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Re: [OpenBabel-scripting] Cluster

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

On Mar 11, 2008, at 4:36 AM, Jurgens de Bruin wrote:

>  was wondering if OB has any functionalities that can be applied to  
> a library of small molecules??

I'm not sure what you mean. Certainly Open Babel can handle libraries,  
doing splitting, merging, batch conversion, etc. Almost all functions  
can be run across a library file. That's what Open Babel is designed  
to do.

If, however, what you mean is to run "clustering" statistical  
analysis, then no. We do not have any functions for statistical  
analysis at all. Other packages (e.g., R) are better suited for this  
IMHO.

Cheers,
-Geoff

[OpenBabel-scripting] Cluster

[Jurgens de B. <deb...@gm...>]

Hi

I was wondering if OB has any functionalities that can be applied to a
library of small molecules??

Thanx

-- 
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет

Jurgens de Bruin

[OpenBabel-scripting] ANN: Pybel paper published

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

Geoff, Chris and I have just published a paper on Pybel which
describes the rationale behind the Python bindings and Pybel, as well
as their implementation. We would appreciate if you could reference
this publication if you use the Python bindings to OpenBabel to obtain
results for publication:

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit
Noel M O'Boyle, Chris Morley and Geoffrey R Hutchison.
Chemistry Central Journal 2008, 2:5.
http://www.journal.chemistrycentral.com/content/2/1/5

Background

Scripting languages such as Python are ideally suited to common
programming tasks in cheminformatics such as data analysis and parsing
information from files. However, for reasons of efficiency,
cheminformatics toolkits such as the OpenBabel toolkit are often
implemented in compiled languages such as C++. We describe Pybel, a
Python module that provides access to the OpenBabel toolkit.

Results

Pybel wraps the direct toolkit bindings to simplify common tasks such
as reading and writing molecular files and calculating fingerprints.
Extensive use is made of Python iterators to simplify loops such as
that over all the molecules in a file. A Pybel Molecule can be easily
interconverted to an OpenBabel OBMol to access those methods or
attributes not wrapped by Pybel.

Conclusion

Pybel allows cheminformaticians to rapidly develop Python scripts that
manipulate chemical information. It is open source, available
cross-platform, and offers the power of the OpenBabel toolkit to
Python programmers.

Regards,
   Noel

Re: [OpenBabel-scripting] openbabel installation problems

[<gil...@we...>]

Hello Noel,

renaming the DLLs gave also no change...


I will try to get it running on Linux,
may be I can use the prebuild from BioRPMS / UMDNJ.
But this may take some time...

Noel, 
many, many thanks for your patience and your help !
I fully appreciate your support and 
your attitude to solve problems like this.

Best regards

Gilbert




	
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Re: [OpenBabel-scripting] openbabel installation problems

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

On 22/02/2008, gil...@we... <gil...@we...> wrote:
> Hi Noel,
>
>  I tried the search for the dlls you proposed.
>  I found some and deinstalled or renamed those who could lead to confusion. (see attachment)
>  After reboot no change: DLL load failed
>  Same is true for the borrowed PC.
>
>  Installing OpenBabelGUI went without problems and runs without problems.
>  I replaced the 5 dlls in the site-packackes folder with those from the OpenBabelGUI folder: no change
>
>  I would like to come back to the error message
>
>
>  Python 2.4.4 (#71, Oct 18 2006, 08:34:43) [MSC v.1310 32 bit (Intel)] on win32
>
> Type "help", "copyright", "credits" or "license" for more information.
>
> >>> import openbabel
>  Traceback (most recent call last):
>
>   File "<stdin>", line 1, in ?
>   File "C:\Programme\Python24\Lib\site-packages\openbabel.py", line 7, in ?
>
>     import _openbabel
>  ImportError: DLL load failed: Diese Anwendung konnte nicht gestartet werden, wei
>  l die Anwenungskonfiguration nicht korrekt ist. Zur Problembehebung sollten Sie
>  die Anwendung neu installieren.
>  >>>
>
> Does the error message itself make any sense to you ('wrong configuration') ?
>  Is there may be a problem when the _openbabel.pyd was build,
>  may be something special to german OS ?
>  I googled for problems with .pyd loading genaral and there are some posts,
>  though I couldn't see something that helps me (which of course means nothing).
>
>  Are there any other openbabel users with german WinXP out there,
>  who use it without problems ?
I think you will need to ask this question as a separate email, as
many people probably are not following this thread.

The error message seems to be very general. I don't know what it is
referring to exactly. As one last attempt, try renaming the DLLs that
we provide, in particular iconv.dll. There's no need to reboot. Just
rename the DLL, and restart python, and try the import.

Other options:
(1) You might want to try compiling OpenBabel and the Pybel extension
yourself on Windows. This will take a little bit of time to setup if
you haven't done it before, and it may not work in any case (for the
same mysterious reason). However, if you're interested I can give you
specific instructions on how to do this. If you are interesting in
seeing how Microsoft Visual C++ works, you might be interested in
looking at this in any case.
(2) Install Linux, either dual boot or under a virtual machine (e.g.
the free VMWare player). This is not very convenient though.

Noel

>  Many thanks again for your help !
>
>  Best regards
>
>  Gilbert
>
>
>
>
>
>  > -----Ursprüngliche Nachricht-----
>  > Von: "Noel O'Boyle" <bao...@gm...>
>  > Gesendet: 20.02.08 18:17:33
>  > An: "gil...@we..." <gil...@we...>
>  > CC: ope...@li..., "Chris Morley" <c.m...@ga...>
>
> > Betreff: Re: [OpenBabel-scripting] openbabel installation problems
>
>
> This is really disappointing. :-/
>  >
>  > The question is, what's the difference between your computer and mine? You have the same files installed (thanks for the output of 'dir'). There are two possibilities here: something to do with German Windows (I don't know why this would be), or something to do with a mixup of different DLLs on your system. You could search your computer for other DLLs with the same name as zlib1.dll, iconv.dll, libinchi.dll, libxml2.dll and OpenBabelDLL.dll but which are not identical. Then you could try renaming them while you test the import. (Don't forget to rename them back!)
>  >
>  > The other thing to try is to install OpenBabelGUI, and test that it is working fine. If that doesn't work, then the problem isn't the Python stuff, it's OpenBabel stuff and maybe Chris will be able to help...
>  >
>  > I appreciate you helping us sort this out, because if you have this problem, other people will have it too. But I think these are the last ideas I can think of :-/
>  >
>  > -------- One quick google search later -----
>  >
>  > I've just found that iconv.dll is used for characterset conversion. I wonder if this could be the problem. (See http://www.linuxinfor.com/german/PHP-Manual/ref.iconv.html for some information...)
>  >
>  > If you can, try the ideas above, and let us know the results. We can consider where to go from there.
>  >
>  > Noel
>  >
>  >
>
>
> _________________________________________________________________________
>
> In 5 Schritten zur eigenen Homepage. Jetzt Domain sichern und gestalten!
>  Nur 3,99 EUR/Monat! http://www.maildomain.web.de/?mc=021114
>
>
>

Re: [OpenBabel-scripting] openbabel installation problems

[<gil...@we...>]

Hi Noel,

I tried the search for the dlls you proposed.
I found some and deinstalled or renamed those who could lead to confusion. (see attachment)
After reboot no change: DLL load failed
Same is true for the borrowed PC.

Installing OpenBabelGUI went without problems and runs without problems.
I replaced the 5 dlls in the site-packackes folder with those from the OpenBabelGUI folder: no change

I would like to come back to the error message

Python 2.4.4 (#71, Oct 18 2006, 08:34:43) [MSC v.1310 32 bit (Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import openbabel
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "C:\Programme\Python24\Lib\site-packages\openbabel.py", line 7, in ?
    import _openbabel
ImportError: DLL load failed: Diese Anwendung konnte nicht gestartet werden, wei
l die Anwenungskonfiguration nicht korrekt ist. Zur Problembehebung sollten Sie
die Anwendung neu installieren.
>>>
Does the error message itself make any sense to you ('wrong configuration') ?
Is there may be a problem when the _openbabel.pyd was build, 
may be something special to german OS ?
I googled for problems with .pyd loading genaral and there are some posts,
though I couldn't see something that helps me (which of course means nothing).

Are there any other openbabel users with german WinXP out there,
who use it without problems ?

Many thanks again for your help !

Best regards

Gilbert





> -----Ursprüngliche Nachricht-----
> Von: "Noel O'Boyle" <bao...@gm...>
> Gesendet: 20.02.08 18:17:33
> An: "gil...@we..." <gil...@we...>
> CC: ope...@li..., "Chris Morley" <c.m...@ga...>
> Betreff: Re: [OpenBabel-scripting] openbabel installation problems

This is really disappointing. :-/
> 
> The question is, what's the difference between your computer and mine? You have the same files installed (thanks for the output of 'dir'). There are two possibilities here: something to do with German Windows (I don't know why this would be), or something to do with a mixup of different DLLs on your system. You could search your computer for other DLLs with the same name as zlib1.dll, iconv.dll, libinchi.dll, libxml2.dll and OpenBabelDLL.dll but which are not identical. Then you could try renaming them while you test the import. (Don't forget to rename them back!)
> 
> The other thing to try is to install OpenBabelGUI, and test that it is working fine. If that doesn't work, then the problem isn't the Python stuff, it's OpenBabel stuff and maybe Chris will be able to help...
> 
> I appreciate you helping us sort this out, because if you have this problem, other people will have it too. But I think these are the last ideas I can think of :-/
> 
> -------- One quick google search later -----
> 
> I've just found that iconv.dll is used for characterset conversion. I wonder if this could be the problem. (See http://www.linuxinfor.com/german/PHP-Manual/ref.iconv.html for some information...)
> 
> If you can, try the ideas above, and let us know the results. We can consider where to go from there.
> 
> Noel
> 
> 

_________________________________________________________________________
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Re: [OpenBabel-scripting] openbabel installation problems

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

This is really disappointing. :-/

The question is, what's the difference between your computer and mine? You
have the same files installed (thanks for the output of 'dir'). There are
two possibilities here: something to do with German Windows (I don't know
why this would be), or something to do with a mixup of different DLLs on
your system. You could search your computer for other DLLs with the same
name as zlib1.dll, iconv.dll, libinchi.dll, libxml2.dll and
OpenBabelDLL.dllbut which are not identical. Then you could try
renaming them while you test
the import. (Don't forget to rename them back!)

The other thing to try is to install OpenBabelGUI, and test that it is
working fine. If that doesn't work, then the problem isn't the Python stuff,
it's OpenBabel stuff and maybe Chris will be able to help...

