From: DeVill <de...@cs...> - 2007-03-09 13:26:06
|
Hi! I would like to use direct mysql connection to a database in a plugin. = Can you please tell me if there is a way to add MySQLdb module to PyMOL? = if yes, then how? Bye DeVill |
From: Jerome P. <j.p...@pa...> - 2007-03-09 13:58:36
|
Hi, Take a look on this plugin: http://pymol-plugins.sourceforge.net/dbsearch.html Cheers, Jerome Pansanel Le vendredi 9 mars 2007 14:24, DeVill a =C3=A9crit=C2=A0: > Hi! > > I would like to use direct mysql connection to a database in a plugin. Can > you please tell me if there is a way to add MySQLdb module to PyMOL? if > yes, then how? > > Bye > DeVill |
From: DeVill <dev...@gm...> - 2007-03-09 14:22:39
|
Hi! I end up with the same problem. Just like this plugin i tried: import MySQLdb but I get this error message, when starting up pymol: Exception in plugin 'dbsearch' -- Traceback follows... Traceback (most recent call last): File "C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\PMGApp.py", line 156, in initialize_plugins __builtin__.__import__(mod_name) File "C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\startup\dbsearch.py", line 54, in ? import MySQLdb ImportError: No module named MySQLdb Error: unable to initialize plugin 'dbsearch'. Bye DeVill 2007/3/9, Jerome Pansanel <j.p...@pa...>: > > Hi, > > Take a look on this plugin: > http://pymol-plugins.sourceforge.net/dbsearch.html > > Cheers, > > Jerome Pansanel > > Le vendredi 9 mars 2007 14:24, DeVill a =E9crit: > > Hi! > > > > I would like to use direct mysql connection to a database in a plugin. > Can > > you please tell me if there is a way to add MySQLdb module to PyMOL? if > > yes, then how? > > > > Bye > > DeVill > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDEV > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Jerome P. <j.p...@pa...> - 2007-03-09 16:13:52
|
Hi, You can get MySQL python from here: http://sourceforge.net/projects/mysql-python Jerome Le vendredi 9 mars 2007 15:22, DeVill a =C3=A9crit=C2=A0: > Hi! > > I end up with the same problem. Just like this plugin i tried: > import MySQLdb > > but I get this error message, when starting up pymol: > > Exception in plugin 'dbsearch' -- Traceback follows... > Traceback (most recent call last): > File "C:\Program Files\DeLano Scientific\PyMOL/modules\pmg_tk\PMGApp.py= ", > line 156, in initialize_plugins > __builtin__.__import__(mod_name) > File "C:\Program Files\DeLano > Scientific\PyMOL/modules\pmg_tk\startup\dbsearch.py", line 54, in ? > import MySQLdb > ImportError: No module named MySQLdb > Error: unable to initialize plugin 'dbsearch'. > > Bye > DeVill > > 2007/3/9, Jerome Pansanel <j.p...@pa...>: > > Hi, > > > > Take a look on this plugin: > > http://pymol-plugins.sourceforge.net/dbsearch.html > > > > Cheers, > > > > Jerome Pansanel > > > > Le vendredi 9 mars 2007 14:24, DeVill a =C3=A9crit: > > > Hi! > > > > > > I would like to use direct mysql connection to a database in a plugin. > > > > Can > > > > > you please tell me if there is a way to add MySQLdb module to PyMOL? = if > > > yes, then how? > > > > > > Bye > > > DeVill > > > > -----------------------------------------------------------------------= =2D- > > Take Surveys. Earn Cash. Influence the Future of IT > > Join SourceForge.net's Techsay panel and you'll get the chance to share > > your > > opinions on IT & business topics through brief surveys-and earn cash > > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID= =3DDEVDEV > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: DeVill <dev...@gm...> - 2007-03-09 18:54:38
|
Hi! I know that as well... what I don't know is how to install it under PyMOL. If I were using simply python, than that would be no big deal, I did that a 1000 times: setup.py --build; setup.py --intall Presently I'm using the windows version of PyMol, and installing a separate python interpreter, and installing MySQLdb module didn't help. When I tried to start PyMOL and enter into command line: run setup.py --build, it didn't work as well, as it wants to find the file = " setup.py --build". Any other ideas? Thnx DeVill 2007/3/9, Jerome Pansanel <j.p...@pa...