' before
‘;’ token
openbabel_python.cpp:43996: error: expected
primary-expression before ‘)’ token
../../src/residue.h: At global scope:
../../src/residue.h:305: warning: ‘OpenBabel::Residue’
defined but not used
../../src/residue.h:348: warning:
‘OpenBabel::ElemDesc’ defined but not used
../../src/residue.h:380: warning: ‘OpenBabel::ResNo’
defined but not used
../../src/residue.h:381: warning: ‘OpenBabel::ElemNo’
defined but not used
error: command 'gcc' failed with exit status 1

Please tell me how to fix this.

Re: [OpenBabel-scripting] Ruby-Open Babel not Still Not Working (detailed)

[richard a. <ric...@ya...>]

Looks like my message got cut off. Here's the rest of
it:

type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vectorBond_emptyq___(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:4945: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4949: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vectorResidue__SWIG_3(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:5263: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5267: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vectorResidue(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:5314: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5323: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vectorResidue___len__(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:5373: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5377: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vectorResidue_emptyq___(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:5405: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5409: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vectorRing__SWIG_3(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:5723: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5727: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vectorRing(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:5774: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5783: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vectorRing___len__(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:5833: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5837: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vectorRing_emptyq___(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:5865: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5869: warning: dereferencing
type-punned pointer will break strict-aliasing rules
gcc -shared  -L"/usr/lib64" -o openbabel_wrap.so
openbabel_wrap.o  -lruby -lopenbabel  -lpthread -ldl
-lcrypt -lm   -lc


The following files are created:

openbabel_wrap.o
openbabel_wrap.so

(12) irb

(13) require 'openbabel_wrap'

produces:

irb(main):001:0> require 'openbabel_wrap'
(eval): [BUG] Segmentation fault
ruby 1.8.5 (2006-08-25) [x86_64-linux-gnu]

Aborted

As I mentioned before, if I remove the OBAtom, OBBond,
and OBMol definitions from Init_openbabel_wrap (last
function), the Ruby module is loaded without
segfaulting. I can also remove everything from the
respective stanzas except the first line and still I
get a segfault, so I'm guessing this is where the
error happens.

Would someone be willing to go through this series of
steps to verify that the problem is not related to my
system's configuration (my version of Ruby, my
platform, my compiler, etc.)

cheers,
Rich

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[OpenBabel-scripting] Ruby-Open Babel not Still Not Working (detailed)

[richard a. <ric...@ya...>]

I upgraded to SWIG 1.3.29, as Geoff suggested. After
compiling the swig wrapper, I still get a segfault on
loading the Ruby module.

Before submitting a bug report to SWIG, I wanted to
make sure I was doing this correctly. So here is my
process in detail. I'm using Open Babel 2.0.2, Ruby
1.8.5, and Mandriva Linux 2007 amd64.

(1) ./configure, make, and (as root) make install OB

(2) cd into OPENBABEL/scripts

(3) edit openbabel.i: comment out line 27 (Swig can't
find std_list.i for Ruby - it works for Python,
though). Change line 5 to %module openbabel_wrap
(don't want to risk a collision w/ installed openbabel
library)

(4) generate the SWIG wrapper:

swig -ruby -c++ -I../src openbabel.i

This generates lots of warnings that don't appear when
the argument is -python instead of -ruby (maybe this
is the problem):

