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Re: [OpenBabel-scripting] installing openbabel python

[Swank, C. <Cra...@nr...>]

Hello Noel,
Are you referring to the instructions at http://openbabel.org/docs/2.3.0/UseTheLibrary/PythonInstall.html?  Those are the instructions I've been following.  There is no mention on those instructions about any of the errors I've encountered.

I've been trying this once again on my home computer, and was, once again, able to build and install the python bindings by editing the setup.py.  I've set the LD_LIBRARY_PATH, as the instructions suggest, to /usr/local/lib.  In the python prompt I get this error:

>>> import pybel
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/craig/src/opv/lib/python2.6/site-packages/pybel.py", line 16, in <module>
    import openbabel as ob
  File "/Users/craig/src/opv/lib/python2.6/site-packages/openbabel.py", line 56, in <module>
    _openbabel = swig_import_helper()
  File "/Users/craig/src/opv/lib/python2.6/site-packages/openbabel.py", line 52, in swig_import_helper
    _mod = imp.load_module('_openbabel', fp, pathname, description)
ImportError: dlopen(/Users/craig/src/opv/lib/python2.6/site-packages/_openbabel.so, 2): Symbol not found: __ZTVN9OpenBabel20OBRMSDConformerScoreE
  Referenced from: /Users/craig/src/opv/lib/python2.6/site-packages/_openbabel.so
  Expected in: dynamic lookup


Is my LD_LIBRARY_PATH incorrect if I've done a default build and install of openbabel?

Just in case this helps, here is where the default install went:

/usr/local/lib/openbabel
/usr/local/include/openbabel-2.0


Craig

Re: [OpenBabel-scripting] installing openbabel python

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

Hi Craig,

If you are building OB 2.3.0, please see the instructions on our website.

- Noel

On 2 November 2010 14:10, Swank, Craig <Cra...@nr...> wrote:
> Hello,
> I have built openbabel on Snow Leopard and am now trying to build the python bindings.  After I build and installed openbabel, I cd'd to the scripts/python directory and ran python setup.py build.  setup.py failed because it tries to copy openbabel.py onto itself with this line:
>
> shutil.copyfile(os.path.join(srcdir, "openbabel.py"), "openbabel.py")
>
> I then tried to fix this error by changing that part of setup.py:
>
>    try:
>        shutil.copyfile(os.path.join(srcdir, "pybel_py%dx.py" % sys.version_info[0]), "pybel.py")
>        shutil.copyfile(os.path.join(srcdir, "openbabel.py"), "openbabel.py")
>    except shutil.Error:
>        pass
>
> It then fails because it can't find an openbabel header.  I tried to fix this by changing the definition of obExtention from:
>
> obExtension = Extension('_openbabel',
>                 [os.path.join(srcdir, "openbabel-python.cpp")],
>                 include_dirs=[os.path.join(srcdir, "..", "..", "include"),
>                               os.path.join("..", "include")],
>                 library_dirs=[os.path.join("..", "lib")],
>                 libraries=['openbabel']
>                 )
>
> to:
>
> obExtension = Extension('_openbabel',
>                 [os.path.join(srcdir, "openbabel-python.cpp")],
>                 include_dirs=[os.path.join(srcdir, "..", "..", "build", "include"),
>                               os.path.join("..", "..", "include")],
>                 library_dirs=[os.path.join("..", "..", "lib")],
>                 libraries=['openbabel']
>                 )
>
> The build and install seemed to work at this point, but when I'm in a python prompt I get this error:
>
>>>> import openbabel
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
>  File "/Users/cswank/src/opv/lib/python2.6/site-packages/openbabel.py", line 56, in <module>
>    _openbabel = swig_import_helper()
>  File "/Users/cswank/src/opv/lib/python2.6/site-packages/openbabel.py", line 52, in swig_import_helper
>    _mod = imp.load_module('_openbabel', fp, pathname, description)
> ImportError: dlopen(/Users/cswank/src/opv/lib/python2.6/site-packages/_openbabel.so, 2): Symbol not found: __ZTVN9OpenBabel20OBRMSDConformerScoreE
>  Referenced from: /Users/cswank/src/opv/lib/python2.6/site-packages/_openbabel.so
>  Expected in: flat namespace
>  in /Users/cswank/src/opv/lib/python2.6/site-packages/_openbabel.so
>
>
> I tried setting the LD_LIBRARY_PATH like the install instructions suggest, but it makes no difference.
>
> Does anyone know what I'm doing wrong?
>
> Thanks,
>
> Craig
> ------------------------------------------------------------------------------
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> _______________________________________________
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>

[OpenBabel-scripting] installing openbabel python

[Swank, C. <Cra...@nr...>]

Hello,
I have built openbabel on Snow Leopard and am now trying to build the python bindings.  After I build and installed openbabel, I cd'd to the scripts/python directory and ran python setup.py build.  setup.py failed because it tries to copy openbabel.py onto itself with this line:

shutil.copyfile(os.path.join(srcdir, "openbabel.py"), "openbabel.py")