I appreciate you helping us sort this out, because if you have this problem,
other people will have it too. But I think these are the last ideas I can
think of :-/

-------- One quick google search later -----

I've just found that iconv.dll is used for characterset conversion. I wonder
if this could be the problem. (See
http://www.linuxinfor.com/german/PHP-Manual/ref.iconv.html for some
information...)

If you can, try the ideas above, and let us know the results. We can
consider where to go from there.

Noel

On 20/02/2008, gil...@we... <gil...@we...> wrote:
>
> Hello Noel,
>
> thanks again for your help.
>
> > -----Ursprüngliche Nachricht-----
> > Von: "Noel O'Boyle"
> > Gesendet: 18.02.08 11:36:33
> > An: "gil...@we..."
> > CC: ope...@li...
> > Betreff: Re: [OpenBabel-scripting] openbabel installation problems
>
>
> >
> > (Please cc to the mailing list)
> >
> > On 17/02/2008, gil...@we... wrote:
> > > Hello Noel,
> > >
> > > thank you for your fast reply.
> > > I appreciate that you do this in your free time.
> > >
> > > >
> > > > I have a couple of questions or suggestions to try:
> > > > (1) Is this the full error message? "ImportError: DLL load
> failed:..."
> > > ok, not too smart... :-| I delete the rest of the message, because it
> was in german,
> > > telling that the _openbabel.dll could not be started because its
> configuration would not be correct.
> >
> > Did a message pop up on the screen too? Like a little Alert box?
> No, there was nothing like that - just the message as shown below.
>
>
> >
> > > I deinstalled all python now and installed from python-2.4.4.msi,
> which looked ok to me.
> > > Then I installed openbabel-python-1.2.2.py2.4, but get the same
> problems (now the complete message):
> > >
> > > ----------------------------------------------------
> > > Python 2.4.4 (#71, Oct 18 2006, 08:34:43) [MSC v.1310 32 bit (Intel)]
> on win32
> > > Type "copyright", "credits" or "license()" for more information.
> > >
> > > ****************************************************************
> > > ...
> > > ****************************************************************
> > >
> > > IDLE 1.1.4
> > > >>> import openbabel
> > >
> > > Traceback (most recent call last):
> > > File "", line 1, in -toplevel-
> > > import openbabel
> > > File "C:ProgrammePython24Libsite-packagesopenbabel.py", line 7, in
> -toplevel-
> > > import _openbabel
> > > ImportError: DLL load failed: Diese Anwendung konnte nicht gestartet
> werden, weil die Anwenungskonfiguration nicht korrekt ist. Zur
> Problembehebung sollten Sie die Anwendung neu installieren.
> > > ---------------------------------------------------
> > >
> > > The python installation for 2.5 came from ActiveState, so I thought
> that the problems might have come from there...
> >
> > Me too - but it seems that this is not the problem in the end :-/
> >
> > > > (2) Could you start python with "python -v", and give the output
> that
> > > > is shown after you type "import openbabel"
> > > That's interessting. When I try to start python in Win cmd shell from
> c:,
> > > I get an error telling me, that python could not be found.
> > > Do you think that should be with a proper installation?
> > > The pythonpath should be in the registry and should be callable from
> everywhere, right ?
> >
> > No - that's actually incorrect. First of all, you are confusing
> > "PYTHONPATH" and "PATH". Just like in Linux, the system uses the PATH
> > to find executables, so you can't just run python at the command
> > prompt until you add C:ProgramsPython24 to the PATH. To do this, you
> > need to use Control Panel/System/Advanced or so (be careful!).
> >
> > PYTHONPATH, for the record, is a variable that Python searches when
> > you type "import whatever", it looks for a file called whatever.py or
> > a directory called whatever in each of the directories in your
> > PYTHONPATH. Again, you can set this environment variable in Control
> > Panel.
> >
> > > On the other hand, the openbabel installer found the python 2.4version in the registry without problems.
> > That uses a key in the registry. Not the PATH.
> Hmmm, ok, thanks, got it.
>
> >
> > > When I cd to the python folder an try again, I get the messages in the
> attached file. (error.txt)
> > > > (3) Can you list the contents of
> > > > C:ProgrammePython25libsite-packages (e.g. use the 'dir' command)
> > > >>> import sys
> > > >>> print sys.path
> > > ['C:\Programme\Python24\Lib\idlelib',
> 'C:\Programme\Python24\python24.zip', 'C:\Programme\Python24',
> 'C:\Programme\Python24\DLLs', 'C:\Programme\Python24\lib',
> 'C:\Programme\Python24\lib\plat-win', 'C:\Programme\Python24\lib\lib-tk',
> 'C:\Programme\Python24\lib\site-packages']
> > >
> > > Seems to be ok...
> >
> > My question is still the same. Can you list the contents of
> > C:\Programme\Python24\lib\site-packages? (I want to make sure that
> > all of the openbabel files have been installed)
>
> Sorry, I got you completly wrong. Here it is:
>
> Verzeichnis von C:ProgrammePython24Libsite-packages
>
> 17.02.2008 01:54 .
>
> 17.02.2008 01:54 ..
> 27.06.2007 12:24 892.928 iconv.dll
> 17.02.2008 01:45 isapi
> 27.06.2007 12:24 724.992 libinchi.dll
> 27.06.2007 12:24 876.032 libxml2.dll
> 27.08.2007 18:22 257.308 openbabel.py
> 17.02.2008 00:45 405.848 openbabel.pyc
> 17.02.2008 00:45 405.848 openbabel.pyo
> 09.07.2007 14:02 1.466.368 OpenBabelDLL.dll
> 17.02.2008 00:45 openbabel_data
> 27.08.2007 18:24 16.541 pybel.py
> 17.02.2008 00:45 18.705 pybel.pyc
> 17.02.2008 00:45 18.705 pybel.pyo
> 17.02.2008 01:54 pysqlite2
> 26.01.2004 23:01 141 pythoncom.py
> 17.02.2008 01:45 245 pythoncom.pyc
> 17.02.2008 01:45 245 pythoncom.pyo
> 17.02.2008 01:45 pythonwin
> 23.09.2006 02:52 450 pywin32-210-py2.6.egg-info
> 23.09.2006 01:52 2.141.131 PyWin32.chm
> 10.10.2004 20:06 69 pywin32.pth
> 23.09.2006 02:50 5 pywin32.version.txt
> 17.02.2008 01:45 pywin32_system32
> 28.10.2005 20:15 121 README.txt
> 17.02.2008 01:45 win32
> 17.02.2008 01:45 win32com
> 17.02.2008 01:45 win32comext
> 27.06.2007 12:24 59.904 zlib1.dll
> 27.08.2007 18:23 1.875.968 _openbabel.pyd>
>
>
> > > > (4) When you run "import openbabel", make sure you are in an empty
> > > > directory (just to avoid any problems)
> > > Do you mean from another folder than the python folder, then see
> above...
> >
> > No - I mean an empty directory (although it looks like this is not the
> > problem). To run Python, just use "C:Program FilesPython24python"
> > instead of just "python".
>
> That works fine:
> C:>c:programmepython24python
> Python 2.4.4 (#71, Oct 18 2006, 08:34:43) [MSC v.1310 32 bit (Intel)] on
> win32
> Type "help", "copyright", "credits" or "license" for more information.
> >>>
>
>
> >
> > > > (5) I have not tested PythonWin. Could you install the regular
> Python
> > > > 2.4, for example, and try using the installer for Python 2.4? (Try
> > > > Python 2.4 rather than 2.5, as otherwise it may cause some
> confusion)
> > > ->(1)
> > >
> > > A python installation error then ?
> > > I am sure I have admin rights, its my private PC.
> > > To check again, I installed SQLite (pysqlite-2.4.1.win32-py2.4)
> > > and it worked without problems.
> > > Then I installed pywin32, no problems...
> > >
> > > Do you have any ideas ?
> >
> > (A1) Hmmm. Did you say that you also installed OpenBabelGUI? If so,
> > can you confirm that "babel -H" is working (please attach the output)?
> > If so, then rename the OpenBabel folder to something different, and
> > try "import openbabel" from Python again. (The reason is that the
> > OpenBabel folder *is* on the PATH, and may be conflicting with the DLL
> > supplied with Python OpenBabel)
>
>
> Actually, OpenBabelGUI is not installed, but it once was.
> 'babel -H' gives an error now (can't find babel...)
> But when I checked the PATH (via Control Panel/System/Advanced)
> there was still a path set to an OpenBabel installation.
> I removed it, rebooted, but it still gives me the error of not being able
> to start '_openbabel.dll'.
>
> >
> > (A2) Take a look at Control Panel/Add and Remove Programs. Is
> > "Microsoft Visual 2005 C++ Redistributable" listed? This is needed for
> > the Python bindings, and should have been installed by the installer.
> Thats installed.
>
> >
> > This is a tough one. Have you tried installing on another computer
> > just to see if you have the same problem??
> I did, but this was on a machine, where I do not have admin rights
> and OpenBabel complains about that during installation anyway, so I did
> not mention it.
> Interesstingly, I get the same error of not being able to start
> '_openbabel.dll'.
> If this dll needs registration, aka admin rights, then no wonder....
> But then what about my private machine where I have admin rights ?
>
> Yesterday I borrowed another machine, where I have admin rights.
> I tried with Python 2.5 and afterwards 2.4, together with the
> corresponding OpenBabels
> and it didn't work, same errors. This machine has never seen OpenBabelGUI.
> There is a Python2.2 preinstalled, but Openbabel was properly
> copied/installed to the newer version.
> In fact, the installer crashed when I tried to install
> openbabel-python-1.2.2.py2.4 on python 2.2... (no surprise)
>
> Noel, if you can make something out of all this, I really would be happy.
> I see a lot of applications for me using OpenBabel.
> However, if I am the only one with these problems and you see no principal
> problem with OpenBabel installation,
> then you might have better use for your time ...
>
> Many thanks again
> Regards
> Gilbert
>
>
>
> In 5 Schritten zur eigenen Homepage. Jetzt Domain sichern und gestalten!
>
> Nur 3,99 EUR/Monat! *http://www.maildomain.web.de/?mc=021114*<http://www.maildomain.web.de/?mc=021114>
>
>

Re: [OpenBabel-scripting] openbabel installation problems

[<gil...@we...>]

Hello Noel,

thanks again for your help.

> -----Ursprüngliche Nachricht-----
> Von: "Noel O'Boyle" <BAO...@GM...>
> Gesendet: 18.02.08 11:36:33
> An: "gil...@we..." <GIL...@WE...>
> CC: ope...@li...
> Betreff: Re: [OpenBabel-scripting] openbabel installation problems


> 
> (Please cc to the mailing list)
> 
> On 17/02/2008, gil...@we... <GIL...@WE...>wrote:
> > Hello Noel,
> >
> > thank you for your fast reply.
> > I appreciate that you do this in your free time.
> >
> > >
> > > I have a couple of questions or suggestions to try:
> > > (1) Is this the full error message? "ImportError: DLL load failed:..."
> > ok, not too smart... :-| I delete the rest of the message, because it was in german,
> > telling that the _openbabel.dll could not be started because its configuration would not be correct.
> 
> Did a message pop up on the screen too? Like a little Alert box?
No, there was nothing like that - just the message as shown below.


