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Re: [OpenBabel-scripting] std::vector< OBInternalCoord * >

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

For the record, running the following code:

grep -h definition xml/classOpenBabel_1_1*.xml | grep "vector<" |
sed 's/std:://g' | sed 's/<definition>//g' | sed 's/<\/definition>//g'
| sed 's/&gt;/\>/g' | sed 's/\&lt;/\</g' | sed 's/< /</g' | sed 's/
\*/\*/g' | sed 's/ >/>/g' | sed 's/\&amp;/\&/g' | sed 's/ \&/\&/g' |
sed 's/::iterator//g' | awk '{for (i=1; i<NF; i++) {printf("%s ",
$i);}; printf("\n");}' | grep -v "&" | grep -v "_" | sort | uniq

gives:
vector<bool>
vector<double*>
vector<double>
vector<GasteigerState*>
vector<int>
vector<int>*
vector<OBAngle>
vector<OBAtom*>
vector<OBBond*>
vector<OBChemTsfm*>
vector<OBElement*>
vector<OBExternalBond>
vector<OBExternalBond>*
vector<OBGenericData*>
vector<OBInternalCoord*>
vector<OBMol*>
vector<OBMol>
vector<OBResidue*>
vector<OBRing*>
vector<OBRotor*>
vector<OBRotorRule*>
vector<OBSmartsPattern*>
vector<OBTorsion>
vector<pair<int,int>>
vector<pair<OBAtom**,vector<int>>>
vector<pair<OBSmartsPattern*, double>>
vector<pair<OBSmartsPattern*, vector<int>>>
vector<pair<OBSmartsPattern*,int>>
vector<pair<OBSmartsPattern*,pair<int,int>>>
vector<pair<OBSmartsPattern*,string>>
vector<pair<OBSmartsPattern*,vector<double>>>
vector<pair<pair<int,int>,int>>
vector<pair<string,int>>
vector<quad<OBAtom*, OBAtom*, OBAtom*, OBAtom*>>
vector<string>
vector<triple<OBAtom*,OBAtom*,double>>
vector<unsigned char*>
vector<unsigned int>
vector<unsigned short>
vector<vector<double>>
vector<vector<int>>
vector<vector<pair <unsigned int, double>>>
vector<vector<pair<string,int>>>
vector<vector<string>>
vector<vector<unsigned int>>
vector<vector<vector3>>
vector<vector3>

We should probably add the lot.

Noel

On 11/07/07, Noel O'Boyle <bao...@gm...> wrote:
> I'm working on identifying (basically, by grepping the Doxygen XML
> docs) any remaining std::vector templates included in OpenBabel that
> we need to wrap . This will mean that no more users will have to
> complain about this problem...
>
> Noel
>
> On 08/07/07, Geoffrey Hutchison <ge...@ge...> wrote:
> >
> > On Jun 28, 2007, at 11:54 PM, wr...@hu... wrote:
> >
> > > Has the proper data structure been wrapped to another name or is it
> > > missing?
> > > I appreciate any response, thank you.
> >
> > No, at the moment, it's missing. If you have SWIG (1.3.30), you can
> > easily regenerate the Python (or other) bindings.
> >
> > You edit the openbabel-python.i file, look for the %template () lines
> > and add something like:
> >
> > %template (vectorpICoord)   vector<OBBInternalCoord *>
> >
> > Then take a look at:
> > http://openbabel.sourceforge.net/wiki/Developer:Building
> >
> > Cheers,
> > -Geoff
> >
> > -------------------------------------------------------------------------
> > This SF.net email is sponsored by DB2 Express
> > Download DB2 Express C - the FREE version of DB2 express and take
> > control of your XML. No limits. Just data. Click to get it now.
> > http://sourceforge.net/powerbar/db2/
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
>

Re: [OpenBabel-scripting] std::vector< OBInternalCoord * >

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

I'm working on identifying (basically, by grepping the Doxygen XML
docs) any remaining std::vector templates included in OpenBabel that
we need to wrap . This will mean that no more users will have to
complain about this problem...

Noel

On 08/07/07, Geoffrey Hutchison <ge...@ge...> wrote:
>
> On Jun 28, 2007, at 11:54 PM, wr...@hu... wrote:
>
> > Has the proper data structure been wrapped to another name or is it
> > missing?
> > I appreciate any response, thank you.
>
> No, at the moment, it's missing. If you have SWIG (1.3.30), you can
> easily regenerate the Python (or other) bindings.
>
> You edit the openbabel-python.i file, look for the %template () lines
> and add something like:
>
> %template (vectorpICoord)   vector<OBBInternalCoord *>
>
> Then take a look at:
> http://openbabel.sourceforge.net/wiki/Developer:Building
>
> Cheers,
> -Geoff
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

[OpenBabel-scripting] ANN: openbabel-python 1.2.1 for Windows

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

Announcing the release of the OpenBabel module for Python, version
1.2.1, for Windows, available from
http://openbabel.sourceforge.net/wiki/Install.