I then tried to fix this error by changing that part of setup.py:

    try:                                                                                                   
        shutil.copyfile(os.path.join(srcdir, "pybel_py%dx.py" % sys.version_info[0]), "pybel.py")          
        shutil.copyfile(os.path.join(srcdir, "openbabel.py"), "openbabel.py")                              
    except shutil.Error:                                                                                   
        pass  

It then fails because it can't find an openbabel header.  I tried to fix this by changing the definition of obExtention from:

obExtension = Extension('_openbabel',                                                                      
                 [os.path.join(srcdir, "openbabel-python.cpp")],                                           
                 include_dirs=[os.path.join(srcdir, "..", "..", "include"),                                
                               os.path.join("..", "include")],                                             
                 library_dirs=[os.path.join("..", "lib")],                                                 
                 libraries=['openbabel']                                                                   
                 )   

to:

obExtension = Extension('_openbabel',                                                                      
                 [os.path.join(srcdir, "openbabel-python.cpp")],                                           
                 include_dirs=[os.path.join(srcdir, "..", "..", "build", "include"),                       
                               os.path.join("..", "..", "include")],                                       
                 library_dirs=[os.path.join("..", "..", "lib")],                                           
                 libraries=['openbabel']                                                                   
                 ) 

The build and install seemed to work at this point, but when I'm in a python prompt I get this error:

>>> import openbabel
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/cswank/src/opv/lib/python2.6/site-packages/openbabel.py", line 56, in <module>
    _openbabel = swig_import_helper()
  File "/Users/cswank/src/opv/lib/python2.6/site-packages/openbabel.py", line 52, in swig_import_helper
    _mod = imp.load_module('_openbabel', fp, pathname, description)
ImportError: dlopen(/Users/cswank/src/opv/lib/python2.6/site-packages/_openbabel.so, 2): Symbol not found: __ZTVN9OpenBabel20OBRMSDConformerScoreE
  Referenced from: /Users/cswank/src/opv/lib/python2.6/site-packages/_openbabel.so
  Expected in: flat namespace
 in /Users/cswank/src/opv/lib/python2.6/site-packages/_openbabel.so


I tried setting the LD_LIBRARY_PATH like the install instructions suggest, but it makes no difference.

Does anyone know what I'm doing wrong?

Thanks,

Craig

[OpenBabel-scripting] ANNOUNCE: Open Babel 2.3.0 Release

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

I am very happy to finally announce the release of Open Babel 2.3.0, the next major release of the open source chemistry toolbox.

Open Babel has been downloaded over 160,000 times and is used in over 40 projects.

This release represents a major update and should be a stable upgrade, strongly recommended for all users of Open Babel. Highlights include a completely rewritten stereochemistry engine, Spectrophore descriptor generation, 2D depiction, improved 3D coordinate generation, conformer searching, and more. Many formats are improved or added, including CIF, PDBQT, SVG, and more. Improved developer API and scripting support and many, many bug fixes are also included.

What's new? See the full release notes at:
http://openbabel.org/wiki/Open_Babel_2.3.0

See the new user guide at:
http://openbabel.org/docs/2.3.0/

See the updated developer documentation at:
http://openbabel.org/api/2.3/

To download, see:
http://sourceforge.net/projects/openbabel/files/

For more information, see the project website at:
http://openbabel.org/

I would like to personally thank a few people for extra effort in improving this release. In alphabetical order Chris Morley, Noel O'Boyle, Tim Vandermeersch, and Silicos NV, which donated their Spectrophore(TM) framework to Open Babel 2.3.

This is a community project and we couldn't have made this release without you. Many thanks to all the contributors to Open Babel including those of you who submitted feedback, bug reports, and code.

Cheers,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: ge...@pi...
web: http://hutchison.chem.pitt.edu/

Re: [OpenBabel-scripting] WriteMapList using Perl

[jseco <js...@mm...>]

  Hi All,

       I have recently installed Openbabel on my computer and trying to
develop some code merging OB and Perl, but unfortunately, I have noticed the
documentation present is not large enough to my comprehension because of my
programming limitations.
     I have the same problem in how to access to the data of GetUMapList().
I have also read the post, but it seems was not clearly fixed it. I have
tried the following code to finally confirm the $maplist is a HASH (using
Scalar::Util, because Data::Dumper gave me  $VAR1 = bless(
{},'Chemistry::OpenBabel::vvInt' );  but I do not know how to interpret...)
and I have unsuccessfully tried all perlistic ways to access to a given hash
but I do not know how to really access to the content, even trying the
solutions posted here. 
     Am I missing anything ?, because the foreach loop does not return
anything.