> 
> > I deinstalled all python now and installed from python-2.4.4.msi, which looked ok to me.
> > Then I installed openbabel-python-1.2.2.py2.4, but get the same problems (now the complete message):
> >
> > ----------------------------------------------------
> > Python 2.4.4 (#71, Oct 18 2006, 08:34:43) [MSC v.1310 32 bit (Intel)] on win32
> > Type "copyright", "credits" or "license()" for more information.
> >
> > ****************************************************************
> > ...
> > ****************************************************************
> >
> > IDLE 1.1.4
> > >>> import openbabel
> >
> > Traceback (most recent call last):
> > File "<PYSHELL#0>", line 1, in -toplevel-
> > import openbabel
> > File "C:ProgrammePython24Libsite-packagesopenbabel.py", line 7, in -toplevel-
> > import _openbabel
> > ImportError: DLL load failed: Diese Anwendung konnte nicht gestartet werden, weil die Anwenungskonfiguration nicht korrekt ist. Zur Problembehebung sollten Sie die Anwendung neu installieren.
> > ---------------------------------------------------
> >
> > The python installation for 2.5 came from ActiveState, so I thought that the problems might have come from there...
> 
> Me too - but it seems that this is not the problem in the end :-/
> 
> > > (2) Could you start python with "python -v", and give the output that
> > > is shown after you type "import openbabel"
> > That's interessting. When I try to start python in Win cmd shell from c:,
> > I get an error telling me, that python could not be found.
> > Do you think that should be with a proper installation?
> > The pythonpath should be in the registry and should be callable from everywhere, right ?
> 
> No - that's actually incorrect. First of all, you are confusing
> "PYTHONPATH" and "PATH". Just like in Linux, the system uses the PATH
> to find executables, so you can't just run python at the command
> prompt until you add C:ProgramsPython24 to the PATH. To do this, you
> need to use Control Panel/System/Advanced or so (be careful!).
> 
> PYTHONPATH, for the record, is a variable that Python searches when
> you type "import whatever", it looks for a file called whatever.py or
> a directory called whatever in each of the directories in your
> PYTHONPATH. Again, you can set this environment variable in Control
> Panel.
> 
> > On the other hand, the openbabel installer found the python 2.4 version in the registry without problems.
> That uses a key in the registry. Not the PATH.
Hmmm, ok, thanks, got it.

> 
> > When I cd to the python folder an try again, I get the messages in the attached file. (error.txt)
> > > (3) Can you list the contents of
> > > C:ProgrammePython25libsite-packages (e.g. use the 'dir' command)
> > >>> import sys
> > >>> print sys.path
> > ['C:\Programme\Python24\Lib\idlelib', 'C:\Programme\Python24\python24.zip', 'C:\Programme\Python24', 'C:\Programme\Python24\DLLs', 'C:\Programme\Python24\lib', 'C:\Programme\Python24\lib\plat-win', 'C:\Programme\Python24\lib\lib-tk', 'C:\Programme\Python24\lib\site-packages']
> >
> > Seems to be ok...
> 
> My question is still the same. Can you list the contents of
> C:\Programme\Python24\lib\site-packages? (I want to make sure that
> all of the openbabel files have been installed)

Sorry, I got you completly wrong. Here it is:

Verzeichnis von C:ProgrammePython24Libsite-packages

17.02.2008 01:54 .

17.02.2008 01:54 ..
27.06.2007 12:24 892.928 iconv.dll
17.02.2008 01:45 isapi
27.06.2007 12:24 724.992 libinchi.dll
27.06.2007 12:24 876.032 libxml2.dll
27.08.2007 18:22 257.308 openbabel.py
17.02.2008 00:45 405.848 openbabel.pyc
17.02.2008 00:45 405.848 openbabel.pyo
09.07.2007 14:02 1.466.368 OpenBabelDLL.dll
17.02.2008 00:45 openbabel_data
27.08.2007 18:24 16.541 pybel.py
17.02.2008 00:45 18.705 pybel.pyc
17.02.2008 00:45 18.705 pybel.pyo
17.02.2008 01:54 pysqlite2
26.01.2004 23:01 141 pythoncom.py
17.02.2008 01:45 245 pythoncom.pyc
17.02.2008 01:45 245 pythoncom.pyo
17.02.2008 01:45 pythonwin
23.09.2006 02:52 450 pywin32-210-py2.6.egg-info
23.09.2006 01:52 2.141.131 PyWin32.chm
10.10.2004 20:06 69 pywin32.pth
23.09.2006 02:50 5 pywin32.version.txt
17.02.2008 01:45 pywin32_system32
28.10.2005 20:15 121 README.txt
17.02.2008 01:45 win32
17.02.2008 01:45 win32com
17.02.2008 01:45 win32comext
27.06.2007 12:24 59.904 zlib1.dll
27.08.2007 18:23 1.875.968 _openbabel.pyd> 


> > > (4) When you run "import openbabel", make sure you are in an empty
> > > directory (just to avoid any problems)
> > Do you mean from another folder than the python folder, then see above...
> 
> No - I mean an empty directory (although it looks like this is not the
> problem). To run Python, just use "C:Program FilesPython24python"
> instead of just "python".

That works fine:
C:>c:programmepython24python
Python 2.4.4 (#71, Oct 18 2006, 08:34:43) [MSC v.1310 32 bit (Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>>


> 
> > > (5) I have not tested PythonWin. Could you install the regular Python
> > > 2.4, for example, and try using the installer for Python 2.4? (Try
> > > Python 2.4 rather than 2.5, as otherwise it may cause some confusion)
> > ->(1)
> >
> > A python installation error then ?
> > I am sure I have admin rights, its my private PC.
> > To check again, I installed SQLite (pysqlite-2.4.1.win32-py2.4)
> > and it worked without problems.
> > Then I installed pywin32, no problems...
> >
> > Do you have any ideas ?
> 
> (A1) Hmmm. Did you say that you also installed OpenBabelGUI? If so,
> can you confirm that "babel -H" is working (please attach the output)?
> If so, then rename the OpenBabel folder to something different, and
> try "import openbabel" from Python again. (The reason is that the
> OpenBabel folder *is* on the PATH, and may be conflicting with the DLL
> supplied with Python OpenBabel)


Actually, OpenBabelGUI is not installed, but it once was.
'babel -H' gives an error now (can't find babel...)
But when I checked the PATH (via Control Panel/System/Advanced)
there was still a path set to an OpenBabel installation.
I removed it, rebooted, but it still gives me the error of not being able to start '_openbabel.dll'.

> 
> (A2) Take a look at Control Panel/Add and Remove Programs. Is
> "Microsoft Visual 2005 C++ Redistributable" listed? This is needed for
> the Python bindings, and should have been installed by the installer.
Thats installed.

> 
> This is a tough one. Have you tried installing on another computer
> just to see if you have the same problem??
I did, but this was on a machine, where I do not have admin rights
and OpenBabel complains about that during installation anyway, so I did not mention it.
Interesstingly, I get the same error of not being able to start '_openbabel.dll'.
If this dll needs registration, aka admin rights, then no wonder....
But then what about my private machine where I have admin rights ?

Yesterday I borrowed another machine, where I have admin rights.
I tried with Python 2.5 and afterwards 2.4, together with the corresponding OpenBabels
and it didn't work, same errors. This machine has never seen OpenBabelGUI.
There is a Python2.2 preinstalled, but Openbabel was properly copied/installed to the newer version.
In fact, the installer crashed when I tried to install openbabel-python-1.2.2.py2.4 on python 2.2... (no surprise)

Noel, if you can make something out of all this, I really would be happy.
I see a lot of applications for me using OpenBabel.
However, if I am the only one with these problems and you see no principal problem with OpenBabel installation,
then you might have better use for your time ...


Many thanks again
Regards
Gilbert




	
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Re: [OpenBabel-scripting] openbabel installation problems

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

(Please cc to the mailing list)

On 17/02/2008, gil...@we... <gil...@we...> wrote:
> Hello Noel,
>
> thank you for your fast reply.
> I appreciate  that you do this in your free time.
>
> >
> > I have a couple of questions or suggestions to try:
> > (1) Is this the full error message? "ImportError: DLL load failed:..."
> ok, not too smart... :-|  I delete the rest of the message, because it was in german,
> telling that the _openbabel.dll could not be started because its configuration would not  be correct.

Did a message pop up on the screen too? Like a little Alert box?

> I deinstalled all python now and installed from python-2.4.4.msi, which looked ok to me.
> Then I installed openbabel-python-1.2.2.py2.4, but get the same problems (now the complete message):
>
> ----------------------------------------------------
> Python 2.4.4 (#71, Oct 18 2006, 08:34:43) [MSC v.1310 32 bit (Intel)] on win32
> Type "copyright", "credits" or "license()" for more information.
>
>     ****************************************************************
> ...
>     ****************************************************************
>
> IDLE 1.1.4
> >>> import openbabel
>
> Traceback (most recent call last):
>   File "<pyshell#0>", line 1, in -toplevel-
>     import openbabel
>   File "C:\Programme\Python24\Lib\site-packages\openbabel.py", line 7, in -toplevel-
>     import _openbabel
> ImportError: DLL load failed: Diese Anwendung konnte nicht gestartet werden, weil die Anwenungskonfiguration nicht korrekt ist. Zur Problembehebung sollten Sie die Anwendung neu installieren.
> ---------------------------------------------------
>
> The python installation for 2.5 came from ActiveState, so I thought that the problems might have come from there...

Me too - but it seems that this is not the problem in the end :-/

> > (2) Could you start python with "python -v", and give the output that
> > is shown after you type "import openbabel"
> That's interessting. When I try to start python in Win cmd shell from c:,
> I get an error telling me, that python could not be found.
> Do you think that should be with a proper installation?
> The pythonpath should be in the registry and should be callable from everywhere, right ?

No - that's actually incorrect. First of all, you are confusing
"PYTHONPATH" and "PATH". Just like in Linux, the system uses the PATH
to find executables, so you can't just run python at the command
prompt until you add C:\Programs\Python24 to the PATH. To do this, you
need to use Control Panel/System/Advanced or so (be careful!).

PYTHONPATH, for the record, is a variable that Python searches when
you type "import whatever", it looks for a file called whatever.py or
a directory called whatever in each of the directories in your
PYTHONPATH. Again, you can set this environment variable in Control
Panel.