../src/math/vector3.h:114: Warning(389): operator[]
ignored (consider using %extend)
../src/math/vector3.h:123: Warning(362): operator=
ignored
../src/math/vector3.h:130: Warning(378): operator!=
ignored
../src/math/vector3.h:180: Warning(365): operator+=
ignored
../src/math/vector3.h:187: Warning(366): operator-=
ignored
../src/math/vector3.h:194: Warning(365): operator+=
ignored
../src/math/vector3.h:201: Warning(366): operator-=
ignored
../src/math/vector3.h:208: Warning(367): operator*=
ignored
../src/math/vector3.h:215: Warning(368): operator/=
ignored
../src/math/vector3.h:217: Warning(367): operator*=
ignored
../src/bitvec.h:121: Warning(362): operator= ignored
../src/bitvec.h:122: Warning(371): operator&= ignored
../src/bitvec.h:123: Warning(372): operator|= ignored
../src/bitvec.h:128: Warning(372): operator|= ignored
../src/bitvec.h:129: Warning(370): operator^= ignored
../src/bitvec.h:130: Warning(366): operator-= ignored
../src/bitvec.h:131: Warning(365): operator+= ignored
../src/bitvec.h:136: Warning(389): operator[] ignored
(consider using %extend)
../src/generic.h:152: Warning(362): operator= ignored
../src/generic.h:170: Warning(362): operator= ignored
../src/generic.h:279: Warning(362): operator= ignored
../src/generic.h:310: Warning(362): operator= ignored
../src/generic.h:364: Warning(362): operator= ignored
../src/generic.h:399: Warning(362): operator= ignored
../src/generic.h:437: Warning(362): operator= ignored
../src/generic.h:483: Warning(362): operator= ignored
../src/generic.h:531: Warning(362): operator= ignored
../src/generic.h:567: Warning(362): operator= ignored
../src/generic.h:598: Warning(362): operator= ignored
../src/mol.h:87: Warning(362): operator= ignored
../src/mol.h:233: Warning(362): operator= ignored
../src/mol.h:785: Warning(362): operator= ignored
../src/mol.h:786: Warning(365): operator+= ignored
../src/ring.h:62: Warning(362): operator= ignored
../src/parsmart.h:207: Warning(362): operator= ignored
../src/oberror.h:162: Warning(401): Nothing known
about base class 'std::stringbuf'. Ignored.
../src/obconversion.h:175: Warning(401): Nothing known
about base class 'std::binary_function<char const
*,char const *,bool >'. Ignored.
../src/obconversion.h:175: Warning(401): Maybe you
forgot to instantiate 'std::binary_function<char const
*,char const *,bool >' using %template.
openbabel.i:33: Warning(801): Wrong class name
(corrected to `VectorInt')
openbabel.i:33: Warning(801): Wrong class name
(corrected to `VectorInt')
openbabel.i:34: Warning(801): Wrong class name
(corrected to `VvInt')
openbabel.i:34: Warning(801): Wrong class name
(corrected to `VvInt')
openbabel.i:35: Warning(801): Wrong class name
(corrected to `VectorDouble')
openbabel.i:35: Warning(801): Wrong class name
(corrected to `VectorDouble')
openbabel.i:36: Warning(801): Wrong class name
(corrected to `VVector3')
openbabel.i:36: Warning(801): Wrong class name
(corrected to `VVector3')
openbabel.i:38: Warning(801): Wrong class name
(corrected to `VectorMol')
openbabel.i:38: Warning(801): Wrong class name
(corrected to `VectorMol')
openbabel.i:39: Warning(801): Wrong class name
(corrected to `VectorBond')
openbabel.i:39: Warning(801): Wrong class name
(corrected to `VectorBond')
openbabel.i:40: Warning(801): Wrong class name
(corrected to `VectorResidue')
openbabel.i:40: Warning(801): Wrong class name
(corrected to `VectorResidue')
openbabel.i:41: Warning(801): Wrong class name
(corrected to `VectorRing')
openbabel.i:41: Warning(801): Wrong class name
(corrected to `VectorRing')
../src/math/vector3.h:57: Warning(801): Wrong class
name (corrected to `Vector3')
../src/math/vector3.h:57: Warning(801): Wrong class
name (corrected to `Vector3')
../src/math/vector3.h:126: Warning(503): Can't wrap
'operator <<' unless renamed to a valid identifier.
../src/math/vector3.h:129: Warning(503): Can't wrap
'operator ==' unless renamed to a valid identifier.
../src/math/vector3.h:137: Warning(503): Can't wrap
'operator +' unless renamed to a valid identifier.
../src/math/vector3.h:142: Warning(503): Can't wrap
'operator -' unless renamed to a valid identifier.
../src/math/vector3.h:147: Warning(503): Can't wrap
'operator -' unless renamed to a valid identifier.
../src/math/vector3.h:152: Warning(503): Can't wrap
'operator *' unless renamed to a valid identifier.
../src/math/vector3.h:157: Warning(503): Can't wrap
'operator *' unless renamed to a valid identifier.
../src/math/vector3.h:162: Warning(503): Can't wrap
'operator /' unless renamed to a valid identifier.
../src/math/vector3.h:171: Warning(503): Can't wrap
'operator *' unless renamed to a valid identifier.
../src/math/vector3.h:225: Warning(503): Can't wrap
'OpenBabel::dot' unless renamed to a valid identifier.
../src/math/vector3.h:228: Warning(503): Can't wrap
'OpenBabel::cross' unless renamed to a valid
identifier.
../src/math/vector3.h:231: Warning(503): Can't wrap
'OpenBabel::vectorAngle' unless renamed to a valid
identifier.
../src/math/vector3.h:235: Warning(503): Can't wrap
'OpenBabel::CalcTorsionAngle' unless renamed to a
valid identifier.
../src/oberror.h:162: Warning(801): Wrong class name
(corrected to `ObLogBuf')