OpenBabel is a chemical toolbox designed to speak the many languages
of chemical data. It's an open, collaborative project allowing anyone
to search, convert, analyze, or store data from molecular modeling,
chemistry, solid-state materials, biochemistry, or related areas. This
Python module allows you to access this popular C++ library in your
Python scripts.

New features in 1.2.1:
(1) Descriptor values for LogP, MR and PSA can be calculated
(2) Incorporates all bug fixes included in the recent OpenBabel 2.1.1

New features in 1.2:
(1) Data fields in file formats like MOL2 and SDF can now be accessed and edited
(2) Unit cell data in crystallographic file formats such as CIF can
now be accessed
(3) A list of all detected input and output file formats can be accessed

Core features:
(1) Read and write over 80 molecular file formats
(2) Access molecular properties like molecular weight, formula, charge
(3) Daylight-type fingerprints and calculation of the Tanimoto coefficient
(4) SMARTS pattern matching
(5) Graph algorithms such as the Smallest Set of Smallest Rings (SSSR)
and Depth-First Iteration over atoms

Documentation:
(1) The Python module: http://openbabel.sourceforge.net/wiki/Python
(2) The C++ toolkit: http://openbabel.sourceforge.net/api/2.1.0/index.shtml
(3) The OpenBabel web site: http://openbabel.sourceforge.net

Support:
(1) If you have any questions, send an email to
ope...@li...
(2) Report a bug at http://sourceforge.net/tracker/?atid=428740&group_id=40728

Regards,
  baoilleach
  (on behalf of the OpenBabel development team)

Re: [OpenBabel-scripting] std::vector< OBInternalCoord * >

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

On Jun 28, 2007, at 11:54 PM, wr...@hu... wrote:

> Has the proper data structure been wrapped to another name or is it  
> missing?
> I appreciate any response, thank you.

No, at the moment, it's missing. If you have SWIG (1.3.30), you can  
easily regenerate the Python (or other) bindings.

You edit the openbabel-python.i file, look for the %template () lines  
and add something like:

%template (vectorpICoord)   vector<OBBInternalCoord *>

Then take a look at:
http://openbabel.sourceforge.net/wiki/Developer:Building

Cheers,
-Geoff

[OpenBabel-scripting] ANNOUNCE: Open Babel 2.1 Release

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

I am pleased to announce the release of Open Babel 2.1.1, the latest  
stable version of the open source chemistry toolbox.

This release represents a stable bug-fix release and is highly  
recommended for all users, even those who have not had problems with  
2.1.0. It includes fixes for several important crashes, and many,  
many bug fixes and improvements.

What's new? See the full release notes at:
http://openbabel.sourceforge.net/wiki/Open_Babel_2.1.1

To download, see:
http://sourceforge.net/project/showfiles.php? 
group_id=40728&package_id=32894&release_id=521581

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

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 and many thanks,
-Geoff

[OpenBabel-scripting] Some example code

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

I've posted some example Pybel code at:
http://baoilleach.blogspot.com/2007/07/pybel-just-how-unique-are-your.html

which shows how to analyse a dataset to look for unique molecules and
duplicates.

Regards,
   Noel

Re: [OpenBabel-scripting] ADME

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

On Jul 2, 2007, at 8:55 AM, Noel O'Boyle wrote:

> The attached Python file

...

That reminds me. We need to add another SVN trunk to the repository  
for contributed scripts.
http://openbabel.svn.sourceforge.net/viewvc/openbabel/contributed/trunk/

This will make it easier to gather up contributed C++, Python, Perl,  
etc. code and reference them from the wiki.

Cheers,
-Geoff

Re: [OpenBabel-scripting] Problem reading PDB with Python bindings under windows

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

On 02/07/07, Jens Thomas <j.m...@dl...> wrote:
> Hello,
>
> Sorry for not replying before, but I was away with no access to email.
>
> Neither of the files was compressed when I was using them - I only
> compressed them for sending them to the list.
>
>  From Noel's email it seems that the problem with PDB files has already
> been fixed, and so I presume that the next version of the windows
> binaries will be o.k.
>
> Is there a timetable for when new binaries will become available?

Well, if you're referring to the Python Windows module, it'll be after
the release of 2.1.1. Depending on whether there are any problems, it
should be within a week or two of that.