> On the other hand, the openbabel installer found the python 2.4 version in the registry without problems.
That uses a key in the registry. Not the PATH.

> When I cd to the python folder an try again, I get the messages in the attached file. (error.txt)
> > (3) Can you list the contents of
> > C:\Programme\Python25\lib\site-packages\ (e.g. use the 'dir' command)
> >>> import sys
> >>> print sys.path
> ['C:\\Programme\\Python24\\Lib\\idlelib', 'C:\\Programme\\Python24\\python24.zip', 'C:\\Programme\\Python24', 'C:\\Programme\\Python24\\DLLs', 'C:\\Programme\\Python24\\lib', 'C:\\Programme\\Python24\\lib\\plat-win', 'C:\\Programme\\Python24\\lib\\lib-tk', 'C:\\Programme\\Python24\\lib\\site-packages']
>
> Seems to be ok...

My question is still the same. Can you list the contents of
C:\\Programme\\Python24\\lib\\site-packages? (I want to make sure that
all of the openbabel files have been installed)

> > (4) When you run "import openbabel", make sure you are in an empty
> > directory (just to avoid any problems)
> Do you mean from another folder than the python folder, then see above...

No - I mean an empty directory (although it looks like this is not the
problem). To run Python, just use "C:\Program Files\Python24\python"
instead of just "python".

> > (5) I have not tested PythonWin. Could you install the regular Python
> > 2.4, for example, and try using the installer for Python 2.4? (Try
> > Python 2.4 rather than 2.5, as otherwise it may cause some confusion)
>    ->(1)
>
> A python installation error then ?
> I am sure I have admin rights, its my private PC.
> To check again, I installed SQLite (pysqlite-2.4.1.win32-py2.4)
> and it worked without problems.
> Then I installed pywin32, no problems...
>
> Do you have any ideas ?

(A1) Hmmm. Did you say that you also installed OpenBabelGUI? If so,
can you confirm that "babel -H" is working (please attach the output)?
If so, then rename the OpenBabel folder to something different, and
try "import openbabel" from Python again. (The reason is that the
OpenBabel folder *is* on the PATH, and may be conflicting with the DLL
supplied with Python OpenBabel)

(A2) Take a look at Control Panel/Add and Remove Programs. Is
"Microsoft Visual 2005 C++ Redistributable" listed? This is needed for
the Python bindings, and should have been installed by the installer.

This is a tough one. Have you tried installing on another computer
just to see if you have the same problem??

Regards,
    Noel

Re: [OpenBabel-scripting] openbabel installation problems

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

Hello Gilbert,



On 15/02/2008, gil...@we... <gil...@we...> wrote:
> Hi all,
>
> I wanted to install openbabel and pybel modules on WinXP (with admin rights)
> using the openbabel-python-1.2.2.py2.5 installer, but I got
>
> PythonWin 2.5.1 (r251:54863, May  1 2007, 17:47:05) [MSC v.1310 32 bit (Intel)] on win32.
> Portions Copyright 1994-2006 Mark Hammond - see 'Help/About PythonWin' for further copyright information.
> >>> import openbabel
> Traceback (most recent call last):
>   File "<interactive input>", line 1, in <module>
>   File "C:\Programme\Python25\lib\site-packages\openbabel.py", line 7, in <module>
>     import _openbabel
> ImportError: DLL load failed:...
> >>>
>
> I already reinstalled OB, but I still doesn't work.
>
> The installation protocoll looks ok to me and ends with
>
> 300 Run Script: [python25.dll]C:\Programme\Python25\Scripts\openbabel_postinstall.py
> *** Installation finished 2008/02/15 21:41 ***
>
>
> I am new to python, so I might do something wrong or miss something.
> As far as I understood, there is no need to build with 'python setup.py build'
> on windows as there is the installer, but is this correct?
> (I didn't find a setup.py for babel, though...)

It sounds like you are doing everything correctly. There is no need to
run "python setup.py build" on Windows, as we have already done this.
All you need is the installer.

> Could anyone please help me ?

I have a couple of questions or suggestions to try:
(1) Is this the full error message? "ImportError: DLL load failed:..."
(2) Could you start python with "python -v", and give the output that
is shown after you type "import openbabel"
(3) Can you list the contents of
C:\Programme\Python25\lib\site-packages\ (e.g. use the 'dir' command)
(4) When you run "import openbabel", make sure you are in an empty
directory (just to avoid any problems)
(5) I have not tested PythonWin. Could you install the regular Python
2.4, for example, and try using the installer for Python 2.4? (Try
Python 2.4 rather than 2.5, as otherwise it may cause some confusion)

Regards,
   Noel

> Thanks a lot
>
> Gilbert
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

[OpenBabel-scripting] openbabel installation problems

[<gil...@we...>]

Hi all,

I wanted to install openbabel and pybel modules on WinXP (with admin rights)
using the openbabel-python-1.2.2.py2.5 installer, but I got

PythonWin 2.5.1 (r251:54863, May  1 2007, 17:47:05) [MSC v.1310 32 bit (Intel)] on win32.
Portions Copyright 1994-2006 Mark Hammond - see 'Help/About PythonWin' for further copyright information.
>>> import openbabel
Traceback (most recent call last):
  File "<interactive input>", line 1, in <module>
  File "C:\Programme\Python25\lib\site-packages\openbabel.py", line 7, in <module>
    import _openbabel
ImportError: DLL load failed:...
>>> 

I already reinstalled OB, but I still doesn't work.

The installation protocoll looks ok to me and ends with

300 Run Script: [python25.dll]C:\Programme\Python25\Scripts\openbabel_postinstall.py
*** Installation finished 2008/02/15 21:41 ***


I am new to python, so I might do something wrong or miss something.
As far as I understood, there is no need to build with 'python setup.py build'
on windows as there is the installer, but is this correct?
(I didn't find a setup.py for babel, though...)

Could anyone please help me ?

Thanks a lot

Gilbert

Re: [OpenBabel-scripting] Compiling ruby extensions continued

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

After googling, I see that the solution to my earlier problem (see
email below) was described in Rich's post:
http://www.nabble.com/Ruby-Open-Babel-in-2.1.1-td14109532.html

I've updated the Makefile to perform the correction described by Rich
(not yet checked in).

After doing this, everything is AOK:

oboyle@calvin:~/openbabel-trunk/scripts/ruby$ export RUBYLIB=.
oboyle@calvin:~/openbabel-trunk/scripts/ruby$ irb
irb(main):001:0> require 'openbabel'
(eval): warning: already initialized constant VectorData
=> true
irb(main):002:0> require 'examples/load_benzene.rb'
Benzene has 6 heavy atoms.
Benzene has 12 total atoms.
The molecular weight of benzene is 78.11184.
=> true

So...in summary:
(1) %include fingerprint.h causes the error previously reported, and
this is not yet resolved
(2) Where in the procedure is it possible to specify a DESTDIR for
installing the Ruby extension module? (For Python/Perl, it's done at
the last install step, with a --prefix)