     Thanks in advance!!


use Chemistry::OpenBabel;
use Scalar::Util;


my $smiles = "c1cc(CC(=O)CN)ccc1";
my $obMol = new Chemistry::OpenBabel::OBMol;
my $obConversion = new Chemistry::OpenBabel::OBConversion;
$obConversion->SetInFormat("smi");
$obConversion->ReadString($obMol,$smiles);
my $obsmartpattern = new Chemistry::OpenBabel::OBSmartsPattern;
$obsmartpattern->Init('C(=O)');
$obsmartpattern->Match($obMol);
my $maplist = $obsmartpattern->GetMapList();
print UNIVERSAL::isa($maplist,'HASH');

foreach my $index1 (sort {$a cmp $b} keys %{$maplist}) {
        printf "index is %s\n",$index;
}

-- 
View this message in context: http://open-babel.957263.n4.nabble.com/WriteMapList-using-Perl-tp957583p2543611.html
Sent from the openbabel-scripting mailing list archive at Nabble.com.

Re: [OpenBabel-scripting] Problem of Calling OB with PHP

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

> $results=shell_exec('/usr/local/bin/python
> /home/monkey/Monkey0.01/selected.py -p '.$_POST['types'].' -s -1'.' -l
> '.$_POST['classlabel'].' -i '.$uploadfile_train.' -o '.$ig_anal_out.'
> 2>&1');

I'd check in your python script, but I'm willing to bet that the shell environment is very different.

If you post to the regular openbabel-discuss mailing list, there are many people who have run OB from a web service, and I'm sure someone could give you tips and/or sample code.

Best regards,
-Geoff

[OpenBabel-scripting] Problem of Calling OB with PHP

[Jie S. <jie...@gm...>]

Dear all,

I am now trying to built a web-based calculation server. It will work like this:

Using PHP call the python script in linux.

The script could run well in the terminal of linux, but the same
commands can not run successfully under PHP calling (using
"shell_exec")

The error listed:

Traceback (most recent call last):
 File "/home/monkey/Monkey0.01/selected.py", line 137, in
   main(sys.argv[1:])
 File "/home/monkey/Monkey0.01/selected.py", line 74, in main
   import getopt, string, readsdf
 File "/home/monkey/Monkey0.01/readsdf.py", line 33, in
   import pybel as pb
 File "/home/monkey/program/OB-2.2.3/lib/python2.6/site-packages/pybel.py",
line 16, in
   import openbabel as ob
 File "/home/monkey/program/OB-2.2.3/lib/python2.6/site-packages/openbabel.py",
line 36, in
   _openbabel = swig_import_helper()
 File "/home/monkey/program/OB-2.2.3/lib/python2.6/site-packages/openbabel.py",
line 35, in swig_import_helper
   return _mod
UnboundLocalError: local variable '_mod' referenced before assignment


The calling line in PHP is:

$results=shell_exec('/usr/local/bin/python
/home/monkey/Monkey0.01/selected.py -p '.$_POST['types'].' -s -1'.' -l
'.$_POST['classlabel'].' -i '.$uploadfile_train.' -o '.$ig_anal_out.'
2>&1');

BTW, this command can run successfully in the terminal after translation.
and we have exclude following reasons:
1. safe mode is already off
2. The shell command is right
3. there is no problem with "permission" issues.


I am grateful if anyone can help me.

Best regards,

Sincerely,

Re: [OpenBabel-scripting] Problem reading text date from OBElementTable

[Dan K. <da...@sb...>]

  Thanks Noel,

I wasn't sure if it was a bug since I am new to both Iron Python and 
OpenBabel.

Dan

On 8/26/2010 12:44 PM, Noel O'Boyle wrote:
> Hi Dan,
>
> I filed a bug: https://sourceforge.net/tracker/?func=detail&aid=3053762&group_id=40728&atid=428740
>
> I'll update up when it gets sorted out. If you find other examples of
> similar problems, can you just add them to the bug report (you may
> have to create an a/c on source forge to do this, I forget).
>
> - Noel
>
> On 25 August 2010 23:54, Dan Kimberling<da...@sb...>  wrote:
>>   Thanks Noel,
>>
>> I am CCing this to the list.
>>
>> Dan
>>
>> On 8/25/2010 12:10 PM, Noel O'Boyle wrote:
>>> Can you cc the message to the list?
>>>
>>> I'll look into the problem when I get a chance, but there's something
>>> funny going on.
>>>
>>> - Noel
>>>
>>> On 25 August 2010 15:56, Dan Kimberling<da...@sb...>    wrote:
>>>>   On 8/25/2010 2:22 AM, Noel O'Boyle wrote:
>>>>> On 25 August 2010 02:54, Dan Kimberling<da...@sb...>      wrote:
>>>>>> Hi,
>>>>>>
>>>>>> This is the message  that got accidentally deleted.
>>>>>>
>>>>>> I just started using OpenBabel with Iron Python. I am new to each so
>>>>>> i'm
>>>>>> not sure if this a bug or user error.
>>>>>>
>>>>>> When I try to get an element name or symbol using:
>>>>>>
>>>>>> import clr
>>>>>> clr.AddReference("OBDotNet.dll")
>>>>>> import OpenBabel as ob
>>>>>>
>>>>>> etab = ob.OBElementTable()
>>>>>> name = str(etab.GetName(8))
>>>>> Try just name = etab.GetName(8)
>>>>>
>>>>>> print(name)
>>>>>>
>>>>>> I get an error:
>>>>>> Message: Attempted to read or write protected memory. This is often an
>>>>>> indication that other memory is corrupt.
>>>>>>
>>>>>> When I try to get a numeric value such as mass, everything works fine.
>>>>>>
>>>>>> Dan
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
>>>>>> Be part of this innovative community and reach millions of netbook
>>>>>> users
>>>>>> worldwide. Take advantage of special opportunities to increase revenue
>>>>>> and
>>>>>> speed time-to-market. Join now, and jumpstart your future.
>>>>>> http://p.sf.net/sfu/intel-atom-d2d
>>>>>> _______________________________________________
>>>>>> OpenBabel-scripting mailing list
>>>>>> Ope...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>>>>>
>>>> Thanks Noel but that's what I tried first and got the same result.
>>>>
>>>> I still get the message:
>>>> "Message: Attempted to read or write protected memory. This is often an
>>>> indication that other memory is corrupt."
>>>>
>>>> This only happens when I try to read a text attribute. Numeric data works
>>>> as
>>>> expected.
>>>>
>>>> Dan
>>>>
>>