> I've tried to reproduce the error with the NWCHEM output, but can't and
> have absolutely no idea why.  I did confirm that it crashed several
> times before sending the email so I'm going to resort to the thoroughly
> lame excuse that it must just have been one of those gremlins that makes
> Windows such an entertaining platform to use... ;-)  Anyway, please
> accept my apologies for raising what seems to be a red herring.
>
> It's good to hear that other codes are making use of openbabel and that
> there are moves to increase support for quantum data - I look forward to
> trying them out when they become available.

> Best wishes,
>
> Jens
>
>
>
> Chris Morley wrote:
> > Are the input files compressed? The automatic decompression of gz files
> > is not active under Windows. The nwo file seems to work ok when
> > separately decompressed.
> > There may be a case for reactivating the decompression, because the
> > problem was with compression during output. I'll look again at this but
> > I doubt it would be ready for v2.1.1.
> > Chris
> >
> > Noel O'Boyle wrote:
> >
> >> The PDB issue seems to have been fixed by r1997:
> >>    http://cia.vc/stats/project/openbabel/.message/e0048
> >>
> >> I assume that the NW-Chem error is unrelated...
> >>
> >> On 25/06/07, Noel O'Boyle <bao...@gm...> wrote:
> >>
> >>> On 24/06/07, Geoffrey Hutchison <ge...@ge...> wrote:
> >>>
> >>>> On Jun 22, 2007, at 1:29 PM, Jens Thomas wrote:
> >>>>
> >>>>
> >>>>> I've successfully managed to port our CCP1GUI application to Open
> >>>>> Babel and it works fine under Linux and Mac. However, I'm currently
> >>>>> hitting rather a lot of segmentation violations when reading in
> >>>>> files on Windows.
> >>>>>
> >>>> ...
> >>>>
> >>>>> Changing the input format to 'nwo' and reading in the attached nw-
> >>>>> chem output file (optim_c6h6.nwo) also generates similar errors,
> >>>>> although a simple .xyz or .car file seems to work fine.
> >>>>>
> >>>>> Is this a known problem, or should I file this as a bug? I've
> >>>>> looked in Bugzilla and couldn't find anything, but it seemed such
> >>>>> an obvious problem that I was wondering if I wasn't missing
> >>>>> something somewhere.
> >>>>>
> >>>> I would qualify this as a clear bug. The scripting support on Windows
> >>>> is still quite new and has not received the same level of testing on
> >>>> Linux or Mac. (Noel uses Linux and I use Mac.)
> >>>>
> >>> I note that babel has the same error, so it is a general windows
> >>> issue, and not related to scripting...(P.S. I do use Windows too, but
> >>> the only test I run is reading and writing SMILES and SDF. In future,
> >>> we should get the full conversion test suite working on windows)
> >>>
> >>>
> >>>> So please, please file a bug report and provide whatever you can as
> >>>> far as a backtrace or debugging report.
> >>>>
> >>>> Thanks!
> >>>> -Geoff
> >>>>
> >>>> P.S. Glad to hear that CCP1GUI is using Open Babel. The GAMESS-US
> >>>> folks are partially funding a graduate student to improve support for
> >>>> quantum data, and Molekel has a few pending patches (for cubes, etc.)
> >>>> as well. Please forward any changes you have -- they'd be really
> >>>> appreciated.
> >>>>
> >>>> -------------------------------------------------------------------------
> >>>> This SF.net email is sponsored by DB2 Express
> >>>> Download DB2 Express C - the FREE version of DB2 express and take
> >>>> control of your XML. No limits. Just data. Click to get it now.
> >>>> http://sourceforge.net/powerbar/db2/
> >>>> _______________________________________________
> >>>> OpenBabel-scripting mailing list
> >>>> Ope...@li...
> >>>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >>>>
> >>>>
> >> -------------------------------------------------------------------------
> >> This SF.net email is sponsored by DB2 Express
> >> Download DB2 Express C - the FREE version of DB2 express and take
> >> control of your XML. No limits. Just data. Click to get it now.
> >> http://sourceforge.net/powerbar/db2/
> >> _______________________________________________
> >> OpenBabel-scripting mailing list
> >> Ope...@li...
> >> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >>
> >>
> >
> >
> > -------------------------------------------------------------------------
> > This SF.net email is sponsored by DB2 Express
> > Download DB2 Express C - the FREE version of DB2 express and take
> > control of your XML. No limits. Just data. Click to get it now.
> > http://sourceforge.net/powerbar/db2/
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
> >
>
>
> --
> ===================================================================
> Jens Thomas,                email:  j.m...@dl...
> STFC Daresbury Lab,         tel:    +44-1925-603849
> Warrington,                 fax:    +44-1925-603634
> WA4 4AD,  UK.               http:   http://www.cse.scitech.ac.uk
> ===================================================================
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] ADME

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

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Re: [OpenBabel-scripting] Problem reading PDB with Python bindings under windows

[Jens T. <j.m...@dl...>]

Hello,

Sorry for not replying before, but I was away with no access to email.