Regards,
   Noel

On 24/01/2008, Noel O'Boyle <bao...@gm...> wrote:
> Mea culpa. Running make in openbabel/script correctly sets the
> location of the library and header files to wherever they have been
> installed:
>
> (cd ruby; ruby extconf.rb \
>   --with-openbabel-include=/home/oboyle/not-backed-up/tree/include/openbabel-2.0
>  \
>   --with-openbabel-lib=/home/oboyle/not-backed-up/tree/lib )
> checking for main() in -lopenbabel... yes
> creating Makefile
> sed -e 's/rb_define_module(\"Openbabel\")/rb_define_module(\"OpenBabel\")/' <rub
> y/openbabel_ruby.cpp >ruby/openbabel_ruby.new
> mv ruby/openbabel_ruby.new ruby/openbabel_ruby.cpp
>
> I made the Ruby interface file identical to that from Python, but get
> the same error as previously. If I comment out fingerprint.h,
> everything compiles.
>
> However, I am unsure how to test. How do I install? "make install"
> wants to install in /usr/lib or so. If I set DESTDIR in the Makefile
> (by hand) it puts it in a local directory. I then can set RUBYLIB to
> point to this. Is this correct? Shouldn't there be a .rb file
> somewhere that I can 'require'. If I require 'openbabel' (i.e.
> openbabel.so) it just says:
>
> irb(main):001:0> require 'openbabel'
> LoadError: /home/noel/tree/usr/local/lib/site_ruby/1.8/i486-linu
> x/openbabel.so: undefined symbol: Init_openbabel - /home/oboyle/tr
> ee/usr/local/lib/site_ruby/1.8/i486-linux/openbabel.so
>         from /home/oboyle/tree/usr/local/lib/site_ruby/1.8/i486-li
> nux/openbabel.so
>         from (irb):1
>
> Side issue regarding interface files: To avoid repeating ourselves, I
> suggest factoring out the common parts and using a include statement.
> I think the original rationale was that we thought it would be better
> to decouple the different scripting languages but it seems that this
> is not necessary, and causes maintenance problems...
>
> Noel
>
> On 23/01/2008, richard apodaca <ric...@ya...> wrote:
> > Noel,
> >
> > Just for laughs, what happens when you try to compile
> > the Ruby extension using the default install
> > directories? (i.e. install as per the tutorial)
> >
> > I've never seen the error you're getting and it makes
> > me wonder if the root cause might be in the way Ruby
> > Open Babel being compiled, not in the SWIG wrapper per
> > se.
> >
> > Cheers,
> > Rich
> >
> > --- Chris Morley <c.m...@ds...> wrote:
> >
> > > The base class version of the virtual function
> > > OBFingerprint::DescribeBits is called for
> > > fingerprints like FP2 (the
> > > default). I'm not sure why there are problems with
> > > the Ruby SWIG and not
> > > the Python SWIG. The function needs to be virtual,
> > > public, but it does
> > > not have to be in line as at present and it could
> > > probably be const. If
> > > the fault caused by returning a std::string I don't
> > > see an easy way
> > > round it. I could try modifying the C++ to see if I
> > > can get the Ruby
> > > SWIG to compile, but this won't be until tomorrow.
> > >
> > > Chris
> > >
> > > Noel O'Boyle wrote:
> > > > Regarding the error below, would I be right in
> > > saying that there is no
> > > > need to wrap OBFingerprint::DescribeBits? This
> > > function will never be
> > > > called in the base class.
> > > >
> > > > ---------- Forwarded message ----------
> > > > From: Noel O'Boyle <bao...@gm...>
> > > > Date: 22 Jan 2008 09:24
> > > > Subject: Re: [OpenBabel-scripting] Using Ruby with
> > > local install of OpenBabel
> > > > To: richard apodaca <ric...@ya...>
> > > > Cc: ope...@li...
> > > >
> > > > Unfortunately, make failed as follows:
> > > >
> > > > $ make
> > > > g++ -I. -I. -I/usr/lib/ruby/1.8/i486-linux -I.
> > > -I../../include  -fPIC -Wall -g -
> > > > fno-strict-aliasing -O2  -fPIC   -c
> > > openbabel_ruby.cpp
> > > > In file included from
> > > ../../include/openbabel/obutil.h:23,
> > > >                  from openbabel_ruby.cpp:1720:
> > > > ../../include/openbabel/babelconfig.h:18:1:
> > > warning: "EXTERN" redefined
> > > > In file included from
> > > /usr/lib/ruby/1.8/i486-linux/ruby.h:28,
> > > >                  from openbabel_ruby.cpp:809:
> > > > /usr/lib/ruby/1.8/i486-linux/defines.h:203:1:
> > > warning: this is the location of t
> > > > he previous definition
> > > > openbabel_ruby.cpp: In function 'VALUE
> > > _wrap_OBFingerprint_describe_bits__SWIG_0
> > > > (int, VALUE*, VALUE)':
> > > > openbabel_ruby.cpp:44781: error: assignment of
> > > read-only location
> > > > openbabel_ruby.cpp: In function 'VALUE
> > > _wrap_OBFingerprint_describe_bits__SWIG_1
> > > > (int, VALUE*, VALUE)':
> > > > openbabel_ruby.cpp:44830: error: assignment of
> > > read-only location
> > > > make: *** [openbabel_ruby.o] Error 1
> > > >
> > > > Regards,
> > > >    Noel
> > > >
> > > > On 21/01/2008, richard apodaca
> > > <ric...@ya...> wrote:
> > > >> Hello Noel,
> > > >>
> > > >> Although I haven't tried it myself, I believe
> > > this
> > > >> should be handled by the extconf.rb script as
> > > outlined
> > > >> in these instructions:
> > > >>
> > > >>
> > >
> > http://depth-first.com/articles/2007/04/09/painless-installation-of-ruby-open-babel
> > > >>
> > > >> If not, could you attach the error message(s)
> > > you're
> > > >> receiving?
> > > >>
> > > >> Cheers,
> > > >> Rich
> > > >>
> > > >> --- Noel O'Boyle <bao...@gm...> wrote:
> > > >>
> > > >>> I would appreciate if a Ruby expert could tell
> > > me
> > > >>> how to compile the
> > > >>> Ruby extensions by linking against an OpenBabel
> > > >>> library in a
> > > >>> non-standard location (i.e. not /usr/lib but
> > > >>> /home/oboyle/lib).
> > > >>>
> > > >>> Regards,
> > > >>>    Noel
> > > >>>
> > > >>>
> > > >>
> > >
> > -------------------------------------------------------------------------
> > > >>> This SF.net email is sponsored by: Microsoft
> > > >>> Defy all challenges. Microsoft(R) Visual Studio
> > > >>> 2008.
> > > >>>
> > > >>
> > >
> > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> > > >>> _______________________________________________
> > > >>> OpenBabel-scripting mailing list
> > > >>> Ope...@li...
> > > >>>
> > > >>
> > >
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> > > >>
> > > >> ___________________________________
> > > >>
> > > >> Richard L. Apodaca
> > > >>
> > > >> http://depth-first.com      Blog
> > > >> http://metamolecular.com    Company
> > > >>
> > > >>
> > >
> > -------------------------------------------------------------------------
> > > >> This SF.net email is sponsored by: Microsoft
> > > >> Defy all challenges. Microsoft(R) Visual Studio
> > > 2008.
> > > >>
> > >
> > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> > > >> _______________________________________________
> > > >> OpenBabel-scripting mailing list
> > > >> Ope...@li...
> > > >>
> > >
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> > > >>
> > > >
> > >
> > >
> > >
> > -------------------------------------------------------------------------
> > > This SF.net email is sponsored by: Microsoft
> > > Defy all challenges. Microsoft(R) Visual Studio
> > > 2008.
> > >
> > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> > > _______________________________________________
> > > OpenBabel-scripting mailing list
> > > Ope...@li...
> > >
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> > >
> >
> >
> > ___________________________________
> >
> > Richard L. Apodaca
> >
> > http://depth-first.com      Blog
> > http://metamolecular.com    Company
> >
> > -------------------------------------------------------------------------
> > This SF.net email is sponsored by: Microsoft
> > Defy all challenges. Microsoft(R) Visual Studio 2008.
> > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
>

[OpenBabel-scripting] Compiling ruby extensions continued

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

Mea culpa. Running make in openbabel/script correctly sets the
location of the library and header files to wherever they have been
installed:

(cd ruby; ruby extconf.rb \
  --with-openbabel-include=/home/oboyle/not-backed-up/tree/include/openbabel-2.0
 \
  --with-openbabel-lib=/home/oboyle/not-backed-up/tree/lib )
checking for main() in -lopenbabel... yes
creating Makefile
sed -e 's/rb_define_module(\"Openbabel\")/rb_define_module(\"OpenBabel\")/' <rub
y/openbabel_ruby.cpp >ruby/openbabel_ruby.new
mv ruby/openbabel_ruby.new ruby/openbabel_ruby.cpp

I made the Ruby interface file identical to that from Python, but get
the same error as previously. If I comment out fingerprint.h,
everything compiles.

However, I am unsure how to test. How do I install? "make install"
wants to install in /usr/lib or so. If I set DESTDIR in the Makefile
(by hand) it puts it in a local directory. I then can set RUBYLIB to
point to this. Is this correct? Shouldn't there be a .rb file
somewhere that I can 'require'. If I require 'openbabel' (i.e.
openbabel.so) it just says:

irb(main):001:0> require 'openbabel'
LoadError: /home/noel/tree/usr/local/lib/site_ruby/1.8/i486-linu
x/openbabel.so: undefined symbol: Init_openbabel - /home/oboyle/tr
ee/usr/local/lib/site_ruby/1.8/i486-linux/openbabel.so
        from /home/oboyle/tree/usr/local/lib/site_ruby/1.8/i486-li
nux/openbabel.so
        from (irb):1

Side issue regarding interface files: To avoid repeating ourselves, I
suggest factoring out the common parts and using a include statement.
I think the original rationale was that we thought it would be better
to decouple the different scripting languages but it seems that this
is not necessary, and causes maintenance problems...

Noel

On 23/01/2008, richard apodaca <ric...@ya...> wrote:
> Noel,
>
> Just for laughs, what happens when you try to compile
> the Ruby extension using the default install
> directories? (i.e. install as per the tutorial)
>
> I've never seen the error you're getting and it makes
> me wonder if the root cause might be in the way Ruby
> Open Babel being compiled, not in the SWIG wrapper per
> se.
>
> Cheers,
> Rich
>
> --- Chris Morley <c.m...@ds...> wrote:
>
> > The base class version of the virtual function
> > OBFingerprint::DescribeBits is called for
> > fingerprints like FP2 (the
> > default). I'm not sure why there are problems with
> > the Ruby SWIG and not
> > the Python SWIG. The function needs to be virtual,
> > public, but it does
> > not have to be in line as at present and it could
> > probably be const. If
> > the fault caused by returning a std::string I don't
> > see an easy way
> > round it. I could try modifying the C++ to see if I
> > can get the Ruby
> > SWIG to compile, but this won't be until tomorrow.
> >
> > Chris
> >
> > Noel O'Boyle wrote:
> > > Regarding the error below, would I be right in
> > saying that there is no
> > > need to wrap OBFingerprint::DescribeBits? This
> > function will never be
> > > called in the base class.
> > >
> > > ---------- Forwarded message ----------
> > > From: Noel O'Boyle <bao...@gm...>
> > > Date: 22 Jan 2008 09:24
> > > Subject: Re: [OpenBabel-scripting] Using Ruby with
> > local install of OpenBabel
> > > To: richard apodaca <ric...@ya...>
> > > Cc: ope...@li...
> > >
> > > Unfortunately, make failed as follows:
> > >
> > > $ make
> > > g++ -I. -I. -I/usr/lib/ruby/1.8/i486-linux -I.
> > -I../../include  -fPIC -Wall -g -
> > > fno-strict-aliasing -O2  -fPIC   -c
> > openbabel_ruby.cpp
> > > In file included from
> > ../../include/openbabel/obutil.h:23,
> > >                  from openbabel_ruby.cpp:1720:
> > > ../../include/openbabel/babelconfig.h:18:1:
> > warning: "EXTERN" redefined
> > > In file included from
> > /usr/lib/ruby/1.8/i486-linux/ruby.h:28,
> > >                  from openbabel_ruby.cpp:809:
> > > /usr/lib/ruby/1.8/i486-linux/defines.h:203:1:
> > warning: this is the location of t
> > > he previous definition
> > > openbabel_ruby.cpp: In function 'VALUE
> > _wrap_OBFingerprint_describe_bits__SWIG_0
> > > (int, VALUE*, VALUE)':
> > > openbabel_ruby.cpp:44781: error: assignment of
> > read-only location
> > > openbabel_ruby.cpp: In function 'VALUE
> > _wrap_OBFingerprint_describe_bits__SWIG_1
> > > (int, VALUE*, VALUE)':
> > > openbabel_ruby.cpp:44830: error: assignment of
> > read-only location
> > > make: *** [openbabel_ruby.o] Error 1
> > >
> > > Regards,
> > >    Noel
> > >
> > > On 21/01/2008, richard apodaca
> > <ric...@ya...> wrote:
> > >> Hello Noel,
> > >>
> > >> Although I haven't tried it myself, I believe
> > this
> > >> should be handled by the extconf.rb script as
> > outlined
> > >> in these instructions:
> > >>
> > >>
> >
> http://depth-first.com/articles/2007/04/09/painless-installation-of-ruby-open-babel
> > >>
> > >> If not, could you attach the error message(s)
> > you're
> > >> receiving?
> > >>
> > >> Cheers,
> > >> Rich
> > >>
> > >> --- Noel O'Boyle <bao...@gm...> wrote:
> > >>
> > >>> I would appreciate if a Ruby expert could tell
> > me
> > >>> how to compile the
> > >>> Ruby extensions by linking against an OpenBabel
> > >>> library in a
> > >>> non-standard location (i.e. not /usr/lib but
> > >>> /home/oboyle/lib).
> > >>>
> > >>> Regards,
> > >>>    Noel
> > >>>
> > >>>
> > >>
> >
> -------------------------------------------------------------------------
> > >>> This SF.net email is sponsored by: Microsoft
> > >>> Defy all challenges. Microsoft(R) Visual Studio
> > >>> 2008.
> > >>>
> > >>
> >
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> > >>> _______________________________________________
> > >>> OpenBabel-scripting mailing list
> > >>> Ope...@li...
> > >>>
> > >>
> >
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> > >>
> > >> ___________________________________
> > >>
> > >> Richard L. Apodaca
> > >>
> > >> http://depth-first.com      Blog
> > >> http://metamolecular.com    Company
> > >>
> > >>
> >
> -------------------------------------------------------------------------
> > >> This SF.net email is sponsored by: Microsoft
> > >> Defy all challenges. Microsoft(R) Visual Studio
> > 2008.
> > >>
> >
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> > >> _______________________________________________
> > >> OpenBabel-scripting mailing list
> > >> Ope...@li...
> > >>
> >
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> > >>
> > >
> >
> >
> >
> -------------------------------------------------------------------------
> > This SF.net email is sponsored by: Microsoft
> > Defy all challenges. Microsoft(R) Visual Studio
> > 2008.
> >
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> >
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
>
>
> ___________________________________
>
> Richard L. Apodaca
>
> http://depth-first.com      Blog
> http://metamolecular.com    Company
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] Compiling ruby extensions

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

On 23/01/2008, richard apodaca <ric...@ya...> wrote:
> Noel,
>
> Just for laughs, what happens when you try to compile
> the Ruby extension using the default install
> directories? (i.e. install as per the tutorial)

I think you mean following "make install" as root? I'm afraid I cannot
test this, as I don't have the appropriate permissions.

