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Re: [OpenBabel-scripting] [openbabel-scripting] OpenBabel for Python on Windows

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

I'm glad to hear that you have solved the problem. We will release new
versions of OpenBabelGUI and openbabel-python which will include these
DLLs as described here (thanks to Chris for sorting this out):
http://forums.microsoft.com/MSDN/ShowPost.aspx?PostID=164465&SiteID=1

Regards,
    Noel

On 01/02/07, buildez <bu...@bu...> wrote:
>
>
> Hi Noel, I hope a Solution.
> I tested with enthought 2.4.3, standard 2.4.4 and 2.5 using good openbabel
> python packages, with
> python in verbose mode, same result, _openbabel.pyd don't load
> OpenBabelDLL.dll tested
> on 3 machines (P4, WinXP, SP2, French).
> I have tested including (replacing) the dll found in openbabelGUI distrib
> ... same
> Ok yesterday, reading the pyd I found that OpenBabelDLL.dll was a good name
> and
> MCSV8 libraries could be useful. So i introduce msvcp80.dll and msvcr80.dll
> in local dir and
> system32 dir ... same result.
> agreeuuu ...
> Ok, I re-install the 3 versions of openbabelGUI (I used currently 2.00) on
> another machine,
> surprise ... version 2.0.0 works, 2.0.1 works, 2.0.2 don't works, even if
> the command line babel works.
> Checking dll in the 3 distribs, i found that 2.0.1 uses msvcp80.dll,
> msvcr80.dll, and ... msvcm80.dll
> not included in previous test (oh).
> Included the 3 in sites-packages directory ... and it works !
> Just for check, I installed openbabelGUI on another computer in version
> 2.0.2
> GUI don't works, added the 3 libraries picked from a 2.0.1 install, GUI
> works.
> Finally, it's was not critic, just a runtime pb. For C/C++ I use LCC and
> when a new version of
> Visual comes, i have often this dll problem (last time it was msvc71), at
> least one time.
>
> Cool :-) and thanks of your interrest on my pb.
> Perhaps I send you another post another day ... I have a work also on 2D
> images
> generation from SMILES using ideas of Guha and your paper of 2005 in CDK
> news.
>
> Regards
> Fred
>
> --
> View this message in context: http://www.nabble.com/Re%3A-OpenBabel-for-Python-on-Windows-tf3147809.html#a8746358
> Sent from the openbabel-scripting mailing list archive at Nabble.com.
>
>
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Re: [OpenBabel-scripting] [openbabel-scripting] OpenBabel for Python on Windows

[buildez <bu...@bu...>]

Hi Noel, I hope a Solution.
I tested with enthought 2.4.3, standard 2.4.4 and 2.5 using good openbabel
python packages, with
python in verbose mode, same result, _openbabel.pyd don't load
OpenBabelDLL.dll tested
on 3 machines (P4, WinXP, SP2, French).
I have tested including (replacing) the dll found in openbabelGUI distrib
... same
Ok yesterday, reading the pyd I found that OpenBabelDLL.dll was a good name
and 
MCSV8 libraries could be useful. So i introduce msvcp80.dll and msvcr80.dll
in local dir and
system32 dir ... same result.
agreeuuu ...
Ok, I re-install the 3 versions of openbabelGUI (I used currently 2.00) on
another machine, 
surprise ... version 2.0.0 works, 2.0.1 works, 2.0.2 don't works, even if
the command line babel works.
Checking dll in the 3 distribs, i found that 2.0.1 uses msvcp80.dll,
msvcr80.dll, and ... msvcm80.dll
not included in previous test (oh).
Included the 3 in sites-packages directory ... and it works !
Just for check, I installed openbabelGUI on another computer in version
2.0.2
GUI don't works, added the 3 libraries picked from a 2.0.1 install, GUI
works.
Finally, it's was not critic, just a runtime pb. For C/C++ I use LCC and
when a new version of
Visual comes, i have often this dll problem (last time it was msvc71), at
least one time.

Cool :-) and thanks of your interrest on my pb.
Perhaps I send you another post another day ... I have a work also on 2D
images 
generation from SMILES using ideas of Guha and your paper of 2005 in CDK
news.

Regards
Fred

-- 
View this message in context: http://www.nabble.com/Re%3A-OpenBabel-for-Python-on-Windows-tf3147809.html#a8746358
Sent from the openbabel-scripting mailing list archive at Nabble.com.

Re: [OpenBabel-scripting] Atom typing via Perl API

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

On Jan 31, 2007, at 9:51 AM, Kieron Taylor wrote:

> I am looking to assign Dreiding atom types with a view to also  
> using UFF
> which is very similar.

Dreiding atom types should already be available through the  
OBTypeTable class. Use ttab.SetToType("DRE"). Check out data/ 
types.txt -- it's the 14th column.

Of course if you find bugs, please let us know!

Cheers,
-Geoff

Re: [OpenBabel-scripting] [openbabel-scripting] OpenBabel for Python on Windows

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

I've just installed Enthought 1.0.0 with Python 2.4.3, with all of the
default options. When I then install openbabel-python-1.0.py2.4.exe,
and try to import it, it works fine for me.

When I emptied my PATH, I found that it didn't work, but for a
different reason - it could not find iconv.dll. (This file is included
in the OpenBabelGUI release, which is why I did not find this error
before). This is a bug, but I don't think that it's the same bug that
you have found. In my case a window pops up saying that it cannot find
iconv.dll.

In the end, I don't know what exactly is happening. Here are some more idea=
s...
(0) Do all of your tests in an empty folder, and with an empty PATH
and PYTHONPATH. You will need to copy iconv.dll from the OpenBabelGUI
folder into lib/site-packages.
(1) try "python -v" instead of "python" (this means 'verbose').
(2) Search your computer for all DLLs of the same name as the DLLs
installed by openbabel-python, and try to figure out whether there is
a conflict.
(3) ??

Bonne chance,
    Noel

On 31/01/07, Noel O'Boyle <bao...@gm...> wrote:
> I'm afraid that I just don't know what's happening...I will install
> the Enthought Edition of Python, and see whether it works for me...
>
> Noel
>
> On 31/01/07, buildez <bu...@bu...> wrote:
> >
> >
> > Hi Noel,
> > I am sure from version of openbabel module, i have downloaded it
> > on my disk, checked name and launch (not once) installer.
> > tested with stable version and beta.
> > I have checked environment variables, usually i  launch python shell
> > using a batch filled with set commands pointing to the good directories
> > add added to the path including python path, lib\sites-packages ..
> > And Enthought adds at install a lot of pointers (wx, swig ...) to
> > other components.
> > Ok i put off all enthought and let these one
> >
> > PYTHONPATH=3D.;C:\Python24\Lib\Site-Packages;
> > path=3Dc:\python24;c:\python\lib\sites-packages;.;c:\windows\system32
> >
> > trying now with some modules (one of my own, 3 classical)
> >
> > E:\test2>python
> > Python 2.4.3 - Enthought Edition 1.0.0 (#69, Aug  2 2006, 12:09:59) [MS=
C
> > v.1310
> > 32 bit (Intel)] on win32
> > Type "help", "copyright", "credits" or "license" for more information.
> > >>> import build
> > >>> import scipy
> > >>> import numeric
> > Traceback (most recent call last):
> >   File "<stdin>", line 1, in ?
> > ImportError: No module named numeric
> > >>> import numarray
> > >>> import openbabel
> > Traceback (most recent call last):
> >   File "<stdin>", line 1, in ?
> > ImportError: DLL load failed: Cette application ...
> > >>>
> >
> > same pb, now cleaning path and pythonpath
> >
> > E:\test2>python
> > 'python' n'est pas reconnu en tant que commande interne
> > ou externe, un programme ex=E9cutable ou un fichier de commandes.
> >
> > E:\test2>c:\python24\python
> > Python 2.4.3 - Enthought Edition 1.0.0 (#69, Aug  2 2006, 12:09:59) [MS=
C
> > v.1310
> > 32 bit (Intel)] on win32
> > Type "help", "copyright", "credits" or "license" for more information.
> > >>> import build
> > >>> import openbabel
> > Traceback (most recent call last):
> >   File "<stdin>", line 1, in ?
> > ImportError: DLL load failed: Cette application ...
> > >>>
> >
> > i have tryed with and without OpenBabelGUI installed
> > in c:\local\winbabel with last or last-1 versions to chek the
> > required dlls. Same result.
> > What i do is to remove enthougth and install standard Python
> > to check if pb is specific from python distribution (that would
> > be strange but ..)
> >
> > Regards
> > Fred
> >
> >
> > --
> > View this message in context: http://www.nabble.com/Re%3A-OpenBabel-for=
-Python-on-Windows-tf3147809.html#a8729937
> > Sent from the openbabel-scripting mailing list archive at Nabble.com.
> >
> >
> > -----------------------------------------------------------------------=
--
> > Take Surveys. Earn Cash. Influence the Future of IT
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 your
> > opinions on IT & business topics through brief surveys - and earn cash
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=3DDEVDEV
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>