(5) create a new directory called "ruby"

(6) move openbabel_wrap.cxx, generated from SWIG, into
the ruby directory

(7) cd into ruby directory

(8) save the following as "extconf.rb":
require 'mkmf'

dir_config('openbabel')
dir_config('openbabel-2.0')
have_library('openbabel')

create_makefile('openbabel_wrap')

(9) create the makefile:

ruby extconf.rb
--with-openbabel-include='/usr/local/include/openbabel-2.0/openbabel'
--with-openbabel-2.0-include='/usr/local/include/openbabel-2.0'

this produces:

checking for main() in -lopenbabel... yes
creating Makefile

and creates "Makefile"

(10) add the following to line 10 of
openbabel_wrap.cxx:

#include <math.h>

(11) make. This generates the following messages:

g++ -I. -I. -I/usr/lib/ruby/1.8/x86_64-linux-gnu -I.
-I/usr/local/include/openbabel-2.0
-I/usr/local/include/openbabel-2.0/openbabel  -fPIC
-O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-Wall  -fPIC   -c openbabel_wrap.cxx
In file included from
/usr/local/include/openbabel-2.0/openbabel/obutil.h:23,
                 from openbabel_wrap.cxx:1648:
/usr/local/include/openbabel-2.0/openbabel/babelconfig.h:18:1:
warning: "EXTERN" redefined
In file included from
/usr/lib/ruby/1.8/x86_64-linux-gnu/ruby.h:28,
                 from openbabel_wrap.cxx:809:
/usr/lib/ruby/1.8/x86_64-linux-gnu/defines.h:203:1:
warning: this is the location of the previous
definition
openbabel_wrap.cxx: In function ‘int
SWIG_AsPtr_std_string(VALUE, std::string**)’:
openbabel_wrap.cxx:2186: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vectorInt__SWIG_3(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:2455: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vectorInt(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:2509: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vectorInt___len__(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:2568: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vectorInt_emptyq___(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:2604: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vvInt__SWIG_2(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:2874: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vvInt__SWIG_3(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:2918: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:2922: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vvInt(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:2969: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:2978: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:3014: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vvInt___len__(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:3050: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:3054: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vvInt_emptyq___(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:3082: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:3086: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vvInt_push(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:3149: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vvInt___setitem__(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:3273: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vectorDouble__SWIG_3(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:3429: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vectorDouble(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:3483: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vectorDouble___len__(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:3542: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vectorDouble_emptyq___(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:3578: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vVector3__SWIG_3(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:3883: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:3887: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vVector3(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:3934: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:3943: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vVector3___len__(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:3993: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:3997: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vVector3_emptyq___(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:4025: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4029: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vectorMol__SWIG_3(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:4343: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4347: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vectorMol(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:4394: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4403: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vectorMol___len__(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:4453: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4457: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vectorMol_emptyq___(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:4485: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4489: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vectorBond__SWIG_3(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:4803: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4807: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vectorBond(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:4854: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4863: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vectorBond___len__(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:4913: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4917: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vectorBond_emptyq___(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:4945: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4949: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vectorResidue__SWIG_3(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:5263: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5267: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vectorResidue(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:5314: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5323: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vectorResidue___len__(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:5373: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5377: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vectorResidue_emptyq___(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:5405: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5409: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vectorRing__SWIG_3(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:5723: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5727: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_new_vectorRing(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:5774: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5783: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vectorRing___len__(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:5833: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5837: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function ‘VALUE
_wrap_vectorRing_emptyq___(int, VALUE*, VALUE)’:
openbabel_wrap.cxx:5865: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5869: warning: dereferencing
type-punned pointer will break strict-aliasing rules
gcc -shared  -L"/usr/lib64" -o openbabel_wrap.so
openbabel_wrap.o  -lruby -lopenbabel  -lpthread -ldl
-lcrypt -lm   -lc