> I've never seen the error you're getting and it makes
> me wonder if the root cause might be in the way Ruby
> Open Babel being compiled, not in the SWIG wrapper per
> se.

Have you compiled the trunk recently? The functions referred to were
introduced relatively recently (I think).

> Cheers,
> Rich
>
> --- Chris Morley <c.m...@ds...> wrote:
>
> > The base class version of the virtual function
> > OBFingerprint::DescribeBits is called for
> > fingerprints like FP2 (the
> > default). I'm not sure why there are problems with
> > the Ruby SWIG and not
> > the Python SWIG. The function needs to be virtual,
> > public, but it does
> > not have to be in line as at present and it could
> > probably be const. If
> > the fault caused by returning a std::string I don't
> > see an easy way
> > round it. I could try modifying the C++ to see if I
> > can get the Ruby
> > SWIG to compile, but this won't be until tomorrow.
> >
> > Chris
> >
> > Noel O'Boyle wrote:
> > > Regarding the error below, would I be right in
> > saying that there is no
> > > need to wrap OBFingerprint::DescribeBits? This
> > function will never be
> > > called in the base class.
> > >
> > > ---------- Forwarded message ----------
> > > From: Noel O'Boyle <bao...@gm...>
> > > Date: 22 Jan 2008 09:24
> > > Subject: Re: [OpenBabel-scripting] Using Ruby with
> > local install of OpenBabel
> > > To: richard apodaca <ric...@ya...>
> > > Cc: ope...@li...
> > >
> > > Unfortunately, make failed as follows:
> > >
> > > $ make
> > > g++ -I. -I. -I/usr/lib/ruby/1.8/i486-linux -I.
> > -I../../include  -fPIC -Wall -g -
> > > fno-strict-aliasing -O2  -fPIC   -c
> > openbabel_ruby.cpp
> > > In file included from
> > ../../include/openbabel/obutil.h:23,
> > >                  from openbabel_ruby.cpp:1720:
> > > ../../include/openbabel/babelconfig.h:18:1:
> > warning: "EXTERN" redefined
> > > In file included from
> > /usr/lib/ruby/1.8/i486-linux/ruby.h:28,
> > >                  from openbabel_ruby.cpp:809:
> > > /usr/lib/ruby/1.8/i486-linux/defines.h:203:1:
> > warning: this is the location of t
> > > he previous definition
> > > openbabel_ruby.cpp: In function 'VALUE
> > _wrap_OBFingerprint_describe_bits__SWIG_0
> > > (int, VALUE*, VALUE)':
> > > openbabel_ruby.cpp:44781: error: assignment of
> > read-only location
> > > openbabel_ruby.cpp: In function 'VALUE
> > _wrap_OBFingerprint_describe_bits__SWIG_1
> > > (int, VALUE*, VALUE)':
> > > openbabel_ruby.cpp:44830: error: assignment of
> > read-only location
> > > make: *** [openbabel_ruby.o] Error 1
> > >
> > > Regards,
> > >    Noel
> > >
> > > On 21/01/2008, richard apodaca
> > <ric...@ya...> wrote:
> > >> Hello Noel,
> > >>
> > >> Although I haven't tried it myself, I believe
> > this
> > >> should be handled by the extconf.rb script as
> > outlined
> > >> in these instructions:
> > >>
> > >>
> >
> http://depth-first.com/articles/2007/04/09/painless-installation-of-ruby-open-babel
> > >>
> > >> If not, could you attach the error message(s)
> > you're
> > >> receiving?
> > >>
> > >> Cheers,
> > >> Rich
> > >>
> > >> --- Noel O'Boyle <bao...@gm...> wrote:
> > >>
> > >>> I would appreciate if a Ruby expert could tell
> > me
> > >>> how to compile the
> > >>> Ruby extensions by linking against an OpenBabel
> > >>> library in a
> > >>> non-standard location (i.e. not /usr/lib but
> > >>> /home/oboyle/lib).
> > >>>
> > >>> Regards,
> > >>>    Noel
> > >>>
> > >>>
> > >>
> >
> -------------------------------------------------------------------------
> > >>> This SF.net email is sponsored by: Microsoft
> > >>> Defy all challenges. Microsoft(R) Visual Studio
> > >>> 2008.
> > >>>
> > >>
> >
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> > >>> _______________________________________________
> > >>> OpenBabel-scripting mailing list
> > >>> Ope...@li...
> > >>>
> > >>
> >
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> > >>
> > >> ___________________________________
> > >>
> > >> Richard L. Apodaca
> > >>
> > >> http://depth-first.com      Blog
> > >> http://metamolecular.com    Company
> > >>
> > >>
> >
> -------------------------------------------------------------------------
> > >> This SF.net email is sponsored by: Microsoft
> > >> Defy all challenges. Microsoft(R) Visual Studio
> > 2008.
> > >>
> >
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> > >> _______________________________________________
> > >> OpenBabel-scripting mailing list
> > >> Ope...@li...
> > >>
> >
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> > >>
> > >
> >
> >
> >
> -------------------------------------------------------------------------
> > This SF.net email is sponsored by: Microsoft
> > Defy all challenges. Microsoft(R) Visual Studio
> > 2008.
> >
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> >
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
>
>
> ___________________________________
>
> Richard L. Apodaca
>
> http://depth-first.com      Blog
> http://metamolecular.com    Company
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] Compiling ruby extensions

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

Noel,

Just for laughs, what happens when you try to compile
the Ruby extension using the default install
directories? (i.e. install as per the tutorial)

I've never seen the error you're getting and it makes
me wonder if the root cause might be in the way Ruby
Open Babel being compiled, not in the SWIG wrapper per
se.

Cheers,
Rich

--- Chris Morley <c.m...@ds...> wrote:

> The base class version of the virtual function 
> OBFingerprint::DescribeBits is called for
> fingerprints like FP2 (the 
> default). I'm not sure why there are problems with
> the Ruby SWIG and not 
> the Python SWIG. The function needs to be virtual,
> public, but it does 
> not have to be in line as at present and it could
> probably be const. If 
> the fault caused by returning a std::string I don't
> see an easy way 
> round it. I could try modifying the C++ to see if I
> can get the Ruby 
> SWIG to compile, but this won't be until tomorrow.
> 
> Chris
> 
> Noel O'Boyle wrote:
> > Regarding the error below, would I be right in
> saying that there is no
> > need to wrap OBFingerprint::DescribeBits? This
> function will never be
> > called in the base class.
> > 
> > ---------- Forwarded message ----------
> > From: Noel O'Boyle <bao...@gm...>
> > Date: 22 Jan 2008 09:24
> > Subject: Re: [OpenBabel-scripting] Using Ruby with
> local install of OpenBabel
> > To: richard apodaca <ric...@ya...>
> > Cc: ope...@li...
> > 
> > Unfortunately, make failed as follows:
> > 
> > $ make
> > g++ -I. -I. -I/usr/lib/ruby/1.8/i486-linux -I.
> -I../../include  -fPIC -Wall -g -
> > fno-strict-aliasing -O2  -fPIC   -c
> openbabel_ruby.cpp
> > In file included from
> ../../include/openbabel/obutil.h:23,
> >                  from openbabel_ruby.cpp:1720:
> > ../../include/openbabel/babelconfig.h:18:1:
> warning: "EXTERN" redefined
> > In file included from
> /usr/lib/ruby/1.8/i486-linux/ruby.h:28,
> >                  from openbabel_ruby.cpp:809:
> > /usr/lib/ruby/1.8/i486-linux/defines.h:203:1:
> warning: this is the location of t
> > he previous definition
> > openbabel_ruby.cpp: In function 'VALUE
> _wrap_OBFingerprint_describe_bits__SWIG_0
> > (int, VALUE*, VALUE)':
> > openbabel_ruby.cpp:44781: error: assignment of
> read-only location
> > openbabel_ruby.cpp: In function 'VALUE
> _wrap_OBFingerprint_describe_bits__SWIG_1
> > (int, VALUE*, VALUE)':
> > openbabel_ruby.cpp:44830: error: assignment of
> read-only location
> > make: *** [openbabel_ruby.o] Error 1
> > 
> > Regards,
> >    Noel
> > 
> > On 21/01/2008, richard apodaca
> <ric...@ya...> wrote:
> >> Hello Noel,
> >>
> >> Although I haven't tried it myself, I believe
> this
> >> should be handled by the extconf.rb script as
> outlined
> >> in these instructions:
> >>
> >>
>
http://depth-first.com/articles/2007/04/09/painless-installation-of-ruby-open-babel
> >>
> >> If not, could you attach the error message(s)
> you're
> >> receiving?
> >>
> >> Cheers,
> >> Rich
> >>
> >> --- Noel O'Boyle <bao...@gm...> wrote:
> >>
> >>> I would appreciate if a Ruby expert could tell
> me
> >>> how to compile the
> >>> Ruby extensions by linking against an OpenBabel
> >>> library in a
> >>> non-standard location (i.e. not /usr/lib but
> >>> /home/oboyle/lib).
> >>>
> >>> Regards,
> >>>    Noel
> >>>
> >>>
> >>
>
-------------------------------------------------------------------------
> >>> This SF.net email is sponsored by: Microsoft
> >>> Defy all challenges. Microsoft(R) Visual Studio
> >>> 2008.
> >>>
> >>
>
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> >>> _______________________________________________
> >>> OpenBabel-scripting mailing list
> >>> Ope...@li...
> >>>
> >>
>
https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >>
> >> ___________________________________
> >>
> >> Richard L. Apodaca
> >>
> >> http://depth-first.com      Blog
> >> http://metamolecular.com    Company
> >>
> >>
>
-------------------------------------------------------------------------
> >> This SF.net email is sponsored by: Microsoft
> >> Defy all challenges. Microsoft(R) Visual Studio
> 2008.
> >>
>
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> >> _______________________________________________
> >> OpenBabel-scripting mailing list
> >> Ope...@li...
> >>
>
https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >>
> > 
> 
> 
>
-------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio
> 2008.
>
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
>
https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> 


___________________________________

Richard L. Apodaca

http://depth-first.com      Blog
http://metamolecular.com    Company

Re: [OpenBabel-scripting] Compiling ruby extensions

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

On 23/01/2008, Chris Morley <c.m...@ds...> wrote:
> The base class version of the virtual function
> OBFingerprint::DescribeBits is called for fingerprints like FP2 (the
> default). I'm not sure why there are problems with the Ruby SWIG and not
> the Python SWIG. The function needs to be virtual, public, but it does
> not have to be in line as at present and it could probably be const. If
> the fault caused by returning a std::string I don't see an easy way
> round it. I could try modifying the C++ to see if I can get the Ruby
> SWIG to compile, but this won't be until tomorrow.