Re: [OpenBabel-scripting] Problem reading text date from OBElementTable

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

Hi Dan,

I filed a bug: https://sourceforge.net/tracker/?func=detail&aid=3053762&group_id=40728&atid=428740

I'll update up when it gets sorted out. If you find other examples of
similar problems, can you just add them to the bug report (you may
have to create an a/c on source forge to do this, I forget).

- Noel

On 25 August 2010 23:54, Dan Kimberling <da...@sb...> wrote:
>  Thanks Noel,
>
> I am CCing this to the list.
>
> Dan
>
> On 8/25/2010 12:10 PM, Noel O'Boyle wrote:
>>
>> Can you cc the message to the list?
>>
>> I'll look into the problem when I get a chance, but there's something
>> funny going on.
>>
>> - Noel
>>
>> On 25 August 2010 15:56, Dan Kimberling<da...@sb...>  wrote:
>>>
>>>  On 8/25/2010 2:22 AM, Noel O'Boyle wrote:
>>>>
>>>> On 25 August 2010 02:54, Dan Kimberling<da...@sb...>    wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> This is the message  that got accidentally deleted.
>>>>>
>>>>> I just started using OpenBabel with Iron Python. I am new to each so
>>>>> i'm
>>>>> not sure if this a bug or user error.
>>>>>
>>>>> When I try to get an element name or symbol using:
>>>>>
>>>>> import clr
>>>>> clr.AddReference("OBDotNet.dll")
>>>>> import OpenBabel as ob
>>>>>
>>>>> etab = ob.OBElementTable()
>>>>> name = str(etab.GetName(8))
>>>>
>>>> Try just name = etab.GetName(8)
>>>>
>>>>> print(name)
>>>>>
>>>>> I get an error:
>>>>> Message: Attempted to read or write protected memory. This is often an
>>>>> indication that other memory is corrupt.
>>>>>
>>>>> When I try to get a numeric value such as mass, everything works fine.
>>>>>
>>>>> Dan
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
>>>>> Be part of this innovative community and reach millions of netbook
>>>>> users
>>>>> worldwide. Take advantage of special opportunities to increase revenue
>>>>> and
>>>>> speed time-to-market. Join now, and jumpstart your future.
>>>>> http://p.sf.net/sfu/intel-atom-d2d
>>>>> _______________________________________________
>>>>> OpenBabel-scripting mailing list
>>>>> Ope...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>>>>
>>> Thanks Noel but that's what I tried first and got the same result.
>>>
>>> I still get the message:
>>> "Message: Attempted to read or write protected memory. This is often an
>>> indication that other memory is corrupt."
>>>
>>> This only happens when I try to read a text attribute. Numeric data works
>>> as
>>> expected.
>>>
>>> Dan
>>>
>
>

Re: [OpenBabel-scripting] Problem reading text date from OBElementTable

[Dan K. <da...@sb...>]

  Thanks Noel,

I am CCing this to the list.