The following files are created:

openbabel_wrap.o
openbabel_wrap.so

(12) irb

(13) require 'openbabel_wrap'

produces:

irb(main):001:0> require 'openbabel_wrap'
(eval): [BUG] Segmentation fault
ruby 1.8.5 (2006-08-25) [x86_64-linux-gnu]

Aborted

As I mentioned before, if I remove the OBAtom, OBBond,
and OBMol definitions from Init_openbabel_wrap (last
function), the Ruby module is loaded without
segfaulting. I can also remove everything from the
respective stanzas except the first line and still I
get a segfault, so I'm guessing this is where the
error happens.

Would someone be willing to go through this series of
steps to verify that the problem is not related to my
system's configuration (my version of Ruby, my
platform, my compiler, etc.)

cheers,
Rich

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Re: [OpenBabel-scripting] Open Babel-Ruby (almost)

[richard a. <ric...@ya...>]

--- Geoffrey Hutchison <ge...@ge...>
wrote:

> 
> On Oct 10, 2006, at 2:16 AM, richard apodaca wrote:
> 
> > I'm trying to get Ruby scripting to work with Open
> > Babel-2.0.2 and SWIG on Linux.
> 
> What version of SWIG are you using? I'm glad to see
> the progress  
> you've made, but certainly previous versions of the
> Perl and Python  
> wrappers uncovered various bugs with SWIG itself.

1.3.27 on Mandriva Linux 2007. Looks like there is
also a 1.3.29 on SF.

> > With a little tweaking (I needed to add #include
> > <math.h> at the top of the .cxx file), I was able
> to
> > compile openbabel_wrap.cxx against my installed
> > OB-2.0.2 library using make.
> 
> Good to know. It should be possible to inject this
> into the SWIG output.
> 
> > In the case of OBAtom, the offending code is at
> the
> > very start of the class stanza:
> >
> > cOBAtom.klass = rb_define_class_under(mRob,
> "OBAtom",
> > ((swig_class *)
> >
>
SWIGTYPE_p_OpenBabel__OBNodeBase->clientdata)->klass);
> 
> Since the Ruby support in SWIG is relatively new and
> continually  
> improving, I'd suggest grabbing the latest SWIG from
> CVS and giving  
> that a spin first:
> http://www.swig.org/cvs.html

I'll give that a shot.

> If that doesn't work, let's submit this as a SWIG
> bug and see what  
> happens. It's often hard for me to follow the SWIG
> auto-generated code.

You and me both.

> As far as getting autoconf building working, I'll
> see if I can't get  
> that working soon. It turns out that I was missing
> some packages.
> 
> Cheers,
> -Geoff
> 


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Re: [OpenBabel-scripting] Open Babel-Ruby (almost)

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

On Oct 10, 2006, at 2:16 AM, richard apodaca wrote:

> I'm trying to get Ruby scripting to work with Open
> Babel-2.0.2 and SWIG on Linux.

What version of SWIG are you using? I'm glad to see the progress  
you've made, but certainly previous versions of the Perl and Python  
wrappers uncovered various bugs with SWIG itself.

> With a little tweaking (I needed to add #include
> <math.h> at the top of the .cxx file), I was able to
> compile openbabel_wrap.cxx against my installed
> OB-2.0.2 library using make.

Good to know. It should be possible to inject this into the SWIG output.

> In the case of OBAtom, the offending code is at the
> very start of the class stanza:
>
> cOBAtom.klass = rb_define_class_under(mRob, "OBAtom",
> ((swig_class *)
> SWIGTYPE_p_OpenBabel__OBNodeBase->clientdata)->klass);

Since the Ruby support in SWIG is relatively new and continually  
improving, I'd suggest grabbing the latest SWIG from CVS and giving  
that a spin first:
http://www.swig.org/cvs.html

If that doesn't work, let's submit this as a SWIG bug and see what  
happens. It's often hard for me to follow the SWIG auto-generated code.