Re: [OpenBabel-scripting] [openbabel-scripting] OpenBabel for Python on Windows

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

I'm afraid that I just don't know what's happening...I will install
the Enthought Edition of Python, and see whether it works for me...

Noel

On 31/01/07, buildez <bu...@bu...> wrote:
>
>
> Hi Noel,
> I am sure from version of openbabel module, i have downloaded it
> on my disk, checked name and launch (not once) installer.
> tested with stable version and beta.
> I have checked environment variables, usually i  launch python shell
> using a batch filled with set commands pointing to the good directories
> add added to the path including python path, lib\sites-packages ..
> And Enthought adds at install a lot of pointers (wx, swig ...) to
> other components.
> Ok i put off all enthought and let these one
>
> PYTHONPATH=3D.;C:\Python24\Lib\Site-Packages;
> path=3Dc:\python24;c:\python\lib\sites-packages;.;c:\windows\system32
>
> trying now with some modules (one of my own, 3 classical)
>
> E:\test2>python
> Python 2.4.3 - Enthought Edition 1.0.0 (#69, Aug  2 2006, 12:09:59) [MSC
> v.1310
> 32 bit (Intel)] on win32
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import build
> >>> import scipy
> >>> import numeric
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
> ImportError: No module named numeric
> >>> import numarray
> >>> import openbabel
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
> ImportError: DLL load failed: Cette application ...
> >>>
>
> same pb, now cleaning path and pythonpath
>
> E:\test2>python
> 'python' n'est pas reconnu en tant que commande interne
> ou externe, un programme ex=E9cutable ou un fichier de commandes.
>
> E:\test2>c:\python24\python
> Python 2.4.3 - Enthought Edition 1.0.0 (#69, Aug  2 2006, 12:09:59) [MSC
> v.1310
> 32 bit (Intel)] on win32
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import build
> >>> import openbabel
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
> ImportError: DLL load failed: Cette application ...
> >>>
>
> i have tryed with and without OpenBabelGUI installed
> in c:\local\winbabel with last or last-1 versions to chek the
> required dlls. Same result.
> What i do is to remove enthougth and install standard Python
> to check if pb is specific from python distribution (that would
> be strange but ..)
>
> Regards
> Fred
>
>
> --
> View this message in context: http://www.nabble.com/Re%3A-OpenBabel-for-P=
ython-on-Windows-tf3147809.html#a8729937
> Sent from the openbabel-scripting mailing list archive at Nabble.com.
>
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share y=
our
> opinions on IT & business topics through brief surveys - and earn cash
> http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D=
DEVDEV
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> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] Atom typing via Perl API

[Kieron T. <kr...@so...>]

Geoffrey Hutchison wrote:
> 
> On Jan 31, 2007, at 5:36 AM, Noel O'Boyle wrote:
> 
>> It's because nobody has gotten around to it yet, as you say.
>>
>>> I am trying to find ways to use the Patty atom typing in OpenBabel so
>>> that I can assign types for molecular mechanics forcefields. That  part
>>> of the API doesn't appear to be accessible through the Perl hook-in.
> 
> 
> I should point out that Patty isn't actually used by Open Babel  itself 
> anymore -- I had considered making it deprecated and removing  it in 3.0.

Thank you both for your swift responses. I notice the class OBAtomTyper. 
Is this the successor to Patty? Essentially I require an automated 
assignment of atom types according to the rules file in the source 
distribution, the technology that does the job isn't important to me. I 
just found Patty first.

I am going to attempt to extend the Perl module and SWIG parts, but I am 
unfamiliar with a lot of the methodologies used. I will post some code 
patches if I am successful.

> So it's good to hear that you find it useful and want it to stay. Out  
> of curiosity, what force fields do you want? I ask because there's  some 
> limited support in the 2.1 development tree for MM2, MMFF94, and  
> Tripos-like force fields right now. (I don't believe this is  accessible 
> from the scripting interface yet, and I think the atom  typing is still 
> incomplete as well.)

I am looking to assign Dreiding atom types with a view to also using UFF 
which is very similar.

Kieron

Re: [OpenBabel-scripting] [openbabel-scripting] OpenBabel for Python on Windows

[buildez <bu...@bu...>]

Hi Noel,
I am sure from version of openbabel module, i have downloaded it
on my disk, checked name and launch (not once) installer.
tested with stable version and beta.
I have checked environment variables, usually i  launch python shell
using a batch filled with set commands pointing to the good directories
add added to the path including python path, lib\sites-packages ..
And Enthought adds at install a lot of pointers (wx, swig ...) to
other components.
Ok i put off all enthought and let these one

PYTHONPATH=3D.;C:\Python24\Lib\Site-Packages;
path=3Dc:\python24;c:\python\lib\sites-packages;.;c:\windows\system32

trying now with some modules (one of my own, 3 classical)

E:\test2>python
Python 2.4.3 - Enthought Edition 1.0.0 (#69, Aug  2 2006, 12:09:59) [MSC
v.1310
32 bit (Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import build
>>> import scipy
>>> import numeric
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
ImportError: No module named numeric
>>> import numarray
>>> import openbabel
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
ImportError: DLL load failed: Cette application ...
>>>

same pb, now cleaning path and pythonpath

E:\test2>python
'python' n'est pas reconnu en tant que commande interne
ou externe, un programme ex=C3=A9cutable ou un fichier de commandes.

E:\test2>c:\python24\python
Python 2.4.3 - Enthought Edition 1.0.0 (#69, Aug  2 2006, 12:09:59) [MSC
v.1310
32 bit (Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import build
>>> import openbabel
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
ImportError: DLL load failed: Cette application ...
>>>

i have tryed with and without OpenBabelGUI installed
in c:\local\winbabel with last or last-1 versions to chek the
required dlls. Same result.
What i do is to remove enthougth and install standard Python
to check if pb is specific from python distribution (that would
be strange but ..)

Regards
Fred


--=20
View this message in context: http://www.nabble.com/Re%3A-OpenBabel-for-Pyt=
hon-on-Windows-tf3147809.html#a8729937
Sent from the openbabel-scripting mailing list archive at Nabble.com.

