Hy, I've just started working on a Chimera extension. I've tried to import chimera after setting up the CHIMERA os variable, but it gives me this erro message: ***from _chimera import * ImportError: No module named _chimera *Some help? Thank you. Javi * *
Hi Javi, The normal way to work with Python in Chimera is to start Chimera and then show the Chimera Python shell (called IDLE) using menu entry Tools / General Controls / IDLE There is no need to set a CHIMERA environment variable. This uses the Python that is included in the Chimera distribution. Utilizing Chimera modules with your own copy of Python is problematic because the current Chimera uses a modified version of Python. Tom
Tom Goddard's comments are exactly correct, I just want to add some advice. If anyone else will be working on your code, you should try to avoid the "from module_name import *" construct because it makes it more difficult to find the place where a class is defined. Say for example you use a Point object in your code. A person trying to find the definition for Point first has to look through the file using Point to see if it's defined there, then through each module from which you've imported "*" to look for it. It is better to import just the names you are going to use, something like: "from chimera import Point, openModels, Molecule". That statement makes it clear where the definition of Point is going to be found. The other thing is that the "chimera" module imports all the names from _chimera, so typically you import from chimera rather than _chimera. I know that the chimera uses the "from _chimera import *" construct, which seems somewhat hypocritical given the advice above, but it is being used to make C++ classes/functions that "logically" belong in the chimera module available. --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu On Oct 2, 2006, at 5:44 AM, Javier Díez wrote:
Hy, I've just started working on a Chimera extension. I've tried to import chimera after setting up the CHIMERA os variable, but it gives me this erro message: from _chimera import * ImportError: No module named _chimera Some help? Thank you. Javi
_______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Hi again, Thank you for your comments. From now I will never use the import construction I wrote above. But I have got another question. Well, I'm using Eclipse and PyDev Extensions, and I seted the Eclipse Python interpreter option using the Python version included in Chimera. I also included the "share" in the Eclipse, PyDev PYTHONPATH, but it doesn't works. I thought it could work, but it doesn't. I prefer Eclipse (because it is the enviroment I'm used to work with) to the IDLE provided by Chimera. Thank you any way. Javi On 10/2/06, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Tom Goddard's comments are exactly correct, I just want to add some advice. If anyone else will be working on your code, you should try to avoid the "from module_name import *" construct because it makes it more difficult to find the place where a class is defined. Say for example you use a Point object in your code. A person trying to find the definition for Point first has to look through the file using Point to see if it's defined there, then through each module from which you've imported "*" to look for it. It is better to import just the names you are going to use, something like: "from chimera import Point, openModels, Molecule". That statement makes it clear where the definition of Point is going to be found. The other thing is that the "chimera" module imports all the names from _chimera, so typically you import from chimera rather than _chimera. I know that the chimera uses the "from _chimera import *" construct, which seems somewhat hypocritical given the advice above, but it is being used to make C++ classes/functions that "logically" belong in the chimera module available.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
pett@cgl.ucsf.edu
On Oct 2, 2006, at 5:44 AM, Javier Díez wrote:
Hy, I've just started working on a Chimera extension. I've tried to import chimera after setting up the CHIMERA os variable, but it gives me this erro message: ***from _chimera import * ImportError: No module named _chimera *Some help? Thank you. Javi * * _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
We haven't used eclipse with chimera, but we will work with you to get it to work. When it does work, please send what you had to do back to the chimera-dev list. First an aside for non-eclipse users and maybe this would work in eclipse too -- you can use Python's help facility to find out more about chimera internals: in an IDLE window, typing: help(chimera.Point) will give you a lot information about the Point API. Since Point is implemented in C++, you only get the type information for the arguments and the return value, but that information, coupled with the name of the method, tell you a lot. Back to eclipse, the chimera program sets up several environment variables before invoking python. On Linux, it is a shell script and you can see everything it does. On Windows, it's basically the same: (1) set the CHIMERA environment variable to the actual path of the chimera install tree (so without any symbolic links). (2) make sure CHIMERA/bin is in the PATH environment (3) defensively remove the PYTHONHOME and PYTHONPATH environment variables so we don't get packages compiled for a different version of python (e.g, the system one) (4) copy CHIMERPATH environment variable to the PYTHONPATH one (5) set Tcl environment variables: TCL_LIBRARY is CHIMERA\lib\tcl8.4 TCLLIBPATH is {CHIMERA\lib} (6) unset TK_LIBRARY and TIX_LIBRARY environment variables Unix systems replace step 2 with one that set the environment variable for finding shared libaries, ie., LD_LIBRARY_PATH or DYLD_LIBRARY_PATH or ... to CHIMERA/lib. On OS X, we also set the DYLD_FRAMEWORK_PATH. Good luck, Greg Couch UCSF Computer Graphics Lab On Mon, 2 Oct 2006, Javier D�ez wrote:
Date: Mon, 2 Oct 2006 20:38:53 +0200 From: "[ISO-8859-1] Javier D�ez" <jdiezperezj@gmail.com> To: Eric Pettersen <pett@cgl.ucsf.edu> Cc: chimera-dev@cgl.ucsf.edu Subject: Re: [chimera-dev] chimera import
Hi again, Thank you for your comments. From now I will never use the import construction I wrote above. But I have got another question. Well, I'm using Eclipse and PyDev Extensions, and I seted the Eclipse Python interpreter option using the Python version included in Chimera. I also included the "share" in the Eclipse, PyDev PYTHONPATH, but it doesn't works. I thought it could work, but it doesn't. I prefer Eclipse (because it is the enviroment I'm used to work with) to the IDLE provided by Chimera. Thank you any way. Javi