Dan

On 8/25/2010 12:10 PM, Noel O'Boyle wrote:
> Can you cc the message to the list?
>
> I'll look into the problem when I get a chance, but there's something
> funny going on.
>
> - Noel
>
> On 25 August 2010 15:56, Dan Kimberling<da...@sb...>  wrote:
>>   On 8/25/2010 2:22 AM, Noel O'Boyle wrote:
>>> On 25 August 2010 02:54, Dan Kimberling<da...@sb...>    wrote:
>>>> Hi,
>>>>
>>>> This is the message  that got accidentally deleted.
>>>>
>>>> I just started using OpenBabel with Iron Python. I am new to each so i'm
>>>> not sure if this a bug or user error.
>>>>
>>>> When I try to get an element name or symbol using:
>>>>
>>>> import clr
>>>> clr.AddReference("OBDotNet.dll")
>>>> import OpenBabel as ob
>>>>
>>>> etab = ob.OBElementTable()
>>>> name = str(etab.GetName(8))
>>> Try just name = etab.GetName(8)
>>>
>>>> print(name)
>>>>
>>>> I get an error:
>>>> Message: Attempted to read or write protected memory. This is often an
>>>> indication that other memory is corrupt.
>>>>
>>>> When I try to get a numeric value such as mass, everything works fine.
>>>>
>>>> Dan
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
>>>> Be part of this innovative community and reach millions of netbook users
>>>> worldwide. Take advantage of special opportunities to increase revenue
>>>> and
>>>> speed time-to-market. Join now, and jumpstart your future.
>>>> http://p.sf.net/sfu/intel-atom-d2d
>>>> _______________________________________________
>>>> OpenBabel-scripting mailing list
>>>> Ope...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>>>
>> Thanks Noel but that's what I tried first and got the same result.
>>
>> I still get the message:
>> "Message: Attempted to read or write protected memory. This is often an
>> indication that other memory is corrupt."
>>
>> This only happens when I try to read a text attribute. Numeric data works as
>> expected.
>>
>> Dan
>>

Re: [OpenBabel-scripting] Problem reading text date from OBElementTable

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

On 25 August 2010 02:54, Dan Kimberling <da...@sb...> wrote:
> Hi,
>
> This is the message  that got accidentally deleted.
>
> I just started using OpenBabel with Iron Python. I am new to each so i'm
> not sure if this a bug or user error.
>
> When I try to get an element name or symbol using:
>
> import clr
> clr.AddReference("OBDotNet.dll")
> import OpenBabel as ob
>
> etab = ob.OBElementTable()
> name = str(etab.GetName(8))

Try just name = etab.GetName(8)

> print(name)
>
> I get an error:
> Message: Attempted to read or write protected memory. This is often an
> indication that other memory is corrupt.
>
> When I try to get a numeric value such as mass, everything works fine.
>
> Dan
>
>
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users
> worldwide. Take advantage of special opportunities to increase revenue and
> speed time-to-market. Join now, and jumpstart your future.
> http://p.sf.net/sfu/intel-atom-d2d
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

[OpenBabel-scripting] Problem reading text date from OBElementTable

[Dan K. <da...@sb...>]

Hi,

This is the message  that got accidentally deleted.

I just started using OpenBabel with Iron Python. I am new to each so i'm
not sure if this a bug or user error.

When I try to get an element name or symbol using:

import clr
clr.AddReference("OBDotNet.dll")
import OpenBabel as ob

etab = ob.OBElementTable()
name = str(etab.GetName(8))
print(name)

I get an error:
Message: Attempted to read or write protected memory. This is often an
indication that other memory is corrupt.

When I try to get a numeric value such as mass, everything works fine.

Dan

[OpenBabel-scripting] Message about Iron Python deleted by accident

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

Apologies to some one out there,

If you recently sent a message to the list about Iron Python could you
please resend it? I think I may have accidentally deleted it in the
course of spam filtering.

- Noel

Re: [OpenBabel-scripting] Python bindings and Mac installer

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

On Aug 20, 2010, at 7:00 PM, Richard West wrote:

> As you can see (URLs below), I had to tweak a couple of the makefiles for the bindings - it may be possible to fix these upstream in a future OpenBabel release.

Well, if you'd like to test a future Open Babel release, see here. (I believe the Makefile now works fine with Perl.)

https://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-08-03/openbabel-2.3.0b2-20100803-r3942.tar.gz/download

Best regards,
-Geoff

Re: [OpenBabel-scripting] Python bindings and Mac installer

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

On 21 August 2010 00:00, Richard West <rw...@mi...> wrote:
>
> On Aug 17, 2010, at 11:17 PM, Geoffrey Hutchison wrote:
>
>>> Many thanks. I was considering trying to put together a homebrew formula for openbabel. If I find the time do you think this would this be a good idea?
>>
>> Yes, I think this would be great.
>>
>> -Geoff
>
>
> I have created a homebrew formula for open-babel. Not perfect, but it's a decent start, and it seems to work for me on my recently-installed Snow Leopard machine.
>
> If/when it gets accepted into the official repository, users of homebrew on a Mac will be able to just type:
> $ brew install open-babel --python --perl --ruby
> to build the whole lot. (Except there's not yet a formula for oasa).
>
> As you can see (URLs below), I had to tweak a couple of the makefiles for the bindings - it may be possible to fix these upstream in a future OpenBabel release.
>
> Formula:
> http://github.com/rwest/homebrew/blob/e46c339eb1d948a82321edb75d79058fa5b498a6/Library/Formula/open-babel.rb
>
> Commit message:
> http://github.com/rwest/homebrew/commit/e46c339eb1d948a82321edb75d79058fa5b498a6
>
> A good place for suggestions (or encouragement for it to be adopted) would be the ticket at:
> http://github.com/mxcl/homebrew/issues/issue/2247
>
> Have a good weekend, and hopefully I'll bump into some of you at ACS next week (is there a good way to increase the probability of this?)

