Thread: [openbabel-scripting] Windows scripting

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(1) Is Python scripting for Openbabel available in Windows somehow?
(2) Is it necessary to compile? 
(3) What's the current status of Cygwin/OpenBabel compilation?

Regards,
 Noel

On Dec 9, 2005, at 12:17 PM, Noel O'Boyle wrote:

> (1) Is Python scripting for Openbabel available in Windows somehow?

I don't have a Windows box to test. I'm also not sure how it would  
link against the Windows OpenBabel DLLs.

> (2) Is it necessary to compile?

Well, I believe you can get DLLs either from the Open Babel windows  
download or from Chris Morley. Certainly you *can* compile on Windows.

> (3) What's the current status of Cygwin/OpenBabel compilation?

So-so. I know the problem, but haven't had the time to fix it or test  
it.

Cheers,
-Geoff

On Fri, 2005-12-09 at 14:14 -0500, Geoffrey Hutchison wrote:
> On Dec 9, 2005, at 12:17 PM, Noel O'Boyle wrote:
> 
> > (1) Is Python scripting for Openbabel available in Windows somehow?
> 
> I don't have a Windows box to test. I'm also not sure how it would  
> link against the Windows OpenBabel DLLs.

Could I put this on someone's things to do list (i.e. to get the SWIG
interface to OpenBabel working for Python)?

I use Windows at home, so if I want to develop the Python interface to a
decent level, I probably need to have python scripting set up for
Windows. Apparently, I can get access to the MSVC++ compiler here, but
not knowing anything about C++ I am not sure whether I will be able to
get it all to work.

> > (2) Is it necessary to compile?
> 
> Well, I believe you can get DLLs either from the Open Babel windows  
> download or from Chris Morley. Certainly you *can* compile on Windows.
> 
> > (3) What's the current status of Cygwin/OpenBabel compilation?
> 
> So-so. I know the problem, but haven't had the time to fix it or test  
> it.
> 
> Cheers,
> -Geoff

It works!

Add this code to the openbabel.i file to add the patch to the .py library f=
ile:

%pythoncode %{
import sys
import dl
sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)
%}

You may want to add a python snippet to execute this code only if the
architecture is Linux.

Thanks for the help :)

Josh

On 09/12/05, Geoffrey Hutchison <ge...@ge...> wrote:
>
> On Dec 9, 2005, at 12:17 PM, Noel O'Boyle wrote:
>
> > (1) Is Python scripting for Openbabel available in Windows somehow?
>
> I don't have a Windows box to test. I'm also not sure how it would
> link against the Windows OpenBabel DLLs.
>
> > (2) Is it necessary to compile?
>
> Well, I believe you can get DLLs either from the Open Babel windows
> download or from Chris Morley. Certainly you *can* compile on Windows.
>
> > (3) What's the current status of Cygwin/OpenBabel compilation?
>
> So-so. I know the problem, but haven't had the time to fix it or test
> it.
>
> Cheers,
> -Geoff
>
>
> -------------------------------------------------------
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>

How do you regenerate the SWIG interface though? Typing 'make' in
scripts doesn't seem to work.

On Fri, 2005-12-09 at 11:52 -0800, S Joshua Swamidass wrote:
> It works!
> 
> Add this code to the openbabel.i file to add the patch to the .py library file:
> 
> %pythoncode %{
> import sys
> import dl
> sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)
> %}
> 
> You may want to add a python snippet to execute this code only if the
> architecture is Linux.
> 
> Thanks for the help :)
> 
> Josh
> 
> On 09/12/05, Geoffrey Hutchison <ge...@ge...> wrote:
> >
> > On Dec 9, 2005, at 12:17 PM, Noel O'Boyle wrote:
> >
> > > (1) Is Python scripting for Openbabel available in Windows somehow?
> >
> > I don't have a Windows box to test. I'm also not sure how it would
> > link against the Windows OpenBabel DLLs.
> >
> > > (2) Is it necessary to compile?
> >
> > Well, I believe you can get DLLs either from the Open Babel windows
> > download or from Chris Morley. Certainly you *can* compile on Windows.
> >
> > > (3) What's the current status of Cygwin/OpenBabel compilation?
> >
> > So-so. I know the problem, but haven't had the time to fix it or test
> > it.
> >
> > Cheers,
> > -Geoff
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
> > for problems?  Stop!  Download the new AJAX search engine that makes
> > searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >

On Dec 15, 2005, at 7:11 AM, Noel O'Boyle wrote:

> How do you regenerate the SWIG interface though? Typing 'make' in
> scripts doesn't seem to work.

Use the --enable-maintainer-mode flag with configure.

Several people complained with the snapshot series that the SWIG  
wrappers were stopping them from running "make" normally. Please be  
sure you have the latest version of SWIG and you'll be all set.

Cheers,
-Geoff

I cannot get this patch to work, as the inserted lines always come after
the initial "import _openbabel" in openbabel.py. Any thoughts?

Regards,
 Noel

On Fri, 2005-12-09 at 11:52 -0800, S Joshua Swamidass wrote:
> It works!
> 
> Add this code to the openbabel.i file to add the patch to the .py library file:
> 
> %pythoncode %{
> import sys
> import dl
> sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)
> %}
> 
> You may want to add a python snippet to execute this code only if the
> architecture is Linux.
> 
> Thanks for the help :)
> 
> Josh
> 
> On 09/12/05, Geoffrey Hutchison <ge...@ge...> wrote:
> >
> > On Dec 9, 2005, at 12:17 PM, Noel O'Boyle wrote:
> >
> > > (1) Is Python scripting for Openbabel available in Windows somehow?
> >
> > I don't have a Windows box to test. I'm also not sure how it would
> > link against the Windows OpenBabel DLLs.
> >
> > > (2) Is it necessary to compile?
> >
> > Well, I believe you can get DLLs either from the Open Babel windows
> > download or from Chris Morley. Certainly you *can* compile on Windows.
> >
> > > (3) What's the current status of Cygwin/OpenBabel compilation?
> >
> > So-so. I know the problem, but haven't had the time to fix it or test
> > it.
> >
> > Cheers,
> > -Geoff
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
> > for problems?  Stop!  Download the new AJAX search engine that makes
> > searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >

As a quick fix, just move them manually.

Next ry and move them to the front of the openbabel.i file. That
should put it at the first part of the openbabel.py file.  If none of
that works, send a line to the listserve and i"ll poke around some
swig faqs to find the answer.

Josh

On 16/12/05, Noel O'Boyle <no...@ca...> wrote:
> I cannot get this patch to work, as the inserted lines always come after
> the initial "import _openbabel" in openbabel.py. Any thoughts?
>
> Regards,
>  Noel
>
> On Fri, 2005-12-09 at 11:52 -0800, S Joshua Swamidass wrote:
> > It works!
> >
> > Add this code to the openbabel.i file to add the patch to the .py libra=
ry file:
> >
> > %pythoncode %{
> > import sys
> > import dl
> > sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)
> > %}
> >
> > You may want to add a python snippet to execute this code only if the
> > architecture is Linux.
> >
> > Thanks for the help :)
> >
> > Josh
> >
> > On 09/12/05, Geoffrey Hutchison <ge...@ge...> wrote:
> > >
> > > On Dec 9, 2005, at 12:17 PM, Noel O'Boyle wrote:
> > >
> > > > (1) Is Python scripting for Openbabel available in Windows somehow?
> > >
> > > I don't have a Windows box to test. I'm also not sure how it would
> > > link against the Windows OpenBabel DLLs.
> > >
> > > > (2) Is it necessary to compile?
> > >
> > > Well, I believe you can get DLLs either from the Open Babel windows
> > > download or from Chris Morley. Certainly you *can* compile on Windows=
.
> > >
> > > > (3) What's the current status of Cygwin/OpenBabel compilation?
> > >
> > > So-so. I know the problem, but haven't had the time to fix it or test
> > > it.
> > >
> > > Cheers,
> > > -Geoff
> > >
> > >
> > > -------------------------------------------------------
> > > This SF.net email is sponsored by: Splunk Inc. Do you grep through lo=
g files
> > > for problems?  Stop!  Download the new AJAX search engine that makes
> > > searching your log files as easy as surfing the  web.  DOWNLOAD SPLUN=
K!
> > > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick
> > > _______________________________________________
> > > OpenBabel-scripting mailing list
> > > Ope...@li...
> > > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> > >
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log fi=
les
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
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> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