Neither of the files was compressed when I was using them - I only 
compressed them for sending them to the list.

 From Noel's email it seems that the problem with PDB files has already 
been fixed, and so I presume that the next version of the windows 
binaries will be o.k.

Is there a timetable for when new binaries will become available?

I've tried to reproduce the error with the NWCHEM output, but can't and 
have absolutely no idea why.  I did confirm that it crashed several 
times before sending the email so I'm going to resort to the thoroughly 
lame excuse that it must just have been one of those gremlins that makes 
Windows such an entertaining platform to use... ;-)  Anyway, please 
accept my apologies for raising what seems to be a red herring.

It's good to hear that other codes are making use of openbabel and that 
there are moves to increase support for quantum data - I look forward to 
trying them out when they become available.

Best wishes,

Jens



Chris Morley wrote:
> Are the input files compressed? The automatic decompression of gz files 
> is not active under Windows. The nwo file seems to work ok when 
> separately decompressed.
> There may be a case for reactivating the decompression, because the 
> problem was with compression during output. I'll look again at this but 
> I doubt it would be ready for v2.1.1.
> Chris
>
> Noel O'Boyle wrote:
>   
>> The PDB issue seems to have been fixed by r1997:
>>    http://cia.vc/stats/project/openbabel/.message/e0048
>>
>> I assume that the NW-Chem error is unrelated...
>>
>> On 25/06/07, Noel O'Boyle <bao...@gm...> wrote:
>>     
>>> On 24/06/07, Geoffrey Hutchison <ge...@ge...> wrote:
>>>       
>>>> On Jun 22, 2007, at 1:29 PM, Jens Thomas wrote:
>>>>
>>>>         
>>>>> I've successfully managed to port our CCP1GUI application to Open
>>>>> Babel and it works fine under Linux and Mac. However, I'm currently
>>>>> hitting rather a lot of segmentation violations when reading in
>>>>> files on Windows.
>>>>>           
>>>> ...
>>>>         
>>>>> Changing the input format to 'nwo' and reading in the attached nw-
>>>>> chem output file (optim_c6h6.nwo) also generates similar errors,
>>>>> although a simple .xyz or .car file seems to work fine.
>>>>>
>>>>> Is this a known problem, or should I file this as a bug? I've
>>>>> looked in Bugzilla and couldn't find anything, but it seemed such
>>>>> an obvious problem that I was wondering if I wasn't missing
>>>>> something somewhere.
>>>>>           
>>>> I would qualify this as a clear bug. The scripting support on Windows
>>>> is still quite new and has not received the same level of testing on
>>>> Linux or Mac. (Noel uses Linux and I use Mac.)
>>>>         
>>> I note that babel has the same error, so it is a general windows
>>> issue, and not related to scripting...(P.S. I do use Windows too, but
>>> the only test I run is reading and writing SMILES and SDF. In future,
>>> we should get the full conversion test suite working on windows)
>>>
>>>       
>>>> So please, please file a bug report and provide whatever you can as
>>>> far as a backtrace or debugging report.
>>>>
>>>> Thanks!
>>>> -Geoff
>>>>
>>>> P.S. Glad to hear that CCP1GUI is using Open Babel. The GAMESS-US
>>>> folks are partially funding a graduate student to improve support for
>>>> quantum data, and Molekel has a few pending patches (for cubes, etc.)
>>>> as well. Please forward any changes you have -- they'd be really
>>>> appreciated.
>>>>
>>>> -------------------------------------------------------------------------
>>>> This SF.net email is sponsored by DB2 Express
>>>> Download DB2 Express C - the FREE version of DB2 express and take
>>>> control of your XML. No limits. Just data. Click to get it now.
>>>> http://sourceforge.net/powerbar/db2/
>>>> _______________________________________________
>>>> OpenBabel-scripting mailing list
>>>> Ope...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>>>
>>>>         
>> -------------------------------------------------------------------------
>> This SF.net email is sponsored by DB2 Express
>> Download DB2 Express C - the FREE version of DB2 express and take
>> control of your XML. No limits. Just data. Click to get it now.
>> http://sourceforge.net/powerbar/db2/
>> _______________________________________________
>> OpenBabel-scripting mailing list
>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>
>>     
>
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>   


-- 
===================================================================
Jens Thomas,                email:  j.m...@dl...
STFC Daresbury Lab,         tel:    +44-1925-603849
Warrington,                 fax:    +44-1925-603634
WA4 4AD,  UK.               http:   http://www.cse.scitech.ac.uk
===================================================================