Re: [OpenBabel-scripting] Atom typing via Perl API

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

On Jan 31, 2007, at 5:36 AM, Noel O'Boyle wrote:

> It's because nobody has gotten around to it yet, as you say.
>> I am trying to find ways to use the Patty atom typing in OpenBabel so
>> that I can assign types for molecular mechanics forcefields. That  
>> part
>> of the API doesn't appear to be accessible through the Perl hook-in.

I should point out that Patty isn't actually used by Open Babel  
itself anymore -- I had considered making it deprecated and removing  
it in 3.0.

So it's good to hear that you find it useful and want it to stay. Out  
of curiosity, what force fields do you want? I ask because there's  
some limited support in the 2.1 development tree for MM2, MMFF94, and  
Tripos-like force fields right now. (I don't believe this is  
accessible from the scripting interface yet, and I think the atom  
typing is still incomplete as well.)

Cheers,
-Geoff

Re: [OpenBabel-scripting] Atom typing via Perl API

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

It's because nobody has gotten around to it yet, as you say.

patty.h (at least?) needs to be added to openbabel-perl.i. If you have
a recent version of Swig installed, and you've run configure with
--enable-maintainer-mode (all explained on the "Install source code"
page on the wiki), you can add it yourself, and play around with it.
Otherwise, sit tight for a couple of days, and then check out the
latest source from SVN...

Regards,
    Noel

On 31/01/07, Kieron Taylor <kr...@so...> wrote:
> Greetings,
>
> I am trying to find ways to use the Patty atom typing in OpenBabel so
> that I can assign types for molecular mechanics forcefields. That part
> of the API doesn't appear to be accessible through the Perl hook-in.
>
> Is this because nobody got around to it yet, or because the feature can
> be accessed somehow through the other classes such as OBMol or OBConversion?
>
> Does anyone have any recommendations on how else I might get access to
> the output of the atom typer?
>
> Regards,
>
> Kieron Taylor
>
>
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
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>

[OpenBabel-scripting] Atom typing via Perl API

[Kieron T. <kr...@so...>]

Greetings,

I am trying to find ways to use the Patty atom typing in OpenBabel so 
that I can assign types for molecular mechanics forcefields. That part 
of the API doesn't appear to be accessible through the Perl hook-in.

Is this because nobody got around to it yet, or because the feature can 
be accessed somehow through the other classes such as OBMol or OBConversion?

Does anyone have any recommendations on how else I might get access to 
the output of the atom typer?

Regards,

Kieron Taylor

Re: [OpenBabel-scripting] OpenBabel for Python on Windows

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

Hello Fred,

I haven't tested with the Enthought installation, but maybe one of our
users has. As far as I know, there's no reason it shouldn't work with
this also. Here are some ideas and things to test:
(1) Make sure that you have installed the correct version of the
openbabel module. There is one for Python 2.4 and another for Python
2.5.
(2) Open a command prompt. Type:
set PATH=3D
(Then run python from wherever it's installed...)
C:\Program Files\Python2.4\python
>>> import openbabel
(Does this work? The idea is to empty the PATH variable so that it
doesn't look for DLLs in the wrong place)

Let me know if this works. It's possible that the Enthought version
requires something special, but I hope not...I will check this.

Just to check...have you also installed the OpenBabelGUI?

Regards,
    Noel

On 30/01/07, bu...@bu... <bu...@bu...> wrote:
>
> Hi Noel, I have tested openbabel python module
> on a fresh Python install (2.4.3 from entough).
> I had the problem of library load, i have readed some
> posts on linux (use dl module) but not applicable
> on windows (XP SP2, Intel P4).
> I send to you the output (tested with a python
> script first, same error, tested in python shell here)
>
> >>> import openbabel
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
> ImportError: DLL load failed: Cette application n'a pas pu d=DAmarrer car=
 la confi
> guration de l'application est incorrecte. R=DAinstaller l'application pou=
rrait r=DAs
> oudre ce probl=DEme.
>
> all in c:\python24\Lib\sites-packages seems in good place: libinchi.dll,
> libxml2.dll, OpenBabelDLL.dll, zlib1.dll, _openbabel.pyd, openbabel.py,
> openbabel_data ...
> no error found in installer log, openbabel-python-wininst.log and
> in post-install scripts.
> Tryed to remove/reinstall, check environment variables, ok.
>
> tested with version 1.0 and version beta, same results.
>
> Regards,
> Fred
> you can reply also at build at chimie dot ups-tlse dot fr
>
>
> Noel O wrote:
> >
> > Just before Christmas, I made a beta release of openbabel-python for
> > Windows, and I'd appreciate any feedback regarding problems or
> > improvements.
> >
> > It's available for testing from:
> >
> > http://sourceforge.net/project/showfiles.php?group_id=3D40728&package_i=
d=3D215445
> >
> > It requires: (1) a windows like WinXP (sorry to be so vague, but
> > that's all I've tested)
> >                 (2) Python 2.4.x (support for 2.5.x will be included
> > in future releases)
> >
> > It's distributed as a self-installing executable, and can be removed
> > using "Add/Remove Programs".
> >
> > To test, start Python and type "import openbabel". If that works,
> > everything else should work too.
> >
> > A special word of thanks to Chris Morley who overcome all of the
> > technical problems involved in getting the Python bindings to compile
> > on Windows.
> >
> > For those who are interested, this release is based on SVN r1650,
> > patched with r1655,r1656,r1677 and r1680.
> >
> > Regards,
> >    Noel
> >
> > -----------------------------------------------------------------------=
--
> > Take Surveys. Earn Cash. Influence the Future of IT
> > Join SourceForge.net's Techsay panel and you'll get the chance to share
> > your
> > opinions on IT & business topics through brief surveys - and earn cash
> > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=
=3DDEVDEV
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
> >
> Quoted from:
> http://www.nabble.com/OpenBabel-for-Python-on-Windows-tf2916222.html#a814=
9409
>
>

[OpenBabel-scripting] ANN: openbabel-python 1.0 for windows

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

openbabel-python 1.0 for Windows is now available from:

http://sourceforge.net/project/showfiles.php?group_id=40728&package_id=215445

Two releases are available: one for Python 2.4 and another for Python 2.5.

The only difference between this release and the recent beta release
is that the environmental variable BABEL_DATADIR is set by the
installer. This is required for access to the OBFingerprint FP3, for
example.

Regards,
   Noel

[OpenBabel-scripting] OpenBabel for Python on Windows

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

Just before Christmas, I made a beta release of openbabel-python for
Windows, and I'd appreciate any feedback regarding problems or
improvements.

It's available for testing from:
 http://sourceforge.net/project/showfiles.php?group_id=40728&package_id=215445

It requires: (1) a windows like WinXP (sorry to be so vague, but
that's all I've tested)
                (2) Python 2.4.x (support for 2.5.x will be included
in future releases)

It's distributed as a self-installing executable, and can be removed
using "Add/Remove Programs".

To test, start Python and type "import openbabel". If that works,
everything else should work too.

A special word of thanks to Chris Morley who overcome all of the
technical problems involved in getting the Python bindings to compile
on Windows.

For those who are interested, this release is based on SVN r1650,
patched with r1655,r1656,r1677 and r1680.

Regards,
   Noel

Re: [OpenBabel-scripting] Open Babel for Java

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

No dice, I'm afraid - the java result doesn't change, and Python
starts to give the same errors if the dlopenflags stuff is removed
from openbabel.py. Good idea though.