I won't be there, but if you attend Harry's Party
(http://www.mail-archive.com/blu...@li.../msg00944.html)
you will meet many of the blue obeliskers.

> Richard
> ------------------------------------------------------------------------------
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Re: [OpenBabel-scripting] openbabel perl binding problems

[Richard W. <rw...@MI...>]

On Aug 20, 2010, at 7:15 PM, ope...@li... wrote:

> Message: 3
> Date: Tue, 10 Aug 2010 21:28:18 -0400
> From: Dave Nunn <dav...@gm...>
> Subject: [OpenBabel-scripting] openbabel perl binding problems
> To: ope...@li...
> Message-ID:
> 	<AAN...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hello --
> 
> While trying to install the perl bindings for openbabel, I run into the
> following problem:
> 
> $ make
> Skip blib/lib/Chemistry/OpenBabel.pm (unchanged)
> g++ -c  -I../../include -arch x86_64 -arch i386 -arch ppc -g -pipe
> -fno-common -DPERL_DARWIN -fno-strict-aliasing -I/usr/local/include -Os
> -DVERSION=\"1.3.0\" -DXS_VERSION=\"1.3.0\"
> "-I/System/Library/Perl/5.10.0/darwin-thread-multi-2level/CORE"
> openbabel_perl.cpp
> Running Mkbootstrap for Chemistry::OpenBabel ()
> chmod 644 OpenBabel.bs
> rm -f blib/arch/auto/Chemistry/OpenBabel/OpenBabel.bundle
> g++ -shared  -arch x86_64 -arch i386 -arch ppc -bundle -undefined
> dynamic_lookup -L/usr/local/lib openbabel_perl.o -L../../src/.libs
> -lopenbabel -lz  -o blib/arch/auto/Chemistry/OpenBabel/OpenBabel.bundle \
>     \
> 
> i686-apple-darwin10-g++-4.2.1: -bundle not allowed with -dynamiclib
> i686-apple-darwin10-g++-4.2.1: -bundle not allowed with -dynamiclib
> powerpc-apple-darwin10-g++-4.2.1: -bundle not allowed with -dynamiclib
> lipo: can't figure out the architecture type of: /var/tmp//cchi5SMV.out
> make: *** [blib/arch/auto/Chemistry/OpenBabel/OpenBabel.bundle] Error 1
> 
> 
> I get the same results after trying the suggested
> (export MACOSX_DEPLOYMENT_TARGET='10.6');
> Compiling openbabel itself went smoothly, and the installations of both
> openbabel and the perl bindings worked fine on a Mac OSX 10.5 machine today.
> 
> Any suggestions?  Any help greatly appreciated.
> 
> -Dave Nunn

Hi Dave,
I only just saw this (I have the mailing list in digest mode) but ran into the same problem myself while making the homebrew formula from 2.2.3. This is my solution:
After running "perl Makefile.PL" to create the Makefile you have to edit it.
Search and remove all instances of "-bundle" "-arch ppc" and "-arch i386".
Then run make.
You may be able to leave the additional -arch flags, or use i386 instead of x86_64 if you built a 32-bit version of openbabel.
...or use homebrew and try out my formula (see earlier email).
Richard

Re: [OpenBabel-scripting] Python bindings and Mac installer

[Richard W. <rw...@MI...>]

On Aug 17, 2010, at 11:17 PM, Geoffrey Hutchison wrote:

>> Many thanks. I was considering trying to put together a homebrew formula for openbabel. If I find the time do you think this would this be a good idea?
> 
> Yes, I think this would be great.
> 
> -Geoff


I have created a homebrew formula for open-babel. Not perfect, but it's a decent start, and it seems to work for me on my recently-installed Snow Leopard machine.

If/when it gets accepted into the official repository, users of homebrew on a Mac will be able to just type:
$ brew install open-babel --python --perl --ruby
to build the whole lot. (Except there's not yet a formula for oasa).

As you can see (URLs below), I had to tweak a couple of the makefiles for the bindings - it may be possible to fix these upstream in a future OpenBabel release.

Formula:
http://github.com/rwest/homebrew/blob/e46c339eb1d948a82321edb75d79058fa5b498a6/Library/Formula/open-babel.rb

Commit message:
http://github.com/rwest/homebrew/commit/e46c339eb1d948a82321edb75d79058fa5b498a6

A good place for suggestions (or encouragement for it to be adopted) would be the ticket at:
http://github.com/mxcl/homebrew/issues/issue/2247

Have a good weekend, and hopefully I'll bump into some of you at ACS next week (is there a good way to increase the probability of this?)

Richard

Re: [OpenBabel-scripting] Python bindings and Mac installer

[Richard W. <rw...@MI...>]

Many thanks. I was considering trying to put together a homebrew formula for openbabel. If I find the time do you think this would this be a good idea?