On Fri, 2005-12-16 at 09:28 -0800, S Joshua Swamidass wrote:
> As a quick fix, just move them manually.
It does work if I move them manually, that's how I know that this is the
problem. It's possible to add a line to the Makefile, or Makefile.in or
whatever, to add the lines to the start of openbabel.py (not very
elegant though :-).

> Next try and move them to the front of the openbabel.i file.
I tried this, but the Perl wrapper dies as follows:

~/Tools/OpenBabel/openbabel/scripts$ make
/usr/bin/swig -perl5 -c++ -o perl/openbabel_perl.cpp \
        -I../src openbabel.i
openbabel.i:5: Error: Syntax error in input.
../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.
*** No module name specified using %module or -module.
make: *** [perl/openbabel_perl.cpp] Error 1

If I remove the call to the Perl wrapper, and just run the Python
wrapper, the extra Python code still comes after the initial section of
openbabel.py. So, no change.

I think that I should get the latest SWIG, as Geoff recommends - I have
1.3.24, but he used 1.3.27, if that makes a difference.

>  That
> should put it at the first part of the openbabel.py file.  If none of
> that works, send a line to the listserve and i"ll poke around some
> swig faqs to find the answer.

Good luck,
Noel

> 
> On 16/12/05, Noel O'Boyle <no...@ca...> wrote:
> > I cannot get this patch to work, as the inserted lines always come after
> > the initial "import _openbabel" in openbabel.py. Any thoughts?
> >
> > Regards,
> >  Noel
> >
> > On Fri, 2005-12-09 at 11:52 -0800, S Joshua Swamidass wrote:
> > > It works!
> > >
> > > Add this code to the openbabel.i file to add the patch to the .py library file:
> > >
> > > %pythoncode %{
> > > import sys
> > > import dl
> > > sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)
> > > %}
> > >
> > > You may want to add a python snippet to execute this code only if the
> > > architecture is Linux.
> > >
> > > Thanks for the help :)
> > >
> > > Josh
> > >
> > > On 09/12/05, Geoffrey Hutchison <ge...@ge...> wrote:
> > > >
> > > > On Dec 9, 2005, at 12:17 PM, Noel O'Boyle wrote:
> > > >
> > > > > (1) Is Python scripting for Openbabel available in Windows somehow?
> > > >
> > > > I don't have a Windows box to test. I'm also not sure how it would
> > > > link against the Windows OpenBabel DLLs.
> > > >
> > > > > (2) Is it necessary to compile?
> > > >
> > > > Well, I believe you can get DLLs either from the Open Babel windows
> > > > download or from Chris Morley. Certainly you *can* compile on Windows.
> > > >
> > > > > (3) What's the current status of Cygwin/OpenBabel compilation?
> > > >
> > > > So-so. I know the problem, but haven't had the time to fix it or test
> > > > it.
> > > >
> > > > Cheers,
> > > > -Geoff
> > > >
> > > >
> > > > -------------------------------------------------------
> > > > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
> > > > for problems?  Stop!  Download the new AJAX search engine that makes
> > > > searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> > > > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
> > > > _______________________________________________
> > > > OpenBabel-scripting mailing list
> > > > Ope...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> > > >
> >
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
> > for problems?  Stop!  Download the new AJAX search engine that makes
> > searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >