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From: Jens T. <j.m...@dl...> - 2007-06-22 17:29:54
Attachments:
optim_c6h6.nwo.gz
caffeine.pdb.gz
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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 =================================================================== |
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From: Geoffrey H. <ge...@ge...> - 2007-06-24 19:59:11
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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. |
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From: Noel O'B. <bao...@gm...> - 2007-06-25 09:35:42
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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 > |
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From: Noel O'B. <bao...@gm...> - 2007-06-28 15:58:04
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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 > > > |
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From: Chris M. <c.m...@ds...> - 2007-06-28 16:23:28
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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 > |
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From: Jens T. <j.m...@dl...> - 2007-07-02 12:34:48
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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 =================================================================== |
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From: Noel O'B. <bao...@gm...> - 2007-07-02 19:29:39
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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 > |
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