Richard

On Aug 17, 2010, at 9:05 PM, Geoffrey Hutchison <ge...@ge...> wrote:

>> Is there a way to build the python bindings having used the (recommended) v2.2.3 Installer (http://sourceforge.net/projects/openbabel/files/openbabel/2.2.3/OpenBabel-2.2.3.mac.zip/download )
>> or do I need to compile open-babel from source?
> 
> The python bindings are not included in the installer -- they must be built from source code. Next time, I'll make an optional package for the Mac python bindings.
> 
> Best regards,
> -Geoff
> 

Re: [OpenBabel-scripting] Python bindings and Mac installer

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

> Is there a way to build the python bindings having used the (recommended) v2.2.3 Installer (http://sourceforge.net/projects/openbabel/files/openbabel/2.2.3/OpenBabel-2.2.3.mac.zip/download )
> or do I need to compile open-babel from source?

The python bindings are not included in the installer -- they must be built from source code. Next time, I'll make an optional package for the Mac python bindings.

Best regards,
-Geoff

[OpenBabel-scripting] Python bindings and Mac installer

[Richard W. <rw...@MI...>]

Hi,
I have just upgraded my Mac to OS X 10.6 and am reinstalling OpenBabel.
Is there a way to build the python bindings having used the (recommended) v2.2.3 Installer (http://sourceforge.net/projects/openbabel/files/openbabel/2.2.3/OpenBabel-2.2.3.mac.zip/download )
or do I need to compile open-babel from source?
Apologies if this has been answered already, but I couldn't see it obviously in the wiki.
Many thanks,
Richard

Re: [OpenBabel-scripting] openbabel perl binding problems

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

Hi Dave,

Have you tried the latest snapshot?
https://sourceforge.net/projects/openbabel/files/

- Noel

On 11 August 2010 02:28, Dave Nunn <dav...@gm...> wrote:
> Hello --
> While trying to install the perl bindings for openbabel, I run into the
> following problem:
> $ make
> Skip blib/lib/Chemistry/OpenBabel.pm (unchanged)
> g++ -c  -I../../include -arch x86_64 -arch i386 -arch ppc -g -pipe
> -fno-common -DPERL_DARWIN -fno-strict-aliasing -I/usr/local/include -Os
> -DVERSION=\"1.3.0\" -DXS_VERSION=\"1.3.0\"
>  "-I/System/Library/Perl/5.10.0/darwin-thread-multi-2level/CORE"
> openbabel_perl.cpp
> Running Mkbootstrap for Chemistry::OpenBabel ()
> chmod 644 OpenBabel.bs
> rm -f blib/arch/auto/Chemistry/OpenBabel/OpenBabel.bundle
> g++ -shared  -arch x86_64 -arch i386 -arch ppc -bundle -undefined
> dynamic_lookup -L/usr/local/lib openbabel_perl.o -L../../src/.libs
> -lopenbabel -lz  -o blib/arch/auto/Chemistry/OpenBabel/OpenBabel.bundle \
>     \
>
> i686-apple-darwin10-g++-4.2.1: -bundle not allowed with -dynamiclib
> i686-apple-darwin10-g++-4.2.1: -bundle not allowed with -dynamiclib
> powerpc-apple-darwin10-g++-4.2.1: -bundle not allowed with -dynamiclib
> lipo: can't figure out the architecture type of: /var/tmp//cchi5SMV.out
> make: *** [blib/arch/auto/Chemistry/OpenBabel/OpenBabel.bundle] Error 1
>
> I get the same results after trying the suggested
> (export MACOSX_DEPLOYMENT_TARGET='10.6');
> Compiling openbabel itself went smoothly, and the installations of both
> openbabel and the perl bindings worked fine on a Mac OSX 10.5 machine today.
> Any suggestions?  Any help greatly appreciated.
> -Dave Nunn
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
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> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>

[OpenBabel-scripting] openbabel perl binding problems

[Dave N. <dav...@gm...>]

Hello --

While trying to install the perl bindings for openbabel, I run into the
following problem:

$ make
Skip blib/lib/Chemistry/OpenBabel.pm (unchanged)
g++ -c  -I../../include -arch x86_64 -arch i386 -arch ppc -g -pipe
-fno-common -DPERL_DARWIN -fno-strict-aliasing -I/usr/local/include -Os
-DVERSION=\"1.3.0\" -DXS_VERSION=\"1.3.0\"
 "-I/System/Library/Perl/5.10.0/darwin-thread-multi-2level/CORE"
openbabel_perl.cpp
Running Mkbootstrap for Chemistry::OpenBabel ()
chmod 644 OpenBabel.bs
rm -f blib/arch/auto/Chemistry/OpenBabel/OpenBabel.bundle
g++ -shared  -arch x86_64 -arch i386 -arch ppc -bundle -undefined
dynamic_lookup -L/usr/local/lib openbabel_perl.o -L../../src/.libs
-lopenbabel -lz  -o blib/arch/auto/Chemistry/OpenBabel/OpenBabel.bundle \
     \

i686-apple-darwin10-g++-4.2.1: -bundle not allowed with -dynamiclib
i686-apple-darwin10-g++-4.2.1: -bundle not allowed with -dynamiclib
powerpc-apple-darwin10-g++-4.2.1: -bundle not allowed with -dynamiclib
lipo: can't figure out the architecture type of: /var/tmp//cchi5SMV.out
make: *** [blib/arch/auto/Chemistry/OpenBabel/OpenBabel.bundle] Error 1