>: > > Hi, > > You can get MySQL python from here: > http://sourceforge.net/projects/mysql-python > > Jerome > > Le vendredi 9 mars 2007 15:22, DeVill a =E9crit: > > Hi! > > > > I end up with the same problem. Just like this plugin i tried: > > import MySQLdb > > > > but I get this error message, when starting up pymol: > > > > Exception in plugin 'dbsearch' -- Traceback follows... > > Traceback (most recent call last): > > File "C:\Program Files\DeLano > Scientific\PyMOL/modules\pmg_tk\PMGApp.py", > > line 156, in initialize_plugins > > __builtin__.__import__(mod_name) > > File "C:\Program Files\DeLano > > Scientific\PyMOL/modules\pmg_tk\startup\dbsearch.py", line 54, in ? > > import MySQLdb > > ImportError: No module named MySQLdb > > Error: unable to initialize plugin 'dbsearch'. > > > > Bye > > DeVill > > > > 2007/3/9, Jerome Pansanel <j.p...@pa...>: > > > Hi, > > > > > > Take a look on this plugin: > > > http://pymol-plugins.sourceforge.net/dbsearch.html > > > > > > Cheers, > > > > > > Jerome Pansanel > > > > > > Le vendredi 9 mars 2007 14:24, DeVill a =E9crit: > > > > Hi! > > > > > > > > I would like to use direct mysql connection to a database in a > plugin. > > > > > > Can > > > > > > > you please tell me if there is a way to add MySQLdb module to PyMOL= ? > if > > > > yes, then how? > > > > > > > > Bye > > > > DeVill > > > > > > > ------------------------------------------------------------------------- > > > Take Surveys. Earn Cash. Influence the Future of IT > > > Join SourceForge.net's Techsay panel and you'll get the chance to > share > > > your > > > opinions on IT & business topics through brief surveys-and earn cash > > > > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDEV > > > _______________________________________________ > > > PyMOL-users mailing list > > > PyM...@li... > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDEV > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Jerome P. <j.p...@pa...> - 2007-03-09 19:08:08
|
Try to copy MySQLdb into: C:\Program Files\DeLano Scientific\PyMOL\py24\Lib\site-packages\ Jerome Pansanel Le vendredi 9 mars 2007 19:54, DeVill a =C3=A9crit=C2=A0: > Hi! > > I know that as well... what I don't know is how to install it under PyMOL. > If I were using simply python, than that would be no big deal, I did that= a > 1000 times: setup.py --build; setup.py --intall > > Presently I'm using the windows version of PyMol, and installing a separa= te > python interpreter, and installing MySQLdb module didn't help. When I tri= ed > to start PyMOL and enter into command line: > run setup.py --build, it didn't work as well, as it wants to find the file > " setup.py --build". > > Any other ideas? > > Thnx > DeVill > > 2007/3/9, Jerome Pansanel <j.p...@pa...>: > > Hi, > > > > You can get MySQL python from here: > > http://sourceforge.net/projects/mysql-python > > > > Jerome > > > > Le vendredi 9 mars 2007 15:22, DeVill a =C3=A9crit: > > > Hi! > > > > > > I end up with the same problem. Just like this plugin i tried: > > > import MySQLdb > > > > > > but I get this error message, when starting up pymol: > > > > > > Exception in plugin 'dbsearch' -- Traceback follows... > > > Traceback (most recent call last): > > > File "C:\Program Files\DeLano > > > > Scientific\PyMOL/modules\pmg_tk\PMGApp.py", > > > > > line 156, in initialize_plugins > > > __builtin__.__import__(mod_name) > > > File "C:\Program Files\DeLano > > > Scientific\PyMOL/modules\pmg_tk\startup\dbsearch.py", line 54, in ? > > > import MySQLdb > > > ImportError: No module named MySQLdb > > > Error: unable to initialize plugin 'dbsearch'. > > > > > > Bye > > > DeVill > > > > > > 2007/3/9, Jerome Pansanel <j.p...@pa...>: > > > > Hi, > > > > > > > > Take a look on this plugin: > > > > http://pymol-plugins.sourceforge.net/dbsearch.html > > > > > > > > Cheers, > > > > > > > > Jerome Pansanel > > > > > > > > Le vendredi 9 mars 2007 14:24, DeVill a =C3=A9crit: > > > > > Hi! > > > > > > > > > > I would like to use direct mysql connection to a database in a > > > > plugin. > > > > > > Can > > > > > > > > > you please tell me if there is a way to add MySQLdb module to > > > > > PyMOL? > > > > if > > > > > > > yes, then how? > > > > > > > > > > Bye > > > > > DeVill > > > > -----------------------------------------------------------------------= =2D- > > > > > > Take Surveys. Earn Cash. Influence the Future of IT > > > > Join SourceForge.net's Techsay panel and you'll get the chance to > > > > share > > > > > > your > > > > opinions on IT & business topics through brief surveys-and earn cash > > > > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID= =3DDEVDEV > > > > > > _______________________________________________ > > > > PyMOL-users mailing list > > > > PyM...@li... > > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > -----------------------------------------------------------------------= =2D- > > Take Surveys. Earn Cash. Influence the Future of IT > > Join SourceForge.net's Techsay panel and you'll get the chance to share > > your > > opinions on IT & business topics through brief surveys-and earn cash > > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID= =3DDEVDEV > > _______________________________________________ > > PyMOL-users mailing list > > PyM...@li... > > https://lists.sourceforge.net/lists/listinfo/pymol-users |
From: DeVill <dev...@gm...> - 2007-03-09 19:16:55
|
Also tried it :-) 2007/3/9, Jerome Pansanel <j.p...@pa...>: > > Try to copy MySQLdb into: > C:\Program Files\DeLano Scientific\PyMOL\py24\Lib\site-packages\ > > Jerome Pansanel > > Le vendredi 9 mars 2007 19:54, DeVill a =E9crit: > > Hi! > > > > I know that as well... what I don't know is how to install it under > PyMOL. > > If I were using simply python, than that would be no big deal, I did > that a > > 1000 times: setup.py --build; setup.py --intall > > > > Presently I'm using the windows version of PyMol, and installing a > separate > > python interpreter, and installing MySQLdb module didn't help. When I > tried > > to start PyMOL and enter into command line: > > run setup.py --build, it didn't work as well, as it wants to find the > file > > " setup.py --build". > > > > Any other ideas? > > > > Thnx > > DeVill > > > > 2007/3/9, Jerome Pansanel <j.p...@pa...>: > > > Hi, > > > > > > You can get MySQL python from here: > > > http://sourceforge.net/projects/mysql-python > > > > > > Jerome > > > > > > Le vendredi 9 mars 2007 15:22, DeVill a =E9crit: > > > > Hi! > > > > > > > > I end up with the same problem. Just like this plugin i tried: > > > > import MySQLdb > > > > > > > > but I get this error message, when starting up pymol: > > > > > > > > Exception in plugin 'dbsearch' -- Traceback follows... > > > > Traceback (most recent call last): > > > > File "C:\Program Files\DeLano > > > > > > Scientific\PyMOL/modules\pmg_tk\PMGApp.py", > > > > > > > line 156, in initialize_plugins > > > > __builtin__.__import__(mod_name) > > > > File "C:\Program Files\DeLano > > > > Scientific\PyMOL/modules\pmg_tk\startup\dbsearch.py", line 54, in ? > > > > import MySQLdb > > > > ImportError: No module named MySQLdb > > > > Error: unable to initialize plugin 'dbsearch'. > > > > > > > > Bye > > > > DeVill > > > > > > > > 2007/3/9, Jerome Pansanel <j.p...@pa...>: > > > > > Hi, > > > > > > > > > > Take a look on this plugin: > > > > > http://pymol-plugins.sourceforge.net/dbsearch.html > > > > > > > > > > Cheers, > > > > > > > > > > Jerome Pansanel > > > > > > > > > > Le vendredi 9 mars 2007 14:24, DeVill a =E9crit: > > > > > > Hi! > > > > > > > > > > > > I would like to use direct mysql connection to a database in a > > > > > > plugin. > > > > > > > > Can > > > > > > > > > > > you please tell me if there is a way to add MySQLdb module to > > > > > > PyMOL? > > > > > > if > > > > > > > > > yes, then how? > > > > > > > > > > > > Bye > > > > > > DeVill > > > > > > > ------------------------------------------------------------------------- > > > > > > > > Take Surveys. Earn Cash. Influence the Future of IT > > > > > Join SourceForge.net's Techsay panel and you'll get the chance to > > > > > > share > > > > > > > > your > > > > > opinions on IT & business topics through brief surveys-and earn > cash > > > > > > > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDEV > > > > > > > > _______________________________________________ > > > > > PyMOL-users mailing list > > > > > PyM...@li... > > > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > ------------------------------------------------------------------------- > > > Take Surveys. Earn Cash. Influence the Future of IT > > > Join SourceForge.net's Techsay panel and you'll get the chance to > share > > > your > > > opinions on IT & business topics through brief surveys-and earn cash > > > > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDEV > > > _______________________________________________ > > > PyMOL-users mailing list > > > PyM...@li... > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDEV > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users > |