Re: [OpenBabel-scripting] ADME

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

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[OpenBabel-scripting] ADME

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

SGkgYWxsCgpJIHdvdWxkIGxpa2UgdG8ga25vdyB3aGF0IGlzIE9wZW5CYWJlbCdzIGNhcGFiaWxp
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dXRpL3Npb25nL2R1w6wgecO6L9C/0YDQuNCy0LXRggoKSnVyZ2VucyBkZSBCcnVpbgo=

[OpenBabel-scripting] std::vector< OBInternalCoord * >

[<wr...@hu...>]

I was attempting to access the function CartesianToInternal with the
python binding to openbabel. This function has been wrapped, however it
requires a vector of internal coordinate objects. I cannot seem to find a
corresponding vectorInternals object in the bindings. The vector classes
that currently ship with the binding (vers. 1.2) are:
vector3
vectorAngle
vectorBond
vectorData
vectorDouble
vectorInt
vectorMol
vectorResidue
vectorRing
vectorUnsignedInt
Has the proper data structure been wrapped to another name or is it missing?
I appreciate any response, thank you.
     Wilton Wilson

Re: [OpenBabel-scripting] Problem reading PDB with Python bindings under windows

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

Are the input files compressed? The automatic decompression of gz files 
is not active under Windows. The nwo file seems to work ok when 
separately decompressed.
There may be a case for reactivating the decompression, because the 
problem was with compression during output. I'll look again at this but 
I doubt it would be ready for v2.1.1.
Chris

Noel O'Boyle wrote:
> The PDB issue seems to have been fixed by r1997:
>    http://cia.vc/stats/project/openbabel/.message/e0048
> 
> I assume that the NW-Chem error is unrelated...
> 
> On 25/06/07, Noel O'Boyle <bao...@gm...> wrote:
>> On 24/06/07, Geoffrey Hutchison <ge...@ge...> wrote:
>>> On Jun 22, 2007, at 1:29 PM, Jens Thomas wrote:
>>>
>>>> I've successfully managed to port our CCP1GUI application to Open
>>>> Babel and it works fine under Linux and Mac. However, I'm currently
>>>> hitting rather a lot of segmentation violations when reading in
>>>> files on Windows.
>>> ...
>>>> Changing the input format to 'nwo' and reading in the attached nw-
>>>> chem output file (optim_c6h6.nwo) also generates similar errors,
>>>> although a simple .xyz or .car file seems to work fine.
>>>>
>>>> Is this a known problem, or should I file this as a bug? I've
>>>> looked in Bugzilla and couldn't find anything, but it seemed such
>>>> an obvious problem that I was wondering if I wasn't missing
>>>> something somewhere.
>>> I would qualify this as a clear bug. The scripting support on Windows
>>> is still quite new and has not received the same level of testing on
>>> Linux or Mac. (Noel uses Linux and I use Mac.)
>> I note that babel has the same error, so it is a general windows
>> issue, and not related to scripting...(P.S. I do use Windows too, but
>> the only test I run is reading and writing SMILES and SDF. In future,
>> we should get the full conversion test suite working on windows)
>>
>>> So please, please file a bug report and provide whatever you can as
>>> far as a backtrace or debugging report.
>>>
>>> Thanks!
>>> -Geoff
>>>
>>> P.S. Glad to hear that CCP1GUI is using Open Babel. The GAMESS-US
>>> folks are partially funding a graduate student to improve support for
>>> quantum data, and Molekel has a few pending patches (for cubes, etc.)
>>> as well. Please forward any changes you have -- they'd be really
>>> appreciated.
>>>
>>> -------------------------------------------------------------------------
>>> This SF.net email is sponsored by DB2 Express
>>> Download DB2 Express C - the FREE version of DB2 express and take
>>> control of your XML. No limits. Just data. Click to get it now.
>>> http://sourceforge.net/powerbar/db2/
>>> _______________________________________________
>>> OpenBabel-scripting mailing list
>>> Ope...@li...
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>>
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> 

Re: [OpenBabel-scripting] Problem reading PDB with Python bindings under windows

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

The PDB issue seems to have been fixed by r1997:
   http://cia.vc/stats/project/openbabel/.message/e0048

I assume that the NW-Chem error is unrelated...