I get the same results after trying the suggested
(export MACOSX_DEPLOYMENT_TARGET='10.6');
Compiling openbabel itself went smoothly, and the installations of both
openbabel and the perl bindings worked fine on a Mac OSX 10.5 machine today.

Any suggestions?  Any help greatly appreciated.

-Dave Nunn

Re: [OpenBabel-scripting] OBReaction missing from OpenBabel.py

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

It's a bug. Could you file one please and I'll sort it out before the
next release?

- Noel

On 15 July 2010 20:08, A. Heifets <ab...@cs...> wrote:
> I notice that OBReaction [1] is missing from the OpenBabel python
> module.  Is this a bug or a feature?  Other subclasses of OBBase such
> as OBAtom, OBMol, and OBBond are present.
>
> [1] http://openbabel.org/api/2.2.0/classOpenBabel_1_1OBReaction.shtml
>
> Cheers,
> Abe
>
> --
> A. Heifets
> http://www.cs.toronto.edu/~aheifets/
>
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[OpenBabel-scripting] OBReaction missing from OpenBabel.py

[A. H. <ab...@cs...>]

I notice that OBReaction [1] is missing from the OpenBabel python
module.  Is this a bug or a feature?  Other subclasses of OBBase such
as OBAtom, OBMol, and OBBond are present.

[1] http://openbabel.org/api/2.2.0/classOpenBabel_1_1OBReaction.shtml

Cheers,
Abe

--
A. Heifets
http://www.cs.toronto.edu/~aheifets/

Re: [OpenBabel-scripting] Pybel installation problems

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

Hi Ori,

Thanks for that. The error is my fault as Python 3.1 has changed the
print statement to a function. You should instead type the following:
   print(mol.write("sdf"))

Hopefully this should work fine.

- Noel

On 12 May 2010 17:47, ori kalid <ori...@gm...> wrote:
> Hi,
> I've just installed python3.1, open babel 2.2.3 and pybel.
> I ran the tests for pybel installation and I am getting errors on the
> ">>>print mol.write("sdf")" command.
> As advised on the installation website, I am sending you the output from the
> test commands (see below).
>
> What should I do?
>
> Best regards,
>
> Ori
>
> output from test commands:
>
> Microsoft Windows XP [Version 5.1.2600]
> (C) Copyright 1985-2001 Microsoft Corp.
>
> C:\Documents and Settings\ginati>cd C:\Documents and Settings\ginati\My
> Document
> s\Ori\LEDGF\Libaries
>
> C:\Documents and Settings\ginati\My Documents\Ori\XXX\Libaries>babel -V
> Open Babel 2.2.3 -- Aug 18 2009 -- 16:21:20
>
> C:\Documents and Settings\ginati\My Documents\Ori\XXX\Libaries>babel -Hsdf
> sdf  MDL MOL/SDF format
> Reads and writes V2000 and V3000 versions
> Write Options, e.g. -x3
>  3  output V3000 not V2000 (used for >999 atoms/bonds)
>  m  write no properties
>
> Input Options, e.g. -av
>  v  AtomValue in V line is NOT a partial charge
>
>
> Specification at: http://www.mdl.com/downloads/public/ctfile/ctfile.jsp
>
> C:\Documents and Settings\ginati\My Documents\Ori\XXX\Libaries>dir
> "%BABEL_DAT
> ADIR%"\OBGUI.exe
>  Volume in drive C has no label.
>  Volume Serial Number is 34F7-04B6
>
>  Directory of C:\Program Files\OpenBabel-2.2.3
>
> 08/18/2009  06:20 PM         1,253,376 OBGUI.exe
>                1 File(s)      1,253,376 bytes
>                0 Dir(s)  180,960,583,680 bytes free
>
> C:\Documents and Settings\ginati\My
> Documents\Ori\LEDGF\Libaries>c:\Python31\pyt
> hon.exe
> Python 3.1.1 (r311:74483, Aug 17 2009, 17:02:12) [MSC v.1500 32 bit (Intel)]
> on
> win32
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import pybel
>>>> mol = pybel.readstring("smi", "CC(=O)Br")
>>>> mol.make3D()
>>>> print mol.write("sdf")
>   File "<stdin>", line 1
>     print mol.write("sdf")
>             ^
> SyntaxError: invalid syntax
>>>>
>
> ------------------------------------------------------------------------------
>
>
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>
>