From: Peter A. M. <pa...@co...> - 2007-03-09 21:24:13
|
> I know that as well... what I don't know is how to install it under PyMOL. > If I were using simply python, than that would be no big deal, I did that > a > 1000 times: setup.py --build; setup.py --intall > > Presently I'm using the windows version of PyMol, and installing a > separate > python interpreter, and installing MySQLdb module didn't help. When I > tried > to start PyMOL and enter into command line: > run setup.py --build, it didn't work as well, as it wants to find the file > " > setup.py --build". If I'm understanding the situation correctly, you're trying to get MySQLdb into the pymol python, not the seperate python installation. And if there's a seperate python.exe in the windows pymol install, you've probably tried that already (there may not be one with the windows pymol binary). When you try to run setup.py with arguments from the pymol python intpreter, it intprets the arguments as a filename. Have you tried re-setting sys.argv before running setup (aka sys.argv=['setup.py','--build'] ; run setup.py,local )? If I'm understanding the help for the pymol run command correctly, you'd want to use either local or module (so that the global namespace doesn't confuse things). This may do strange things to your pymol install, and might not work, but it seems like it would be worth a try. Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University |
From: DeVill <dev...@gm...> - 2007-03-09 23:18:41
|
Have you tried re-setting sys.argv before running setup (aka sys.argv=['setup.py','--build'] ; run setup.py,local )? If I'm understanding the help for the pymol run command correctly, you'd want to use either local or module (so that the global namespace doesn't confuse things). This may do strange things to your pymol install, and might not work, but it seems like it would be worth a try. |
From: DeVill <dev...@gm...> - 2007-03-09 23:21:15
|
> > Have you tried re-setting sys.argv before running setup (aka > sys.argv=['setup.py','--build'] ; run setup.py,local )? If I'm > understanding the help for the pymol run command correctly, you'd want to > use either local or module (so that the global namespace doesn't confuse > things). Now that finaly got me closer to the solution! :-) This way I could start the setup.py installation. Thx! But now I'm facing another problem: PyMOL>sys.argv=['setup.py','build'] PyMOL>run setup.py, local running build running build_py copying MySQLdb\release.py -> build\lib.win32-2.4\MySQLdb running build_ext Traceback (most recent call last): File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py", line 291, in parse parsing.run_file(exp_path(args[nest][0]),pymol_names,{}) File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parsing.py", line 407, in run_file execfile(file,global_ns,local_ns) File "setup.py", line 19, in ? setup(**metadata) File "C:\Program Files\DeLano Scientific\PyMOL\py24\lib\distutils\core.py", line 166, in setup raise SystemExit, "error: " + str(msg) SystemExit: error: The .NET Framework SDK needs to be installed before building extensions for Python. Where should I install the .NET Framework? Bye DeVill P.S.: sorry for the previous empty E-mail... my client mesd things up a bit :-* |
From: DeVill <dev...@gm...> - 2007-03-10 16:45:01
|
2007/3/10, DeVill <dev...@gm...>: > > Have you tried re-setting sys.argv before running setup (aka > > sys.argv=['setup.py','--build'] ; run setup.py,local )? If I'm > > understanding the help for the pymol run command correctly, you'd want > > to > > use either local or module (so that the global namespace doesn't confuse > > things). > > > Now that finaly got me closer to the solution! :-) This way I could start > the setup.py installation. Thx! > > But now I'm facing another problem: > > PyMOL>sys.argv=['setup.py','build'] > PyMOL>run setup.py, local > running build > running build_py > copying MySQLdb\release.py -> build\lib.win32-2.4\MySQLdb > running build_ext > Traceback (most recent call last): > File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py", > line 291, in parse > parsing.run_file(exp_path(args[nest][0]),pymol_names,{}) > File "C:\Program Files\DeLano > Scientific\PyMOL/modules\pymol\parsing.py", line 407, in run_file > execfile(file,global_ns,local_ns) > File " setup.py", line 19, in ? > setup(**metadata) > File "C:\Program Files\DeLano > Scientific\PyMOL\py24\lib\distutils\core.py", line 166, in setup > raise SystemExit, "error: " + str(msg) > SystemExit: error: The .NET Framework SDK needs to be installed before > building extensions for Python. > > Where should I install the .NET Framework? > > Bye > DeVill > > P.S.: sorry for the previous empty E-mail... my client mesd things up a > bit :-* > > > Hi! Finaly I succesfully installed the .NET framework, the Platform SDK, and so on... a lot o stuff indeed! Now I get another error message saying: running build running build_py copying MySQLdb\release.py -> build\lib.win32-2.4\MySQLdb running build_ext building '_mysql' extension C:\Program Files\Microsoft Visual Studio 8\VC\bin\cl.exe /c /nologo /Ox /MD /W3 /GX /DNDEBUG -Dversion_info=(1,2,2,'final',0) -D__version__=1.2.2"-IC:\Program Files\MySQL\MySQL Server 5.0\include" "-IC:\Program Files\DeLano Scientific\PyMOL\py24\include" "-IC:\Program Files\DeLano Scientific\PyMOL\py24\PC" /Tc_mysql.c /Fobuild\temp.win32-2.4\Release\_mysql.obj /Zl Traceback (most recent call last): File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parser.py", line 291, in parse parsing.run_file(exp_path(args[nest][0]),pymol_names,{}) File "C:\Program Files\DeLano Scientific\PyMOL/modules\pymol\parsing.py", line 407, in run_file execfile(file,global_ns,local_ns) File "setup.py", line 19, in ? setup(**metadata) File "C:\Program Files\DeLano Scientific\PyMOL\py24\lib\distutils\core.py", line 166, in setup raise SystemExit, "error: " + str(msg) SystemExit: error: command '"C:\Program Files\Microsoft Visual Studio 8\VC\bin\cl.exe"' failed with exit status 2 Then I tried to run the compiler in a command prompt: C:\Program Files\DeLano Scientific\PyMOL\MySQLsetup>cl.exe /c /nologo /Ox /MD /W 3 /GX /DNDEBUG -Dversion_info=(1,2,2,'final',0) -D__version__=1.2.2"-IC:\Progra m Files\MySQL\MySQL Server 5.0\include" "-IC:\Program Files\DeLano Scientific\Py MOL\py24\include" "-IC:\Program Files\DeLano Scientific\PyMOL\py24\PC" /Tc_mysql .c /Fobuild\temp.win32-2.4\Release\_mysql.obj /Zl cl : Command line warning D9035 : option 'GX' has been deprecated and will be re moved in a future release cl : Command line warning D9036 : use 'EHsc' instead of 'GX' _mysql.c C:\Program Files\DeLano Scientific\PyMOL\py24\include\Python.h(18) : fatal error C1083: Cannot open include file: 'limits.h': No such file or directory Then I added the include dir of Visual Studio into the command line, and: _mysql.c C:\Program Files\DeLano Scientific\PyMOL\py24\include\Python.h(41) : fatal error C1083: Cannot open include file: 'unistd.h': No such file or directory Now I don't have the faintest idea, where should I get unistd.h from... what it is after all? Dose anyone have any ideas? Bye DeVill |
From: Peter A. M. <pa...@co...> - 2007-03-10 18:23:22
|
> Finaly I succesfully installed the .NET framework, the Platform SDK, and so > on... a lot o stuff indeed! I'm not clear on why you'd need the .NET framework (pymol/python stuff is generally compiled to machine code, not CLR bytecode). One thing to check is that you're using the correct compiler (MS has a dialect of c++ that compiles to CLR bytecode which would probably not work so well as a python module). [snip] > _mysql.c > C:\Program Files\DeLano Scientific\PyMOL\py24\include\Python.h(41) : fatal > error > C1083: Cannot open include file: 'unistd.h': No such file or directory > > Now I don't have the faintest idea, where should I get unistd.h from... what > it is after all? As far as I know, unistd.h is a POSIX (unix) header file. I don't know this is available on windows natively (I believe some versions of windows are supposed to be POSIX compliant, but I'm not sure how compilant they are); possibly the pre-processer definations are not being set correctly. I'd recommend either installing mingw or cywin at this point, and compiling pymol from source, then using the same compilers to build the mysql module. Actually, I'd recommend switching to linux or another unix varient (OS X, one of the bsd's, etc); but that may be more trouble than you're willing to go to for this problem. But possibly someone with more experience in windows programming than I am has a better suggestion. Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University |