On 19/12/06, Geoffrey Hutchison <ge...@ge...> wrote:
>
> On Dec 19, 2006, at 11:58 AM, Noel O'Boyle wrote:
>
> >>      sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)
> >>
> >> I'm not sure what the appropriate fix would be for Java. Basically,
> >> Open Babel loads its file format shared libraries separately from the
> >> library.
>
> I had a brainstorm. At the moment, I don't have time to test this on
> a Linux box, but it might do the trick. What we've been doing is
> hacking Perl and Python wrappers. But what about the C++ library
> itself? Maybe that's the basic culprit...
>
> If you apply this patch (i.e., change the appropriate line in
> dlhandler_unix.cpp) does Java work? Better yet, try editing the
> openbabel.py and rip out the dl.RTLD_GLOBAL bits and see if that works.
>
> (I'm hoping this solves the problem and we don't need something from
> SWIG.)
>
> Cheers,
> -Geoff
>
> Index: dlhandler_unix.cpp
> ===================================================================
> --- dlhandler_unix.cpp  (revision 1679)
> +++ dlhandler_unix.cpp  (working copy)
> @@ -149,7 +149,7 @@ int DLHandler::findFiles (std::vector<st
> bool DLHandler::openLib(const string& lib_name)
> {
> -  return dlopen(lib_name.c_str(), RTLD_LAZY) != 0;
> +  return dlopen(lib_name.c_str(), RTLD_LAZY|RTLD_GLOBAL) != 0;
> }
> const char* DLHandler::getFormatFilePattern()
>
>

Re: [OpenBabel-scripting] Open Babel for Java

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

On Dec 19, 2006, at 11:58 AM, Noel O'Boyle wrote:

>>      sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)
>>
>> I'm not sure what the appropriate fix would be for Java. Basically,
>> Open Babel loads its file format shared libraries separately from the
>> library.

I had a brainstorm. At the moment, I don't have time to test this on  
a Linux box, but it might do the trick. What we've been doing is  
hacking Perl and Python wrappers. But what about the C++ library  
itself? Maybe that's the basic culprit...

If you apply this patch (i.e., change the appropriate line in  
dlhandler_unix.cpp) does Java work? Better yet, try editing the  
openbabel.py and rip out the dl.RTLD_GLOBAL bits and see if that works.

(I'm hoping this solves the problem and we don't need something from  
SWIG.)

Cheers,
-Geoff

Index: dlhandler_unix.cpp
===================================================================
--- dlhandler_unix.cpp  (revision 1679)
+++ dlhandler_unix.cpp  (working copy)
@@ -149,7 +149,7 @@ int DLHandler::findFiles (std::vector<st
bool DLHandler::openLib(const string& lib_name)
{
-  return dlopen(lib_name.c_str(), RTLD_LAZY) != 0;
+  return dlopen(lib_name.c_str(), RTLD_LAZY|RTLD_GLOBAL) != 0;
}
const char* DLHandler::getFormatFilePattern()

Re: [OpenBabel-scripting] Open Babel for Java

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

I didn't get any answer on the SWIG mailing list regarding this...but
I didn't really know how to phrase the question.

Googling doesn't help much but I did find the following links which
might yield some information:
http://forum.java.sun.com/thread.jspa?threadID=786600
http://forum.java.sun.com/thread.jspa?threadID=521235&messageID=2492274
http://java.sun.com/docs/books/jni/download/jni.pdf

Noel

On 18/12/06, Geoffrey Hutchison <ge...@ge...> wrote:
>
> On Dec 17, 2006, at 7:33 PM, richard apodaca wrote:
>
> > But now I get a new series of errors when this code is
> > run:
> ...
> >   /usr/local/lib/openbabel/cifformat.so did not load
> > properly
>
> This sounds like the problems we had with the Python and Perl
> wrappers, e.g.:
> if sys.platform.find(\"linux\") != -1:
>      import dl
>      sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)
>
> I'm not sure what the appropriate fix would be for Java. Basically,
> Open Babel loads its file format shared libraries separately from the
> library. Probably the best solution would be to write to the SWIG
> list and find out if there's a global solution. (Strange that it's
> not an issue with Ruby, evidently.)
>
> As I've learned, adding new languages with SWIG is always an
> adventure. :-)
>
> Thanks guys!
> -Geoff
>

[OpenBabel-scripting] Fwd: Trying to get access to a gzipped SDF file in Python

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

---------- Forwarded message ----------
From: Andreas Karwath <ka...@in...>
Date: 18-Dec-2006 08:25
Subject: Re: [OpenBabel-scripting] Trying to get access to a gzipped
SDF file in Python
To: Noel O'Boyle <bao...@gm...>


Cheers,

I also traced the vbug back to mdlformat.cpp, where a false is
returned as the if(!ifs.getline(buffer,BUFF_SIZE)) return(false);
returns false...


But thanks for the workaround....

ak

On 17.12.2006, at 22:20, Noel O'Boyle wrote:

> I have reproduced the bug. Unfortunately, I don't anticipate an easy
> solution. Streams and Python don't mix very well in the first place.
>
> But here's a workaround in the meanwhile:
>
> import gzip # a standard Python module
> text =3D gzip.open("test.sdf.gz").read()
>
> You now need to use openbabel to read this text (I'm afraid that
> Pybel's readstring currently only reads strings containing a single
> molecule).
>
> import openbabel as ob
> obmol =3D ob.OBMol()
> obconversion =3D ob.OBConversion()
> formatok =3D obconversion.SetInFormat("sdf")
> notatend =3D obconversion.ReadString(obmol, text)
> while notatend:
>     # Do something with obmol
>     obmol =3D ob.OBMol()
>     notatend =3D obconversion.Read(obmol)
>
> Hope this helps...
>
> Noel
>
> On 16/12/06, Andreas Karwath <ka...@in...>
> wrote:
>> I guess you mean:
>>
>> babel -isdf <zipped SDF file> -osmi
>>
>> that works fine...
>>
>> I guess it has something to do with the internal stream (or however
>> it is called).
>>
>> Regards,
>>
>> ak
>>
>>
>> On 15.12.2006, at 18:06, Noel O'Boyle wrote:
>>
>> > Thanks Andreas for letting us know about this problem.
>> >
>> > First of all, can you let us know whether this problem occurs if
>> you
>> > use the babel executable itself to convert the file? (If so, the
>> > problem is nothing to do with the Python bindings)
>> >
>> > Noel
>> >
>> > On 15/12/06, Andreas Karwath <ka...@in...>
>> > wrote:
>> >> Hi all,
>> >>
>> >> I hope I don't have to send this to the developer list...
>> >>
>> >> I have installed the latest version of openbabel (2.1.0b3)
>> >> including the
>> >> python bindings... (openbabel and pybel), Linux Suse 9.2
>> >> I wanted to parse a gzipped SDF file (zipped file size 14 M) to
>> >> extract
>> >> specific molecules (by name), for this I first tried to do the
>> normal
>> >> routine, i.e.:
>> >>
>> >> sdfFileName =3D <someGzippedSDFFile>
>> >> obconversion =3D OBConversion()
>> >> obconversion.SetInFormat("sdf")
>> >> obconversion.SetOutFormat("smi")
>> >> obmol =3D OBMol()
>> >>
>> >> notatend =3D obconversion.ReadFile(obmol,sdfFileName)
>> >> export =3D obconversion.WriteFile(obmol,'myTest.smi')
>> >> while notatend:
>> >>     obconversion.Write(obmol)
>> >>     obmol =3D OBMol()
>> >>     notatend =3D obconversion.Read(obmol)
>> >>
>> >> On a normal (i.e. unzipped) SDF File it works fine. But not on a
>> >> gzipped one
>> >> -> Segmentation Fault. It can only get access the first  single
>> >> molecule
>> >>
>> >> The same is true when using the new pybel lib. -> Segmentation
>> Fault!
>> >>
>> >> I assume that OpenBabel keeps a pointer to the last read molecule
>> >> in the SDF
>> >> file, which would not work when accessing the zipped one...
>> >>
>> >> I don't want to unpack the file, as I have a few hundred of
>> >> those.. (disk
>> >> space!)
>> >>
>> >> Did anyone have the same problem and knows an elegant workaround?
>> >> I guess the problem should occur for other scripting languages as
>> >> well...
>> >>
>> >> Regards,
>> >>
>> >> A. Karwath
>> >> -----------------
>> >>
>> >> Dr. Andreas Karwath
>> >> Machine Learning Lab
>> >> Institute for Computer Science
>> >> Albert-Ludwigs-Universit=E4t Freiburg
>> >> Georges-K=F6hler-Allee 079
>> >> D-79110 Freiburg
>> >> Germany
>> >>
>> >>
>> >>
>> ---------------------------------------------------------------------
>> >> ----
>> >> Take Surveys. Earn Cash. Influence the Future of IT
>> >> Join SourceForge.net's Techsay panel and you'll get the chance to
>> >> share your
>> >> opinions on IT & business topics through brief surveys - and earn
>> >> cash
>> >> http://www.techsay.com/default.php?
>> >> page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV
>> >>
>> >> _______________________________________________
>> >> OpenBabel-scripting mailing list
>> >> Ope...@li...
>> >> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>> >>
>> >>
>> >>
>>
>> Dr. Andreas Karwath
>> Machine Learning Lab
>> Institute for Computer Science
>> Albert-Ludwigs-Universit=E4t Freiburg
>> Georges-K=F6hler-Allee 079
>> D-79110 Freiburg
>> Germany
>> +49 761 203 8029 (office)
>> +49 761 203 8007 (fax)
>> http://www.informatik.uni-freiburg.de/~karwath/ (web)
>> ka...@in... (email)
>> theKnoedel (skype)
>>
>>
>>

Dr. Andreas Karwath
Machine Learning Lab
Institute for Computer Science
Albert-Ludwigs-Universit=E4t Freiburg
Georges-K=F6hler-Allee 079
D-79110 Freiburg
Germany
+49 761 203 8029 (office)
+49 761 203 8007 (fax)
http://www.informatik.uni-freiburg.de/~karwath/ (web)
ka...@in... (email)
theKnoedel (skype)

Re: [OpenBabel-scripting] Open Babel for Java

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

On Dec 17, 2006, at 7:33 PM, richard apodaca wrote:

> But now I get a new series of errors when this code is
> run:
...
>   /usr/local/lib/openbabel/cifformat.so did not load
> properly

This sounds like the problems we had with the Python and Perl  
wrappers, e.g.:
if sys.platform.find(\"linux\") != -1:
     import dl
     sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)

I'm not sure what the appropriate fix would be for Java. Basically,  
Open Babel loads its file format shared libraries separately from the  
library. Probably the best solution would be to write to the SWIG  
list and find out if there's a global solution. (Strange that it's  
not an issue with Ruby, evidently.)

As I've learned, adding new languages with SWIG is always an  
adventure. :-)

Thanks guys!
-Geoff

Re: [OpenBabel-scripting] Open Babel for Java

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

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

> Same happens to me but it runs fine for me (i.e.
> does nothing) with
> the following random changes:
> (1) Add System.loadLibrary("openbabel");
> (2) export LD_LIBRARY_PATH=$PWD:/usr/local/lib

Oh yeah, I forgot the System.loadLibrary call. Adding
it to the constructor gets rid of the
UnsatisfiedLinkError problem:

public class OBTest
{
  public OBTest()
  {
    System.loadLibrary("openbabel");
  }

  public void run()
  {
    OBConversion c = new OBConversion();
  }

  public static void main(String[] args)
  {
    System.out.println("Running OBTest...");

    OBTest test = new OBTest();

    test.run();
  }
}

But now I get a new series of errors when this code is
run:

$ java OBTest
Running OBTest...
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/cmlreactlformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/pubchem.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/cmlformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/xmlformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/APIInterface.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/CSRformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/PQSformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/alchemyformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/amberformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/balstformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/bgfformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/boxformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/cacaoformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/cacheformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/carformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/cccformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/chem3dformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/chemdrawctformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/chemdrawcdxformat.so did
not load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/chemtoolformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/copyformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/crkformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/cssrformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/dmolformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/fastsearchformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/fastaformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/featformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/fhformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/fingerprintformat.so did
not load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/freefracformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/gamessformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/gaussformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/ghemicalformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/gromos96format.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/hinformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/inchiformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/jaguarformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/mdlformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/mmodformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/mpdformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/mol2format.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/molreportformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/mopacformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/mpqcformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/nwchemformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/pcmodelformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/pdbformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/povrayformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/qchemformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/reportformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/rxnformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/shelxformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/smilesformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/thermoformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/tinkerformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/titleformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/turbomoleformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/unichemformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/viewmolformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/xedformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/xyzformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/yasaraformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/zindoformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/cifformat.so did not load
properly

Adding /usr/local/lib or /usr/local/lib/openbabel
(where these fooformat.so files are located) does not
help.

Any ideas?

> 
> Not sure whether 1 or 2 did the magic. BTW, I find
> the presence of two
> completely different libopenbabel.so's very
> confusing - can we rename
> one to libopenbabel-java.so?
> 
> On 17/12/06, richard apodaca
> <ric...@ya...> wrote:
> >
> > --- Geoffrey Hutchison <ge...@ge...>
> > wrote:
> >
> > >
> > > On Dec 16, 2006, at 7:02 PM, richard apodaca
> wrote:
> > >
> > > > 32 compile errors resulting from the 5 classes
> > > listed
> > > > below not being found, it should not be a lot
> of
> > > > effort to get it working.
> > >
> > > No more compile errors, I promise. I added a
> first
> > > stab at a README,
> > > but I can only vouch that it works on Mac OS X.
> >
> > Using revision SVN trunk 1678.
> >
> > Excellent. I went through the steps in the README.
> I
> > needed to modify Step 2 because of the way the
> Linux
> > AMD64 JDK is laid out:
> >
> > (2) g++ -c -fpic openbabel_java.cpp
> -I../../include
> > -I/usr/java/jdk1.5.0_09/include/
> > -I/usr/java/jdk1.5.0_09/include/linux
> >
> > > >> I've tried to follow the README in
> scripts/java
> > > but
> > > >> step 3 gave:
> > > >> g++: libopenbabel.so: No such file or
> directory
> > >
> > > Sorry, that should have been something like:
> > >
> > > g++ -shared -lopenbabel -L/usr/local/lib
> > > openbabel_java.o -o
> > > libopenbabel.so
> >
> > I used the command above and it produced
> > libopenbabel.so. I checked and /usr/local/lib on
> my
> > system contains libopenbabel.so
> >
> > So far so good.
> >
> > I wrote a little test class (saved as OBTest.java
> in
> > the scripts/java directory):
> >
> > public class OBTest
> > {
> >   public OBTest()
> >   {
> >
> >   }
> >
> >   public void run()
> >   {
> >     OBConversion c = new OBConversion();
> >   }
> >
> >   public static void main(String[] args)
> >   {
> >     System.out.println("Running OBTest...");
> >
> >     OBTest test = new OBTest();
> >
> >     test.run();
> >   }
> > }
> >
> > Compiling:
> >
> > javac OBTest.java
> >
> > worked fine.
> >
> > As far as I gather, I need to set LD_LIBRARY_PATH
> to
> > the directory containing libopenbabel.so:
> >
> > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PWD
> >
> > But running the test produces an
> UnsatisfiedLinkError:
> >
> > $ java OBTest
> > Running OBTest...
> > Exception in thread "main"
> > java.lang.UnsatisfiedLinkError:
> > new_OBConversion__SWIG_2
> >  at openbabelJNI.new_OBConversion__SWIG_2(Native
> > Method)
> >  at OBConversion.<init>(OBConversion.java:44)
> >  at OBTest.run(OBTest.java:10)
> >  at OBTest.main(OBTest.java:19)
> >
> > I'm inexperienced with using JNI, so I'm probably
> > doing something wrong.
> >
> > To summarize: I'm able to compile the Open Babel
> JNI
> > wrapper and create the shared library. However,
> > running a simple test class that uses the library
> > gives an UnsatisfiedLinkError.
> >
> > Can someone try to run this test class (or another
> > one) to see if the problem is my system/methods?
> >
> > cheers,
> > Rich
> >
> > ____________________________
> > Richard Apodaca
> > Blog: http://depth-first.com
> >
> > __________________________________________________
> > Do You Yahoo!?
> > Tired of spam?  Yahoo! Mail has the best spam
> protection around
> > http://mail.yahoo.com
> >
> >
>
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> > opinions on IT & business topics through brief
> surveys - and earn cash
> >
>
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
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> >
>
https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
> 