As far as getting autoconf building working, I'll see if I can't get  
that working soon. It turns out that I was missing some packages.

Cheers,
-Geoff

Re: [OpenBabel-scripting] dl module error

[Noel O'B. <bao...@gm...>]

Unfortunately, I don't really know what's going on.

However, it may help others if you can show the very *first* error messages
you get when you run "python setup.py build", because these are likely to be
the main problem. All of the other errors happen because of the main
problem. Please check on the web for how to pipe standard output *and*
standard error to the same file for your shell. In "bash", you use ">&
mybuild.out"

Noel

On 06/10/06, Ahmet Bakan <ah...@pi...> wrote:
>
> I thought my reply was to all, excuse me.
> Babel itself is working.  I installed it as the root.  I have attached
> output for "python setup.py build".  I could not catch all of the output
> in a file.  I have copied last part of the errors and inserted them to the
> end.  The part I couldn't catch is similar to the part in the file.
> Thanks a lot!
> Regards,
> Ahmet
>
> On 10/6/06, Noel O'Boyle <bao...@gm...> wrote:
> >
> > First of all, please send all email to the mailing list. You can 'cc' it
> > to me if you wish, but there are others on the mailing list who will be able
> > to help you more than I can. I have attached the .out files you have sent me
> > to this email.
> >
> > Well, there's nothing obviously wrong to me. I note that you are using a
> > 64-bit system, though. There's a couple more questions which might help us
> > to help you...
> >
> > Does Babel itself work? That is, does the output of "babel -H" list all
> > of the different file formats?
> >
> > Did you install Open Babel globally as root? That is, did you run "make
> > install" as root as described on:
> >     http://openbabel.sourceforge.net/wiki/Install
> >
> > Could you also attach the complete output (errors and all) from "python
> > setup.py build"? (You can catch it using "python setup.py build |&
> > pythonbuild.out")
> >
> > Regards,
> >    Noel
> >
> > On 06/10/06, Ahmet Bakan <ah...@pi...> wrote:
> > >
> > > I am building the latest version 2.0.2.
> > > I have attached configure and make output files.
> > > Thank you very much for your attention.
> > > Regards,
> > > Ahmet
> > >
> > > On 10/6/06, Noel O'Boyle <bao...@gm...> wrote:
> > > >
> > > > What version of OpenBabel are you building?
> > > >
> > > > Can you send configure.out and make.out to this mailing list? The
> > > > problem may be with the OpenBabel compilation, rather than the Python
> > > > wrapper.
> > > >
> > > > (See the instructions at
> > > > http://openbabel.sourceforge.net/wiki/Install on how to create
> > > > configure.out and make.out .)
> > > >
> > > > Regards,
> > > >    Noel
> > > >
> > > > On 06/10/06, Ahmet Bakan <ah...@pi...> wrote:
> > > >
> > > > >  Hi All,
> > > > >
> > > > > I have followed the instructions to install Python wrapper for
> > > > > OpenBabel on Linux.  I have had an error or a warning on every line as I was
> > > > > running the provided setup.py code.
> > > > > Also after the build and install finished I could not import
> > > > > openbabel module due "ImportError: No module named dl".
> > > > > The errors on build and installation is as follows:
> > > > > openbabel_python.cpp:46242: error: `OpenBabel' has not been
> > > > > declared
> > > > > openbabel_python.cpp:46242: error: `OUTOPTIONS' was not declared
> > > > > in this scope
> > > > >
> > > > > If you can figure out that I am missing something, can you please
> > > > > let me know?
> > > > > I use
> > > > > Python 2.4.3
> > > > > [GCC 3.4.5 20051201 (Red Hat 3.4.5-2)] on linux2
> > > > >
> > > > > Thanks in advance.
> > > > > Ahmet
> > > > >
> > > > > --
> > > > > Ahmet Bakan
> > > > > Department of Computational Biology
> > > > > University of Pittsburgh School of Medicine
> > > > > 3501 Fifth Avenue
> > > > > Suite 3064 BST3
> > > > > Pittsburgh, PA  15213-3301
> > > > >
> > > > > -------------------------------------------------------------------------
> > > > > Take Surveys. Earn Cash. Influence the Future of IT
> > > > > Join SourceForge.net's Techsay panel and you'll get the chance to
> > > > > share your
> > > > > opinions on IT & business topics through brief surveys -- and earn
> > > > > cash
> > > > >
> > > > > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> > > > >
> > > > > _______________________________________________
> > > > > OpenBabel-scripting mailing list
> > > > > Ope...@li...
> > > > > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> > > > >
> > > > >
> > > > >
> > > >
> > >
> > >
> > > --
> > > Ahmet Bakan
> > > Department of Computational Biology
> > > University of Pittsburgh School of Medicine
> > > 3501 Fifth Avenue
> > > Suite 3064 BST3
> > > Pittsburgh, PA  15213-3301
> > >
> > >
> >
> >
>
>
> --
> Ahmet Bakan
> Department of Computational Biology
> University of Pittsburgh School of Medicine
> 3501 Fifth Avenue
> Suite 3064 BST3
> Pittsburgh, PA  15213-3301
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share
> your
> opinions on IT & business topics through brief surveys -- and earn cash
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>
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>
>
>