On 25/06/07, Noel O'Boyle <bao...@gm...> wrote:
> On 24/06/07, Geoffrey Hutchison <ge...@ge...> wrote:
> >
> > On Jun 22, 2007, at 1:29 PM, Jens Thomas wrote:
> >
> > > I've successfully managed to port our CCP1GUI application to Open
> > > Babel and it works fine under Linux and Mac. However, I'm currently
> > > hitting rather a lot of segmentation violations when reading in
> > > files on Windows.
> > ...
> > > Changing the input format to 'nwo' and reading in the attached nw-
> > > chem output file (optim_c6h6.nwo) also generates similar errors,
> > > although a simple .xyz or .car file seems to work fine.
> > >
> > > Is this a known problem, or should I file this as a bug? I've
> > > looked in Bugzilla and couldn't find anything, but it seemed such
> > > an obvious problem that I was wondering if I wasn't missing
> > > something somewhere.
> >
> > I would qualify this as a clear bug. The scripting support on Windows
> > is still quite new and has not received the same level of testing on
> > Linux or Mac. (Noel uses Linux and I use Mac.)
>
> I note that babel has the same error, so it is a general windows
> issue, and not related to scripting...(P.S. I do use Windows too, but
> the only test I run is reading and writing SMILES and SDF. In future,
> we should get the full conversion test suite working on windows)
>
> > So please, please file a bug report and provide whatever you can as
> > far as a backtrace or debugging report.
> >
> > Thanks!
> > -Geoff
> >
> > P.S. Glad to hear that CCP1GUI is using Open Babel. The GAMESS-US
> > folks are partially funding a graduate student to improve support for
> > quantum data, and Molekel has a few pending patches (for cubes, etc.)
> > as well. Please forward any changes you have -- they'd be really
> > appreciated.
> >
> > -------------------------------------------------------------------------
> > This SF.net email is sponsored by DB2 Express
> > Download DB2 Express C - the FREE version of DB2 express and take
> > control of your XML. No limits. Just data. Click to get it now.
> > http://sourceforge.net/powerbar/db2/
> > _______________________________________________
> > OpenBabel-scripting mailing list
> > Ope...@li...
> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
> >
>

Re: [OpenBabel-scripting] Segmentation fault

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

On Jun 25, 2007, at 4:28 AM, Pascoe, S (Stephen) wrote:

> I came across this myself the other week.  It is a known bug in  
> 2.1.0 and you can fix it with a small patch.  See the bug report at:

And it's worth mentioning that a 2.1.1 release will come out very  
soon to address this bug and others.

Cheers,
-Geoff

Re: [OpenBabel-scripting] Problem reading PDB with Python bindings under windows

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

On 24/06/07, Geoffrey Hutchison <ge...@ge...> wrote:
>
> On Jun 22, 2007, at 1:29 PM, Jens Thomas wrote:
>
> > I've successfully managed to port our CCP1GUI application to Open
> > Babel and it works fine under Linux and Mac. However, I'm currently
> > hitting rather a lot of segmentation violations when reading in
> > files on Windows.
> ...
> > Changing the input format to 'nwo' and reading in the attached nw-
> > chem output file (optim_c6h6.nwo) also generates similar errors,
> > although a simple .xyz or .car file seems to work fine.
> >
> > Is this a known problem, or should I file this as a bug? I've
> > looked in Bugzilla and couldn't find anything, but it seemed such
> > an obvious problem that I was wondering if I wasn't missing
> > something somewhere.
>
> I would qualify this as a clear bug. The scripting support on Windows
> is still quite new and has not received the same level of testing on
> Linux or Mac. (Noel uses Linux and I use Mac.)

I note that babel has the same error, so it is a general windows
issue, and not related to scripting...(P.S. I do use Windows too, but
the only test I run is reading and writing SMILES and SDF. In future,
we should get the full conversion test suite working on windows)

> So please, please file a bug report and provide whatever you can as
> far as a backtrace or debugging report.
>
> Thanks!
> -Geoff
>
> P.S. Glad to hear that CCP1GUI is using Open Babel. The GAMESS-US
> folks are partially funding a graduate student to improve support for
> quantum data, and Molekel has a few pending patches (for cubes, etc.)
> as well. Please forward any changes you have -- they'd be really
> appreciated.
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
> http://sourceforge.net/powerbar/db2/
> _______________________________________________
> OpenBabel-scripting mailing list
> Ope...@li...
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>

Re: [OpenBabel-scripting] Segmentation fault

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

I came across this myself the other week.  It is a known bug in 2.1.0 =
and you can fix it with a small patch.  See the bug report at:

https://sourceforge.net/tracker/index.php?func=3Ddetail&aid=3D1720529&gro=
up_id=3D40728&atid=3D428740=20

Or go straight to the patch at:

http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/branches/=
openbabel-2-1-x/src/formats/inchiformat.cpp?r1=3D1893&r2=3D1933

Cheers,
Stephen.