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

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Re: [OpenBabel-scripting] Open Babel for Java

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

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

> Same happens to me but it runs fine for me (i.e.
> does nothing) with
> the following random changes:
> (1) Add System.loadLibrary("openbabel");
> (2) export LD_LIBRARY_PATH=$PWD:/usr/local/lib

Oh yeah, I forgot the System.loadLibrary call. Adding
it to the constructor gets rid of the
UnsatisfiedLinkError problem:

public class OBTest
{
  public OBTest()
  {
    System.loadLibrary("openbabel");
  }

  public void run()
  {
    OBConversion c = new OBConversion();
  }

  public static void main(String[] args)
  {
    System.out.println("Running OBTest...");

    OBTest test = new OBTest();

    test.run();
  }
}

But now I get a new series of errors when this code is
run:

$ java OBTest
Running OBTest...
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/cmlreactlformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/pubchem.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/cmlformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/xmlformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/APIInterface.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/CSRformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/PQSformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/alchemyformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/amberformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/balstformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/bgfformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/boxformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/cacaoformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/cacheformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/carformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/cccformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/chem3dformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/chemdrawctformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/chemdrawcdxformat.so did
not load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/chemtoolformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/copyformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/crkformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/cssrformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/dmolformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/fastsearchformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/fastaformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/featformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/fhformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/fingerprintformat.so did
not load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/freefracformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/gamessformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/gaussformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/ghemicalformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/gromos96format.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/hinformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/inchiformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/jaguarformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/mdlformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/mmodformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/mpdformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/mol2format.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/molreportformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/mopacformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/mpqcformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/nwchemformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/pcmodelformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/pdbformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/povrayformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/qchemformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/reportformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/rxnformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/shelxformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/smilesformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/thermoformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/tinkerformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/titleformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/turbomoleformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/unichemformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/viewmolformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/xedformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/xyzformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/yasaraformat.so did not
load properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/zindoformat.so did not load
properly
==============================
*** Open Babel Error  in LoadFormatFiles
  /usr/local/lib/openbabel/cifformat.so did not load
properly

Adding /usr/local/lib or /usr/local/lib/openbabel
(where these fooformat.so files are located) does not
help.

Any ideas?

> 
> Not sure whether 1 or 2 did the magic. BTW, I find
> the presence of two
> completely different libopenbabel.so's very
> confusing - can we rename
> one to libopenbabel-java.so?
> 
> On 17/12/06, richard apodaca
> <ric...@ya...> wrote:
> >
> > --- Geoffrey Hutchison <ge...@ge...>
> > wrote:
> >
> > >
> > > On Dec 16, 2006, at 7:02 PM, richard apodaca
> wrote:
> > >
> > > > 32 compile errors resulting from the 5 classes
> > > listed
> > > > below not being found, it should not be a lot
> of
> > > > effort to get it working.
> > >
> > > No more compile errors, I promise. I added a
> first
> > > stab at a README,
> > > but I can only vouch that it works on Mac OS X.
> >
> > Using revision SVN trunk 1678.
> >
> > Excellent. I went through the steps in the README.
> I
> > needed to modify Step 2 because of the way the
> Linux
> > AMD64 JDK is laid out:
> >
> > (2) g++ -c -fpic openbabel_java.cpp
> -I../../include
> > -I/usr/java/jdk1.5.0_09/include/
> > -I/usr/java/jdk1.5.0_09/include/linux
> >
> > > >> I've tried to follow the README in
> scripts/java
> > > but
> > > >> step 3 gave:
> > > >> g++: libopenbabel.so: No such file or
> directory
> > >
> > > Sorry, that should have been something like:
> > >
> > > g++ -shared -lopenbabel -L/usr/local/lib
> > > openbabel_java.o -o
> > > libopenbabel.so
> >
> > I used the command above and it produced
> > libopenbabel.so. I checked and /usr/local/lib on
> my
> > system contains libopenbabel.so
> >
> > So far so good.
> >
> > I wrote a little test class (saved as OBTest.java
> in
> > the scripts/java directory):
> >
> > public class OBTest
> > {
> >   public OBTest()
> >   {
> >
> >   }
> >
> >   public void run()
> >   {
> >     OBConversion c = new OBConversion();
> >   }
> >
> >   public static void main(String[] args)
> >   {
> >     System.out.println("Running OBTest...");
> >
> >     OBTest test = new OBTest();
> >
> >     test.run();
> >   }
> > }
> >
> > Compiling:
> >
> > javac OBTest.java
> >
> > worked fine.
> >
> > As far as I gather, I need to set LD_LIBRARY_PATH
> to
> > the directory containing libopenbabel.so:
> >
> > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PWD
> >
> > But running the test produces an
> UnsatisfiedLinkError:
> >
> > $ java OBTest
> > Running OBTest...
> > Exception in thread "main"
> > java.lang.UnsatisfiedLinkError:
> > new_OBConversion__SWIG_2
> >  at openbabelJNI.new_OBConversion__SWIG_2(Native
> > Method)
> >  at OBConversion.<init>(OBConversion.java:44)
> >  at OBTest.run(OBTest.java:10)
> >  at OBTest.main(OBTest.java:19)
> >
> > I'm inexperienced with using JNI, so I'm probably
> > doing something wrong.
> >
> > To summarize: I'm able to compile the Open Babel
> JNI
> > wrapper and create the shared library. However,
> > running a simple test class that uses the library
> > gives an UnsatisfiedLinkError.
> >
> > Can someone try to run this test class (or another
> > one) to see if the problem is my system/methods?
> >
> > cheers,
> > Rich
> >
> > ____________________________
> > Richard Apodaca
> > Blog: http://depth-first.com
> >
> > __________________________________________________
> > Do You Yahoo!?
> > Tired of spam?  Yahoo! Mail has the best spam
> protection around
> > http://mail.yahoo.com
> >
> >
>
-------------------------------------------------------------------------
> > Take Surveys. Earn Cash. Influence the Future of
> IT
> > Join SourceForge.net's Techsay panel and you'll
> get the chance to share your
> > opinions on IT & business topics through brief
> surveys - and earn cash
> >
>
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> >
>
https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
> 


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

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Re: [OpenBabel-scripting] Open Babel for Java

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

Same happens to me but it runs fine for me (i.e. does nothing) with
the following random changes:
(1) Add System.loadLibrary("openbabel");
(2) export LD_LIBRARY_PATH=$PWD:/usr/local/lib

Not sure whether 1 or 2 did the magic. BTW, I find the presence of two
completely different libopenbabel.so's very confusing - can we rename
one to libopenbabel-java.so?