It should be noted that the interface files for ruby and python are
not identical (in terms of header files and #includes). This could
also be a factor.

> Chris
>
> Noel O'Boyle wrote:
> > Regarding the error below, would I be right in saying that there is no
> > need to wrap OBFingerprint::DescribeBits? This function will never be
> > called in the base class.
> >
> > ---------- Forwarded message ----------
> > From: Noel O'Boyle <bao...@gm...>
> > Date: 22 Jan 2008 09:24
> > Subject: Re: [OpenBabel-scripting] Using Ruby with local install of OpenBabel
> > To: richard apodaca <ric...@ya...>
> > Cc: ope...@li...
> >
> > Unfortunately, make failed as follows:
> >
> > $ make
> > g++ -I. -I. -I/usr/lib/ruby/1.8/i486-linux -I. -I../../include  -fPIC -Wall -g -
> > fno-strict-aliasing -O2  -fPIC   -c openbabel_ruby.cpp
> > In file included from ../../include/openbabel/obutil.h:23,
> >                  from openbabel_ruby.cpp:1720:
> > ../../include/openbabel/babelconfig.h:18:1: warning: "EXTERN" redefined
> > In file included from /usr/lib/ruby/1.8/i486-linux/ruby.h:28,
> >                  from openbabel_ruby.cpp:809:
> > /usr/lib/ruby/1.8/i486-linux/defines.h:203:1: warning: this is the location of t
> > he previous definition
> > openbabel_ruby.cpp: In function 'VALUE _wrap_OBFingerprint_describe_bits__SWIG_0
> > (int, VALUE*, VALUE)':
> > openbabel_ruby.cpp:44781: error: assignment of read-only location
> > openbabel_ruby.cpp: In function 'VALUE _wrap_OBFingerprint_describe_bits__SWIG_1
> > (int, VALUE*, VALUE)':
> > openbabel_ruby.cpp:44830: error: assignment of read-only location
> > make: *** [openbabel_ruby.o] Error 1
> >
> > Regards,
> >    Noel
> >
> > On 21/01/2008, richard apodaca <ric...@ya...> wrote:
> >> Hello Noel,
> >>
> >> Although I haven't tried it myself, I believe this
> >> should be handled by the extconf.rb script as outlined
> >> in these instructions:
> >>
> >> http://depth-first.com/articles/2007/04/09/painless-installation-of-ruby-open-babel
> >>
> >> If not, could you attach the error message(s) you're
> >> receiving?
> >>
> >> Cheers,
> >> Rich
> >>
> >> --- Noel O'Boyle <bao...@gm...> wrote:
> >>
> >>> I would appreciate if a Ruby expert could tell me
> >>> how to compile the
> >>> Ruby extensions by linking against an OpenBabel
> >>> library in a
> >>> non-standard location (i.e. not /usr/lib but
> >>> /home/oboyle/lib).
> >>>
> >>> Regards,
> >>>    Noel
> >>>
> >>>
> >> -------------------------------------------------------------------------
> >>> This SF.net email is sponsored by: Microsoft
> >>> Defy all challenges. Microsoft(R) Visual Studio
> >>> 2008.
> >>>
> >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> >>> _______________________________________________
> >>> OpenBabel-scripting mailing list
> >>> Ope...@li...
> >>>
> >> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >>
> >> ___________________________________
> >>
> >> Richard L. Apodaca
> >>
> >> http://depth-first.com      Blog
> >> http://metamolecular.com    Company
> >>
> >> -------------------------------------------------------------------------
> >> This SF.net email is sponsored by: Microsoft
> >> Defy all challenges. Microsoft(R) Visual Studio 2008.
> >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> >> _______________________________________________
> >> OpenBabel-scripting mailing list
> >> Ope...@li...
> >> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >>
> >
>
>

Re: [OpenBabel-scripting] Compiling ruby extensions

[Chris M. <c.m...@ds...>]

The base class version of the virtual function 
OBFingerprint::DescribeBits is called for fingerprints like FP2 (the 
default). I'm not sure why there are problems with the Ruby SWIG and not 
the Python SWIG. The function needs to be virtual, public, but it does 
not have to be in line as at present and it could probably be const. If 
the fault caused by returning a std::string I don't see an easy way 
round it. I could try modifying the C++ to see if I can get the Ruby 
SWIG to compile, but this won't be until tomorrow.

Chris

Noel O'Boyle wrote:
> Regarding the error below, would I be right in saying that there is no
> need to wrap OBFingerprint::DescribeBits? This function will never be
> called in the base class.
> 
> ---------- Forwarded message ----------
> From: Noel O'Boyle <bao...@gm...>
> Date: 22 Jan 2008 09:24
> Subject: Re: [OpenBabel-scripting] Using Ruby with local install of OpenBabel
> To: richard apodaca <ric...@ya...>
> Cc: ope...@li...
> 
> Unfortunately, make failed as follows:
> 
> $ make
> g++ -I. -I. -I/usr/lib/ruby/1.8/i486-linux -I. -I../../include  -fPIC -Wall -g -
> fno-strict-aliasing -O2  -fPIC   -c openbabel_ruby.cpp
> In file included from ../../include/openbabel/obutil.h:23,
>                  from openbabel_ruby.cpp:1720:
> ../../include/openbabel/babelconfig.h:18:1: warning: "EXTERN" redefined
> In file included from /usr/lib/ruby/1.8/i486-linux/ruby.h:28,
>                  from openbabel_ruby.cpp:809:
> /usr/lib/ruby/1.8/i486-linux/defines.h:203:1: warning: this is the location of t
> he previous definition
> openbabel_ruby.cpp: In function 'VALUE _wrap_OBFingerprint_describe_bits__SWIG_0
> (int, VALUE*, VALUE)':
> openbabel_ruby.cpp:44781: error: assignment of read-only location
> openbabel_ruby.cpp: In function 'VALUE _wrap_OBFingerprint_describe_bits__SWIG_1
> (int, VALUE*, VALUE)':
> openbabel_ruby.cpp:44830: error: assignment of read-only location
> make: *** [openbabel_ruby.o] Error 1
> 
> Regards,
>    Noel
> 
> On 21/01/2008, richard apodaca <ric...@ya...> wrote:
>> Hello Noel,
>>
>> Although I haven't tried it myself, I believe this
>> should be handled by the extconf.rb script as outlined
>> in these instructions:
>>
>> http://depth-first.com/articles/2007/04/09/painless-installation-of-ruby-open-babel
>>
>> If not, could you attach the error message(s) you're
>> receiving?
>>
>> Cheers,
>> Rich
>>
>> --- Noel O'Boyle <bao...@gm...> wrote:
>>
>>> I would appreciate if a Ruby expert could tell me
>>> how to compile the
>>> Ruby extensions by linking against an OpenBabel
>>> library in a
>>> non-standard location (i.e. not /usr/lib but
>>> /home/oboyle/lib).
>>>
>>> Regards,
>>>    Noel
>>>
>>>
>> -------------------------------------------------------------------------
>>> This SF.net email is sponsored by: Microsoft
>>> Defy all challenges. Microsoft(R) Visual Studio
>>> 2008.
>>>
>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>>> _______________________________________________
>>> OpenBabel-scripting mailing list
>>> Ope...@li...
>>>
>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>
>> ___________________________________
>>
>> Richard L. Apodaca
>>
>> http://depth-first.com      Blog
>> http://metamolecular.com    Company
>>
>> -------------------------------------------------------------------------
>> This SF.net email is sponsored by: Microsoft
>> Defy all challenges. Microsoft(R) Visual Studio 2008.
>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>> _______________________________________________
>> OpenBabel-scripting mailing list
>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>
> 

[OpenBabel-scripting] Compiling ruby extensions

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

Regarding the error below, would I be right in saying that there is no
need to wrap OBFingerprint::DescribeBits? This function will never be
called in the base class.

---------- Forwarded message ----------
From: Noel O'Boyle <bao...@gm...>
Date: 22 Jan 2008 09:24
Subject: Re: [OpenBabel-scripting] Using Ruby with local install of OpenBabel
To: richard apodaca <ric...@ya...>
Cc: ope...@li...