On 10/2/06, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Tom Goddard's comments are exactly correct, I just want to add some advice. If anyone else will be working on your code, you should try to avoid the "from module_name import *" construct because it makes it more difficult to find the place where a class is defined. Say for example you use a Point object in your code. A person trying to find the definition for Point first has to look through the file using Point to see if it's defined there, then through each module from which you've imported "*" to look for it. It is better to import just the names you are going to use, something like: "from chimera import Point, openModels, Molecule". That statement makes it clear where the definition of Point is going to be found. The other thing is that the "chimera" module imports all the names from _chimera, so typically you import from chimera rather than _chimera. I know that the chimera uses the "from _chimera import *" construct, which seems somewhat hypocritical given the advice above, but it is being used to make C++ classes/functions that "logically" belong in the chimera module available.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
pett@cgl.ucsf.edu
On Oct 2, 2006, at 5:44 AM, Javier D�ez wrote:
Hy, I've just started working on a Chimera extension. I've tried to import chimera after setting up the CHIMERA os variable, but it gives me this erro message: ***from _chimera import * ImportError: No module named _chimera *Some help? Thank you. Javi * * _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Greg, First, thank you very much for your help. As your told me, it was a problem with environment variables. Eclipse works now!! and it is easier than I thought. I'll try to explain the way I did it, but sorry about my bad english, I hope you understand what I say. 1)Eclipse: Window (menu) > Preferences... I seted Python interpreter: ...\chimera\bin\python.exe Then I included chimera "share" directory in PYTHONPATH option. Then choose apply and ok. 2)Once I have created a new project, and a new python file or module was created: Go to the Run As (menu option) clicking with right mouse button on the python module. Then select Run ... option and select your file in the Python Run (subtree). Select Enviroment (tab) and mark option "Replace native environment with especified environment. I THINK THAT IS KEY STEP... (Finally you could go to the Refresh tab and apply it to the entire workspace). Well, I think it should works for everybody running Windows or Linux. Thank you so much we keep in contact. Javi. On 10/2/06, Greg Couch <gregc@cgl.ucsf.edu> wrote:
We haven't used eclipse with chimera, but we will work with you to get it to work. When it does work, please send what you had to do back to the chimera-dev list.
First an aside for non-eclipse users and maybe this would work in eclipse too -- you can use Python's help facility to find out more about chimera internals: in an IDLE window, typing:
help(chimera.Point)
will give you a lot information about the Point API. Since Point is implemented in C++, you only get the type information for the arguments and the return value, but that information, coupled with the name of the method, tell you a lot.
Back to eclipse, the chimera program sets up several environment variables before invoking python. On Linux, it is a shell script and you can see everything it does. On Windows, it's basically the same:
(1) set the CHIMERA environment variable to the actual path of the chimera install tree (so without any symbolic links). (2) make sure CHIMERA/bin is in the PATH environment (3) defensively remove the PYTHONHOME and PYTHONPATH environment variables so we don't get packages compiled for a different version of python (e.g, the system one) (4) copy CHIMERPATH environment variable to the PYTHONPATH one (5) set Tcl environment variables: TCL_LIBRARY is CHIMERA\lib\tcl8.4 TCLLIBPATH is {CHIMERA\lib} (6) unset TK_LIBRARY and TIX_LIBRARY environment variables
Unix systems replace step 2 with one that set the environment variable for finding shared libaries, ie., LD_LIBRARY_PATH or DYLD_LIBRARY_PATH or ... to CHIMERA/lib. On OS X, we also set the DYLD_FRAMEWORK_PATH.
Good luck,
Greg Couch UCSF Computer Graphics Lab
On Mon, 2 Oct 2006, Javier Díez wrote:
Date: Mon, 2 Oct 2006 20:38:53 +0200 From: "[ISO-8859-1] Javier Díez" <jdiezperezj@gmail.com> To: Eric Pettersen <pett@cgl.ucsf.edu> Cc: chimera-dev@cgl.ucsf.edu Subject: Re: [chimera-dev] chimera import
Hi again, Thank you for your comments. From now I will never use the import construction I wrote above. But I have got another question. Well, I'm using Eclipse and PyDev Extensions, and I seted the Eclipse Python interpreter option using the Python version included in Chimera. I also included the "share" in the Eclipse, PyDev PYTHONPATH, but it doesn't works. I thought it could work, but it doesn't. I prefer Eclipse (because it is the enviroment I'm used to work with) to the IDLE provided by Chimera. Thank you any way. Javi
On 10/2/06, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Tom Goddard's comments are exactly correct, I just want to add some advice. If anyone else will be working on your code, you should try to avoid the "from module_name import *" construct because it makes it
more
difficult to find the place where a class is defined. Say for example you use a Point object in your code. A person trying to find the definition for Point first has to look through the file using Point to see if it's defined there, then through each module from which you've imported "*" to look for it. It is better to import just the names you are going to use, something like: "from chimera import Point, openModels, Molecule". That statement makes it clear where the definition of Point is going to be found. The other thing is that the "chimera" module imports all the names from _chimera, so typically you import from chimera rather than _chimera. I know that the chimera uses the "from _chimera import *" construct, which seems somewhat hypocritical given the advice above, but it is being used to make C++ classes/functions that "logically" belong in the chimera module available.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
pett@cgl.ucsf.edu
On Oct 2, 2006, at 5:44 AM, Javier Díez wrote:
Hy, I've just started working on a Chimera extension. I've tried to import chimera after setting up the CHIMERA os variable, but it gives me this erro message: ***from _chimera import * ImportError: No module named _chimera *Some help? Thank you. Javi * * _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev
participants (4)
-
Eric Pettersen -
Greg Couch -
Javier Díez -
Thomas Goddard