On 17/12/06, richard apodaca <ric...@ya...> wrote:
>
> --- Geoffrey Hutchison <ge...@ge...>
> wrote:
>
> >
> > On Dec 16, 2006, at 7:02 PM, richard apodaca wrote:
> >
> > > 32 compile errors resulting from the 5 classes
> > listed
> > > below not being found, it should not be a lot of
> > > effort to get it working.
> >
> > No more compile errors, I promise. I added a first
> > stab at a README,
> > but I can only vouch that it works on Mac OS X.
>
> Using revision SVN trunk 1678.
>
> Excellent. I went through the steps in the README. I
> needed to modify Step 2 because of the way the Linux
> AMD64 JDK is laid out:
>
> (2) g++ -c -fpic openbabel_java.cpp -I../../include
> -I/usr/java/jdk1.5.0_09/include/
> -I/usr/java/jdk1.5.0_09/include/linux
>
> > >> I've tried to follow the README in scripts/java
> > but
> > >> step 3 gave:
> > >> g++: libopenbabel.so: No such file or directory
> >
> > Sorry, that should have been something like:
> >
> > g++ -shared -lopenbabel -L/usr/local/lib
> > openbabel_java.o -o
> > libopenbabel.so
>
> I used the command above and it produced
> libopenbabel.so. I checked and /usr/local/lib on my
> system contains libopenbabel.so
>
> So far so good.
>
> I wrote a little test class (saved as OBTest.java in
> the scripts/java directory):
>
> public class OBTest
> {
>   public OBTest()
>   {
>
>   }
>
>   public void run()
>   {
>     OBConversion c = new OBConversion();
>   }
>
>   public static void main(String[] args)
>   {
>     System.out.println("Running OBTest...");
>
>     OBTest test = new OBTest();
>
>     test.run();
>   }
> }
>
> Compiling:
>
> javac OBTest.java
>
> worked fine.
>
> As far as I gather, I need to set LD_LIBRARY_PATH to
> the directory containing libopenbabel.so:
>
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PWD
>
> But running the test produces an UnsatisfiedLinkError:
>
> $ java OBTest
> Running OBTest...
> Exception in thread "main"
> java.lang.UnsatisfiedLinkError:
> new_OBConversion__SWIG_2
>  at openbabelJNI.new_OBConversion__SWIG_2(Native
> Method)
>  at OBConversion.<init>(OBConversion.java:44)
>  at OBTest.run(OBTest.java:10)
>  at OBTest.main(OBTest.java:19)
>
> I'm inexperienced with using JNI, so I'm probably
> doing something wrong.
>
> To summarize: I'm able to compile the Open Babel JNI
> wrapper and create the shared library. However,
> running a simple test class that uses the library
> gives an UnsatisfiedLinkError.
>
> Can someone try to run this test class (or another
> one) to see if the problem is my system/methods?
>
> cheers,
> Rich
>
> ____________________________
> Richard Apodaca
> Blog: http://depth-first.com
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys - and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] Trying to get access to a gzipped SDF file in Python

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

I have reproduced the bug. Unfortunately, I don't anticipate an easy
solution. Streams and Python don't mix very well in the first place.

But here's a workaround in the meanwhile:

import gzip # a standard Python module
text =3D gzip.open("test.sdf.gz").read()

You now need to use openbabel to read this text (I'm afraid that
Pybel's readstring currently only reads strings containing a single
molecule).

import openbabel as ob
obmol =3D ob.OBMol()
obconversion =3D ob.OBConversion()
formatok =3D obconversion.SetInFormat("sdf")
notatend =3D obconversion.ReadString(obmol, text)
while notatend:
     # Do something with obmol
     obmol =3D ob.OBMol()
     notatend =3D obconversion.Read(obmol)

Hope this helps...

Noel

On 16/12/06, Andreas Karwath <ka...@in...> wrote:
> I guess you mean:
>
> babel -isdf <zipped SDF file> -osmi
>
> that works fine...
>
> I guess it has something to do with the internal stream (or however
> it is called).
>
> Regards,
>
> ak
>
>
> On 15.12.2006, at 18:06, Noel O'Boyle wrote:
>
> > Thanks Andreas for letting us know about this problem.
> >
> > First of all, can you let us know whether this problem occurs if you
> > use the babel executable itself to convert the file? (If so, the
> > problem is nothing to do with the Python bindings)
> >
> > Noel
> >
> > On 15/12/06, Andreas Karwath <ka...@in...>
> > wrote:
> >> Hi all,
> >>
> >> I hope I don't have to send this to the developer list...
> >>
> >> I have installed the latest version of openbabel (2.1.0b3)
> >> including the
> >> python bindings... (openbabel and pybel), Linux Suse 9.2
> >> I wanted to parse a gzipped SDF file (zipped file size 14 M) to
> >> extract
> >> specific molecules (by name), for this I first tried to do the normal
> >> routine, i.e.:
> >>
> >> sdfFileName =3D <someGzippedSDFFile>
> >> obconversion =3D OBConversion()
> >> obconversion.SetInFormat("sdf")
> >> obconversion.SetOutFormat("smi")
> >> obmol =3D OBMol()
> >>
> >> notatend =3D obconversion.ReadFile(obmol,sdfFileName)
> >> export =3D obconversion.WriteFile(obmol,'myTest.smi')
> >> while notatend:
> >>     obconversion.Write(obmol)
> >>     obmol =3D OBMol()
> >>     notatend =3D obconversion.Read(obmol)
> >>
> >> On a normal (i.e. unzipped) SDF File it works fine. But not on a
> >> gzipped one
> >> -> Segmentation Fault. It can only get access the first  single
> >> molecule
> >>
> >> The same is true when using the new pybel lib. -> Segmentation Fault!
> >>
> >> I assume that OpenBabel keeps a pointer to the last read molecule
> >> in the SDF
> >> file, which would not work when accessing the zipped one...
> >>
> >> I don't want to unpack the file, as I have a few hundred of
> >> those.. (disk
> >> space!)
> >>
> >> Did anyone have the same problem and knows an elegant workaround?
> >> I guess the problem should occur for other scripting languages as
> >> well...
> >>
> >> Regards,
> >>
> >> A. Karwath
> >> -----------------
> >>
> >> Dr. Andreas Karwath
> >> Machine Learning Lab
> >> Institute for Computer Science
> >> Albert-Ludwigs-Universit=E4t Freiburg
> >> Georges-K=F6hler-Allee 079
> >> D-79110 Freiburg
> >> Germany
> >>
> >>
> >> ---------------------------------------------------------------------
> >> ----
> >> Take Surveys. Earn Cash. Influence the Future of IT
> >> Join SourceForge.net's Techsay panel and you'll get the chance to
> >> share your
> >> opinions on IT & business topics through brief surveys - and earn
> >> cash
> >> http://www.techsay.com/default.php?
> >> page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV
> >>
> >> _______________________________________________
> >> OpenBabel-scripting mailing list
> >> Ope...@li...
> >> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >>
> >>
> >>
>
> Dr. Andreas Karwath
> Machine Learning Lab
> Institute for Computer Science
> Albert-Ludwigs-Universit=E4t Freiburg
> Georges-K=F6hler-Allee 079
> D-79110 Freiburg
> Germany
> +49 761 203 8029 (office)
> +49 761 203 8007 (fax)
> http://www.informatik.uni-freiburg.de/~karwath/ (web)
> ka...@in... (email)
> theKnoedel (skype)
>
>
>

Re: [OpenBabel-scripting] Open Babel for Java

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

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

> 
> On Dec 16, 2006, at 7:02 PM, richard apodaca wrote:
> 
> > 32 compile errors resulting from the 5 classes
> listed
> > below not being found, it should not be a lot of
> > effort to get it working.
> 
> No more compile errors, I promise. I added a first
> stab at a README,  
> but I can only vouch that it works on Mac OS X.