Unfortunately, make failed as follows:

$ make
g++ -I. -I. -I/usr/lib/ruby/1.8/i486-linux -I. -I../../include  -fPIC -Wall -g -
fno-strict-aliasing -O2  -fPIC   -c openbabel_ruby.cpp
In file included from ../../include/openbabel/obutil.h:23,
                 from openbabel_ruby.cpp:1720:
../../include/openbabel/babelconfig.h:18:1: warning: "EXTERN" redefined
In file included from /usr/lib/ruby/1.8/i486-linux/ruby.h:28,
                 from openbabel_ruby.cpp:809:
/usr/lib/ruby/1.8/i486-linux/defines.h:203:1: warning: this is the location of t
he previous definition
openbabel_ruby.cpp: In function 'VALUE _wrap_OBFingerprint_describe_bits__SWIG_0
(int, VALUE*, VALUE)':
openbabel_ruby.cpp:44781: error: assignment of read-only location
openbabel_ruby.cpp: In function 'VALUE _wrap_OBFingerprint_describe_bits__SWIG_1
(int, VALUE*, VALUE)':
openbabel_ruby.cpp:44830: error: assignment of read-only location
make: *** [openbabel_ruby.o] Error 1

Regards,
   Noel

On 21/01/2008, richard apodaca <ric...@ya...> wrote:
> Hello Noel,
>
> Although I haven't tried it myself, I believe this
> should be handled by the extconf.rb script as outlined
> in these instructions:
>
> http://depth-first.com/articles/2007/04/09/painless-installation-of-ruby-open-babel
>
> If not, could you attach the error message(s) you're
> receiving?
>
> Cheers,
> Rich
>
> --- Noel O'Boyle <bao...@gm...> wrote:
>
> > I would appreciate if a Ruby expert could tell me
> > how to compile the
> > Ruby extensions by linking against an OpenBabel
> > library in a
> > non-standard location (i.e. not /usr/lib but
> > /home/oboyle/lib).
> >
> > Regards,
> >    Noel
> >
> >
> -------------------------------------------------------------------------
> > This SF.net email is sponsored by: Microsoft
> > Defy all challenges. Microsoft(R) Visual Studio
> > 2008.
> >
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> >
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
>
>
> ___________________________________
>
> Richard L. Apodaca
>
> http://depth-first.com      Blog
> http://metamolecular.com    Company
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] Using Ruby with local install of OpenBabel

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

I found that mkmf.log had some useful information. The problem was the
-lopenbabel part used to test have_library("openbabel"). After looking
at http://blog.evanweaver.com/files/readme.ext.txt, I tried the
following which worked.
ruby extconf.rb --with-openbabel-lib="../../src/.libs"
--with-openbabel-include="../../include"

(Although "../../include" is specified in extconf.rb, it is only used
if the number of arguments is zero)

Unfortunately, make failed as follows:

$ make
g++ -I. -I. -I/usr/lib/ruby/1.8/i486-linux -I. -I../../include  -fPIC -Wall -g -
fno-strict-aliasing -O2  -fPIC   -c openbabel_ruby.cpp
In file included from ../../include/openbabel/obutil.h:23,
                 from openbabel_ruby.cpp:1720:
../../include/openbabel/babelconfig.h:18:1: warning: "EXTERN" redefined
In file included from /usr/lib/ruby/1.8/i486-linux/ruby.h:28,
                 from openbabel_ruby.cpp:809:
/usr/lib/ruby/1.8/i486-linux/defines.h:203:1: warning: this is the location of t
he previous definition
openbabel_ruby.cpp: In function 'VALUE _wrap_OBFingerprint_describe_bits__SWIG_0
(int, VALUE*, VALUE)':
openbabel_ruby.cpp:44781: error: assignment of read-only location
openbabel_ruby.cpp: In function 'VALUE _wrap_OBFingerprint_describe_bits__SWIG_1
(int, VALUE*, VALUE)':
openbabel_ruby.cpp:44830: error: assignment of read-only location
make: *** [openbabel_ruby.o] Error 1

Regards,
   Noel

On 21/01/2008, richard apodaca <ric...@ya...> wrote:
> Hello Noel,
>
> Although I haven't tried it myself, I believe this
> should be handled by the extconf.rb script as outlined
> in these instructions:
>
> http://depth-first.com/articles/2007/04/09/painless-installation-of-ruby-open-babel
>
> If not, could you attach the error message(s) you're
> receiving?
>
> Cheers,
> Rich
>
> --- Noel O'Boyle <bao...@gm...> wrote:
>
> > I would appreciate if a Ruby expert could tell me
> > how to compile the
> > Ruby extensions by linking against an OpenBabel
> > library in a
> > non-standard location (i.e. not /usr/lib but
> > /home/oboyle/lib).
> >
> > Regards,
> >    Noel
> >
> >
> -------------------------------------------------------------------------
> > This SF.net email is sponsored by: Microsoft
> > Defy all challenges. Microsoft(R) Visual Studio
> > 2008.
> >
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> >
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
>
>
> ___________________________________
>
> Richard L. Apodaca
>
> http://depth-first.com      Blog
> http://metamolecular.com    Company
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] Using Ruby with local install of OpenBabel

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

Hello Noel,

Although I haven't tried it myself, I believe this
should be handled by the extconf.rb script as outlined
in these instructions:

http://depth-first.com/articles/2007/04/09/painless-installation-of-ruby-open-babel

If not, could you attach the error message(s) you're
receiving?

Cheers,
Rich

--- Noel O'Boyle <bao...@gm...> wrote:

> I would appreciate if a Ruby expert could tell me
> how to compile the
> Ruby extensions by linking against an OpenBabel
> library in a
> non-standard location (i.e. not /usr/lib but
> /home/oboyle/lib).
> 
> Regards,
>    Noel
> 
>
-------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio
> 2008.
>
http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
>
https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> 


___________________________________

Richard L. Apodaca

http://depth-first.com      Blog
http://metamolecular.com    Company

[OpenBabel-scripting] Using Ruby with local install of OpenBabel

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

I would appreciate if a Ruby expert could tell me how to compile the
Ruby extensions by linking against an OpenBabel library in a
non-standard location (i.e. not /usr/lib but /home/oboyle/lib).

Regards,
   Noel

Re: [OpenBabel-scripting] [OpenBabel-Devel] Let's fix the Python bindings

[Chris M. <c.m...@ds...>]

Joshua Ballanco wrote:
> Ok, so I've gotten rid of the odd const assignments, but I'm still  
> having issues linking. I'm thinking that it may be related to the  
> following errors that I get when running SWIG:
> 
> ../include/openbabel/plugin.h:39: Warning(401): Nothing known about  
> base class 'std::binary_function<char const *,char const *,bool >'.  
> Ignored.
> ../include/openbabel/plugin.h:39: Warning(401): Maybe you forgot to  
> instantiate 'std::binary_function<char const *,char const *,bool >'  
> using %template.
> ../include/openbabel/oberror.h:197: Warning(401): Nothing known about  
> base class 'std::stringbuf'. Ignored.

I get these warnings (and others) when compiling the SWIG bindings for 
Python (on Windows) - and it goes on to link ok. These functions were 
never intended to be instantiated and the warning may arise because they 
are declared public rather than private. I think your problems are 
elsewhere.

It would probably be worth checking that the #include and %include for 
openbabel files are the same in openbabel-ruby.i as in the latest 
openbabel-python.i
  >
> It seems like most of the symbols that the linker is not finding are  
> parts of (or inherited from parts of) sstream and steambuf. I've been  
> toying around a bit with the std_*.i interface files in SWIG 1.3.33,  
> but so far to little avail. If I have time this weekend I'll try  
> taking a better look at the situation.

Chris

Re: [OpenBabel-scripting] [OpenBabel-Devel] Let's fix the Python bindings

[Joshua B. <Jos...@st...>]

On Jan 18, 2008, at 1:43 PM, Geoffrey Hutchison wrote:

>> Is it a problem with SWIG or with the interface files?
>
> SWIG is, by no means, bug free. It has a hard task -- it must properly
> parse C, C++, etc. and produce useful code.
>
> What version of SWIG are you using?

Ah ha! I was using 1.3.31 (default install on Leopard) figuring it  
close enough to the latest 1.3.33. Apparently, I was wrong.
>
>
>> the interface files, there is no std_list.i file specifically for
>> Ruby. I've substituted the 'std/std_list.i' interface, but I'm not
>> sure if this is a good idea.
>
> I think this is a problem in older versions of SWIG. I'm using 1.3.33,
> which is the latest release.
>
> If you still have problems with the latest SWIG, please send me a
> message and we'll whip up a bug report. They've been pretty responsive
> about fixing problems I've found via Open Babel.

Ok, so I've gotten rid of the odd const assignments, but I'm still  
having issues linking. I'm thinking that it may be related to the  
following errors that I get when running SWIG:

../include/openbabel/plugin.h:39: Warning(401): Nothing known about  
base class 'std::binary_function<char const *,char const *,bool >'.  
Ignored.
../include/openbabel/plugin.h:39: Warning(401): Maybe you forgot to  
instantiate 'std::binary_function<char const *,char const *,bool >'  
using %template.
../include/openbabel/oberror.h:197: Warning(401): Nothing known about  
base class 'std::stringbuf'. Ignored.

It seems like most of the symbols that the linker is not finding are  
parts of (or inherited from parts of) sstream and steambuf. I've been  
toying around a bit with the std_*.i interface files in SWIG 1.3.33,  
but so far to little avail. If I have time this weekend I'll try  
taking a better look at the situation.

Cheers,

Joshua Ballanco
Graduate Student
Department of Chemistry and Chemical Biology
Stevens Institute of Technology
Hoboken, NJ 07030

E-mail: jba...@st...

Re: [OpenBabel-scripting] [OpenBabel-Devel] Let's fix the Python bindings

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

> Is it a problem with SWIG or with the interface files?

SWIG is, by no means, bug free. It has a hard task -- it must properly  
parse C, C++, etc. and produce useful code.

What version of SWIG are you using?

> the interface files, there is no std_list.i file specifically for
> Ruby. I've substituted the 'std/std_list.i' interface, but I'm not
> sure if this is a good idea.

I think this is a problem in older versions of SWIG. I'm using 1.3.33,  
which is the latest release.

If you still have problems with the latest SWIG, please send me a  
message and we'll whip up a bug report. They've been pretty responsive  
about fixing problems I've found via Open Babel.

Cheers,
-Geoff

Re: [OpenBabel-scripting] [OpenBabel-Devel] Let's fix the Python bindings

[Joshua B. <Jos...@st...>]

Noel,

I've merged the changes, and indeed all but two of the compilation  
errors have disappeared. These errors have me perplexed, though, as  
SWIG is trying to make an assignment to a variable that it has  
declared constant. For example:

((std::vector<unsigned int > const &)arg2)[i] = (unsigned int) 
(FIX2INT(o));

I can get around the compilation errors by changing the two places  
where this occurs, but it bothers me that this error pops up at all.  
Is it a problem with SWIG or with the interface files? Also, regarding  
the interface files, there is no std_list.i file specifically for  
Ruby. I've substituted the 'std/std_list.i' interface, but I'm not  
sure if this is a good idea.

Regardless, I'm still having major linking issues. I'll try picking  
through the errors, but it seems like there is something fundamentally  
wrong with the interface file. Oh, and I've resolved the Ruby 1.8.6 vs  
Ruby 1.9.0 difference. For whatever reason, mkmf in Ruby 1.9.0  
suppresses undefined symbols, but then the resulting bundle cannot  
load when 'require'd.

Cheers,

Joshua Ballanco
Graduate Student
Department of Chemistry and Chemical Biology
Stevens Institute of Technology
Hoboken, NJ 07030

E-mail: jba...@st...



On Jan 17, 2008, at 11:21 AM, Noel O'Boyle wrote:

> I need to get a linux compilation set up before I can contribute
> usefully to your efforts. The first thing to do is to try merging the
> recent changes in openbabel-python.i into openbabel-ruby.i (using "svn
> merge" for example), and seeing whether this makes everything better.
>
> Noel