[OpenBabel-scripting] Open Babel-Ruby (almost)

[richard a. <ric...@ya...>]

I'm trying to get Ruby scripting to work with Open
Babel-2.0.2 and SWIG on Linux.

So far I've been able to generate the
openbabel_wrap.cxx file with SWIG from OB's
openbabel.i file and the OB sources. The bottom of
this file contains all of the Ruby module, class, and
method definitions, as expected.

I created an apparently correct extconf.rb file, which
I then used to create a makefile.

With a little tweaking (I needed to add #include
<math.h> at the top of the .cxx file), I was able to
compile openbabel_wrap.cxx against my installed
OB-2.0.2 library using make.

So far so good.

With irb, however, loading the module segfaults:

BUG] Segmentation fault
ruby 1.8.5 (2006-08-25) [x86_64-linux-gnu]

Aborted

Not really that helpful. I was able to trace the
problem to only three class definitions in
obenbabel_wrap.cxx:

OBAtom
OBBond
OBMol

If I remove these three definitions, I can compile the
module, load it through Ruby, and manipulate OB
objects.

In the case of OBAtom, the offending code is at the
very start of the class stanza:

cOBAtom.klass = rb_define_class_under(mRob, "OBAtom",
((swig_class *)
SWIGTYPE_p_OpenBabel__OBNodeBase->clientdata)->klass);

I suspect the same is true for OBBond and OBMol, but
haven't checked.

I initially thought that maybe this problem was linked
to OBAtom inheriting from another OB object. But so
does OBElementTable, for example, and that definition
doesn't cause a segfault.

Any ideas? I'm not very experienced with Ruby
extensions, C, C++, or make, so any information would
be helpful.

cheers,
Rich


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Re: [OpenBabel-scripting] dl module error

[Noel O'B. <bao...@gm...>]

What version of OpenBabel are you building?

Can you send configure.out and make.out to this mailing list? The problem
may be with the OpenBabel compilation, rather than the Python wrapper.

(See the instructions at http://openbabel.sourceforge.net/wiki/Install on
how to create configure.out and make.out.)

Regards,
   Noel

On 06/10/06, Ahmet Bakan <ah...@pi...> wrote:
>
> Hi All,
>
> I have followed the instructions to install Python wrapper for OpenBabel
> on Linux.  I have had an error or a warning on every line as I was running
> the provided setup.py code.
> Also after the build and install finished I could not import openbabel
> module due "ImportError: No module named dl".
> The errors on build and installation is as follows:
> openbabel_python.cpp:46242: error: `OpenBabel' has not been declared
> openbabel_python.cpp:46242: error: `OUTOPTIONS' was not declared in this
> scope
>
> If you can figure out that I am missing something, can you please let me
> know?
> I use
> Python 2.4.3
> [GCC 3.4.5 20051201 (Red Hat 3.4.5-2)] on linux2
>
> Thanks in advance.
> Ahmet
>
> --
> Ahmet Bakan
> Department of Computational Biology
> University of Pittsburgh School of Medicine
> 3501 Fifth Avenue
> Suite 3064 BST3
> Pittsburgh, PA  15213-3301
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share
> your
> opinions on IT & business topics through brief surveys -- and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
>
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>
>