---
Stephen Pascoe  +44 (0)1235 445980
British Atmospheric Data Centre
Rutherford Appleton Laboratory

-----Original Message-----
From: ope...@li... =
[mailto:ope...@li...] On Behalf Of =
Luis Figueiredo
Sent: 31 May 2007 09:35
To: ope...@li...
Subject: [OpenBabel-scripting] Segmentation fault

Hello,

I'm using Open Babel 2.1.0 to convert the structure of molecules in cml =
format to inchi or to smi in order to cross-check information. I started =
to write a simple script in Perl (Perl  5.8.8) to read a file containing =
the structures of several compounds and convert them to inchi.  But I =
got a "Segmentation fault" error message after running the script using =
as input a file containing a single structure. Then I tried to convert =
the structure inside this file using babel command and it worked good, =
without any error.

After some debugging process I did not find the solution for this =
problem and I decided to move to Python (Python 2.5).  Then I wrote a =
simple script to do the same thing:

#  #!/usr/bin/python
#
#  import openbabel
#  import sys
#  import re
#
#  file =3D sys.argv[1]
#  infile =3D open(file,"r")
#
#  while infile:
#     line =3D infile.readline()
#    if re.search("<molecule",line):
#          molecule =3D line
#     elif re.search("</molecule",line):
#          molecule +=3D line
#          obConversion =3D openbabel.OBConversion()
#          obConversion.SetInAndOutFormats("cml", "inchi")
#          mol =3D openbabel.OBMol()
#          obConversion.ReadString(mol, molecule)
#          outMDL =3D obConversion.WriteString(mol)
#          print outMDL
#          break
#      elif len (molecule) > 1:
#          molecule +=3D line

But the result is the same a "Segmentation fault" error. I can get the =
right conversion as in Perl but the script breaks after one conversion.
I can convert everything using a temporary file and convert it using the =
command line, though it would be a brute force approach that I want to =
avoid.

Best greetings

Lu=EDs Figueiredo



-------------------------------------------------------------------------=

This SF.net email is sponsored by DB2 Express Download DB2 Express C - =
the FREE version of DB2 express and take control of your XML. No limits. =
Just data. Click to get it now.
http://sourceforge.net/powerbar/db2/
_______________________________________________
OpenBabel-scripting mailing list
Ope...@li...
https://lists.sourceforge.net/lists/listinfo/openbabel-scripting

Re: [OpenBabel-scripting] Problem reading PDB with Python bindings under windows

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

On Jun 22, 2007, at 1:29 PM, Jens Thomas wrote:

> I've successfully managed to port our CCP1GUI application to Open  
> Babel and it works fine under Linux and Mac. However, I'm currently  
> hitting rather a lot of segmentation violations when reading in  
> files on Windows.
...
> Changing the input format to 'nwo' and reading in the attached nw- 
> chem output file (optim_c6h6.nwo) also generates similar errors,  
> although a simple .xyz or .car file seems to work fine.
>
> Is this a known problem, or should I file this as a bug? I've  
> looked in Bugzilla and couldn't find anything, but it seemed such  
> an obvious problem that I was wondering if I wasn't missing  
> something somewhere.

I would qualify this as a clear bug. The scripting support on Windows  
is still quite new and has not received the same level of testing on  
Linux or Mac. (Noel uses Linux and I use Mac.)

So please, please file a bug report and provide whatever you can as  
far as a backtrace or debugging report.

Thanks!
-Geoff

P.S. Glad to hear that CCP1GUI is using Open Babel. The GAMESS-US  
folks are partially funding a graduate student to improve support for  
quantum data, and Molekel has a few pending patches (for cubes, etc.)  
as well. Please forward any changes you have -- they'd be really  
appreciated.

[OpenBabel-scripting] Problem reading PDB with Python bindings under windows

[Jens T. <j.m...@dl...>]

Hi,

I've successfully managed to port our CCP1GUI application to Open Babel 
and it works fine under Linux and Mac. However, I'm currently hitting 
rather a lot of segmentation violations when reading in files on Windows.

The windows box I'm using is a pentium machine with the latest version 
of Enthought Python 
(http://code.enthought.com/downloads/enthon-python2.4-1.0.0.exe) on it, 
as well as the latest OpenBabel windows gui 
(http://downloads.sourceforge.net/openbabel/OpenBabel2.1.0c_Windows_Installer.exe) 
and python 2.4 bindings 
(http://downloads.sourceforge.net/openbabel/openbabel-python-1.2.py2.4.exe)

Reading in the attached pdb file (caffeine.pdb) crashes the following 
python code:

<code>
import openbabel

filepath='caffeine.pdb'

obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("pdb", "mol2")

mol = openbabel.OBMol()
obConversion.ReadFile(mol, filepath)
</code>

Some information on the error that's generated is:

AppName: python.exe     AppVer: 0.0.0.0         ModName: msvcr80.dll
ModVer: 8.0.50727.762   Offset: 00008a8c

Changing the input format to 'nwo' and reading in the attached nw-chem 
output file (optim_c6h6.nwo) also generates similar errors, although a 
simple .xyz or .car file seems to work fine.