Using revision SVN trunk 1678.

Excellent. I went through the steps in the README. I
needed to modify Step 2 because of the way the Linux
AMD64 JDK is laid out:

(2) g++ -c -fpic openbabel_java.cpp -I../../include
-I/usr/java/jdk1.5.0_09/include/
-I/usr/java/jdk1.5.0_09/include/linux

> >> I've tried to follow the README in scripts/java
> but
> >> step 3 gave:
> >> g++: libopenbabel.so: No such file or directory
> 
> Sorry, that should have been something like:
> 
> g++ -shared -lopenbabel -L/usr/local/lib
> openbabel_java.o -o  
> libopenbabel.so

I used the command above and it produced
libopenbabel.so. I checked and /usr/local/lib on my
system contains libopenbabel.so

So far so good.

I wrote a little test class (saved as OBTest.java in
the scripts/java directory):

public class OBTest
{
  public OBTest()
  {
    
  }

  public void run()
  {
    OBConversion c = new OBConversion();
  }

  public static void main(String[] args)
  {
    System.out.println("Running OBTest...");

    OBTest test = new OBTest();

    test.run();
  }
}

Compiling:

javac OBTest.java

worked fine.

As far as I gather, I need to set LD_LIBRARY_PATH to
the directory containing libopenbabel.so:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PWD

But running the test produces an UnsatisfiedLinkError:

$ java OBTest
Running OBTest...
Exception in thread "main"
java.lang.UnsatisfiedLinkError:
new_OBConversion__SWIG_2
 at openbabelJNI.new_OBConversion__SWIG_2(Native
Method)
 at OBConversion.<init>(OBConversion.java:44)
 at OBTest.run(OBTest.java:10)
 at OBTest.main(OBTest.java:19)

I'm inexperienced with using JNI, so I'm probably
doing something wrong.

To summarize: I'm able to compile the Open Babel JNI
wrapper and create the shared library. However,
running a simple test class that uses the library
gives an UnsatisfiedLinkError.

Can someone try to run this test class (or another
one) to see if the problem is my system/methods?

cheers,
Rich

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

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Re: [OpenBabel-scripting] Open Babel for Java

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

On Dec 16, 2006, at 7:02 PM, richard apodaca wrote:

> 32 compile errors resulting from the 5 classes listed
> below not being found, it should not be a lot of
> effort to get it working.

No more compile errors, I promise. I added a first stab at a README,  
but I can only vouch that it works on Mac OS X.

>> I've tried to follow the README in scripts/java but
>> step 3 gave:
>> g++: libopenbabel.so: No such file or directory

Sorry, that should have been something like:

g++ -shared -lopenbabel -L/usr/local/lib openbabel_java.o -o  
libopenbabel.so

Cheers,
-Geoff

Re: [OpenBabel-scripting] Open Babel for Java

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

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

> What is the current situation with OB/Java?

Hi Noel,

As far as I know, it's in the same state it was in
when I posted my last message. If we can resolve the
32 compile errors resulting from the 5 classes listed
below not being found, it should not be a lot of
effort to get it working.

I'll go through the steps again with the latest SVN to
see if anything has changed.

> 
> I've tried to follow the README in scripts/java but
> step 3 gave:
> g++: libopenbabel.so: No such file or directory
> 
> Noel
> 
> On 07/11/06, richard apodaca
> <ric...@ya...> wrote:
> > Hi Geoff,
> >
> > What a coincidence!
> >
> > In looking through the Java that your
> openbabel-java.i
> > file generated (svn trunk rev 1584), I see the
> cause
> > of the large filenames. The %module directive uses
> > net.sourceforge.openbabel as the name. Change this
> to:
> >
> > %module openbabel
> >
> > The problems with long filenames will disappear.
> But
> > that's not the biggest problem. The autogenerated
> java
> > also wouldn't compile because it was defining
> things
> > like:
> >
> > public interface net.sourceforge.openbabelJNI
> > {
> > ...
> > }
> >
> > when it really should have been generating:
> >
> > package net.sourceforge.openbabel;
> >
> > public interface JNI
> > {
> > ...
> > }
> >
> > and so on. Packages are more of a hassle than
> they're
> > worth at this point. We can always get that part
> > tidied up later.
> >
> > So when I run swig with the '%module openbabel'
> > directive, I get to the same place I was before.
> That
> > is, 32 java compile errors are produced. They
> involve
> > these class definitions that can't be found:
> >
> > OBBitVec
> > matrix3x3
> > OBAromaticTyper
> > OBAtomTyper
> > OBChainsParser
> >
> > In addition, 2 of these errors are apparently
> related
> > to method duplication:
> >
> > OBSmartsPattern.java:107:
> >
>
RestrictedMatch(OBMol,SWIGTYPE_p_std__vectorTstd__pairTint_int_t_t,boolean)
> > is already defined in OBSmartsPattern
> >   public boolean RestrictedMatch(OBMol mol,
> OBBitVec
> > bv, boolean single) {
> >
> > ...
> >
> > OBSmartsPattern.java:111:
> >
>
RestrictedMatch(OBMol,SWIGTYPE_p_std__vectorTstd__pairTint_int_t_t)
> > is already defined in OBSmartsPattern
> >   public boolean RestrictedMatch(OBMol mol,
> OBBitVec
> > bv) {
> >
> > ...
> >
> > cheers,
> > Rich
> >
> > --- Geoffrey Hutchison <ge...@ge...>
> > wrote:
> >
> > >
> > > On Nov 5, 2006, at 9:03 PM, richard apodaca
> wrote:
> > >
> > > > I know Java is technically not a scripting
> > > language,
> > > > but I was wondering if anyone was interested
> in
> > > trying
> > > > to get a Java interface to OB working.
> > >
> > > Actually, there are SWIG generated files for
> Java in
> > > the current SVN
> > > head (much like you describe).
> > >
> > > I had to do some renaming though -- the
> filenames
> > > are so huge that
> > > they can't be archived by tar (i.e., for
> generating
> > > snapshots and
> > > releases). I haven't updated the Makefile to do
> this
> > > automatically yet.
> > >
> > > > (6) on line 1 of openbabel_java.cpp, add
> #include
> > > > <math.h>
> > >
> > > Actually, you can automate this by adding to
> > > openbabel-java.i
> > >
> > > > [produces 32 errors about missing classes such
> as
> > > > OBChainsParser, OBBitVec, matrix3x3,
> > > OBAromaticTyper,
> > > > and so on.]
> > >
> > > If you can get me a full list, I'll definitely
> hack
> > > the SWIG
> > > interface file to generate these.
> > >
> > > Cheers,
> > > -Geoff
> > >
> >
> >
> > ____________________________
> > Richard Apodaca
> > Blog: http://depth-first.com
> >
> >
> >
> >
> >
>
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