Is this a known problem, or should I file this as a bug? I've looked in 
Bugzilla and couldn't find anything, but it seemed such an obvious 
problem that I was wondering if I wasn't missing something somewhere.

Best wishes,

Jens


-- 
===================================================================
Jens Thomas,                email:  j.m...@dl...
STFC Daresbury Lab,         tel:    +44-1925-603849
Warrington,                 fax:    +44-1925-603634
WA4 4AD,  UK.               http:   http://www.cse.scitech.ac.uk
===================================================================

Re: [OpenBabel-scripting] 2D -3D conversion of large datasets

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

It's not possible to generate 3D coordinates from 2D information using
OpenBabel, although babel will happily convert from SMILES to SDF.
It's not possible to use OpenBabel to derive the IUPAC name for a
compound.

Noel

On 21/06/07, an...@av... <an...@av...> wrote:
> Greetings to all
>
> Dear subscribers,
>
> I am interested in knowing the module and name that is required for
> conersion of 2D structure to their 3d formats.Also can I use openbabel to
> name the compounds that I have in the form of a sdf file.
>
>
> Regards
> Anand
>
>
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Re: [OpenBabel-scripting] 2D -3D conversion of large datasets

[<an...@av...>]

Greetings to all

Dear subscribers,

I am interested in knowing the module and name that is required for
conersion of 2D structure to their 3d formats.Also can I use openbabel to
name the compounds that I have in the form of a sdf file.


Regards
Anand

Re: [OpenBabel-scripting] Counting H-bond Donors and Acceptors within a molecule

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

On Jun 15, 2007, at 4:16 AM, markus wrote:

> I searched the OpenBabel Documentation and found, that polar surface
> area is allready implemented as property of a Molecule oject.
...
> Isn't there already a routine to count the number of Donors and
> Acceptors within a Molecule?

There isn't a direct routine, since it's a property for OBAtom.
http://openbabel.sourceforge.net/api/2.1.0/ 
classOpenBabel_1_1OBAtom.shtml#63e02252214e540d56815820715f1ae3

OBAtom::IsHBondDonor()
OBAtom::IsHBondAcceptor()

> If not I should try to do that by smarts matching, i think?

You can always do this, of course. :-)

Cheers,
-Geoff

[OpenBabel-scripting] Counting H-bond Donors and Acceptors within a molecule

[markus <m.k...@tu...>]

Dear babelers,

I'm  quite new to programming as I am actually a pharmacist, but I have 
a quite common problem, as I think:
I want to calculate simple properties of a Molecule, i.e. H bond Donor 
count, H bond Acceptor count, polar surface area...

I searched the OpenBabel Documentation and found, that polar surface 
area is allready implemented as property of a Molecule oject.
Isn't there already a routine to count the number of Donors and 
Acceptors within a Molecule?

If not I should try to do that by smarts matching, i think?

Thannks in advance,

Markus

[OpenBabel-scripting] ANN: openbabel-python 1.2 for Windows

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

Announcing the release of the OpenBabel module for Python, version
1.2, for Windows, available from
http://openbabel.sourceforge.net/wiki/Install.

OpenBabel is a chemical toolbox designed to speak the many languages
of chemical data. It's an open, collaborative project allowing anyone
to search, convert, analyze, or store data from molecular modeling,
chemistry, solid-state materials, biochemistry, or related areas. This
Python module allows you to access this popular C++ library in your
Python scripts.

New features:
(1) Data fields in file formats like MOL2 and SDF can now be accessed and edited
(2) Unit cell data in crystallographic file formats such as CIF can
now be accessed
(3) A list of all detected input and output file formats can be accessed

Core features:
(1) Read and write over 80 molecular file formats
(2) Access molecular properties like molecular weight, formula, charge
(3) Daylight-type fingerprints and calculation of the Tanimoto coefficient
(4) SMARTS pattern matching
(5) Graph algorithms such as the Smallest Set of Smallest Rings (SSSR)
and Depth-First Iteration over atoms

Documentation:
(1) The Python module: http://openbabel.sourceforge.net/wiki/Python
(2) The C++ toolkit: http://openbabel.sourceforge.net/api/2.1.0/index.shtml
(3) The OpenBabel web site: http://openbabel.sourceforge.net

Support:
(1) If you have any questions, send an email to
ope...@li...
(2) Report a bug at http://sourceforge.net/tracker/?atid=428740&group_id=40728

Regards,
   baoilleach
   (on behalf of the OpenBabel development team)

P.S. The Python module is also available for Linux and MacOSX. It is
also possible to use OpenBabel from C++, Perl, Ruby and Java, although
getting these to work on Windows may be more difficult.