Re: [PyMOL] Paths to loaded objects
Hi folks, * Michael Lerner mgler...@gmail.com [2006-08-21 12:26] wrote: I think he means for you to have a Load button as part of your plugin. That button would first record the path to the file and then call through to cmd.load(). Perhaps what Ron needs to do is not use the cmd.load() function but use his own file reading procedure. The lines containing coordinates could be extracted from the file (by recognizing them with a regexp) and passed to the cmd.read_pdbstr() function. The CGO commands could be read separately. Then there is no need to worry about where cmd.load() thinks file is. On 8/19/06, Ron Jacak r...@email.unc.edu wrote: Peter, I'm working on a plugin that reads information appended to the end of PDB files to draw CGO objects. Right now, I have the user specify the filesystem path to the currently loaded objects through the plugin GUI so that I know where to go to find the file. For one object, this isn't so bad. But if users load multiple objects that are in different directories, I will have to change the GUI so that the user has to specify the path to each object loaded. This kind of situation would quickly become tedious. Does PyMOL store the paths for objects that are loaded somewhere? I know I can get the current working directory using getcwd(), so I'm hoping there's a way to get the path to the loaded objects as well. I don't know of a way to get file information from a pymol object, but you could work around this by using a python dictionary (when the pdb file is loaded, store the full path to the file in a dictionary using the pymol object name as the key). I'm not sure I fully understand your suggestion. It sounds to me like what you're saying is that I should add code (e.g. a dictionary) to the importing.py load() function which saves the file information of objects as they're loaded. But then instead of just distributing my plugin, I would have to get users to change their PyMOL source, as well (which I'm not willing to do). Am I understanding correctly? Any other ways around this problem? Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Department of Biochemistry, Queen's University Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.ca http://adelie.biochem.queensu.ca/~rlc
Re: [PyMOL] Paths to loaded objects
I think he means for you to have a Load button as part of your plugin. That button would first record the path to the file and then call through to cmd.load(). Perhaps what Ron needs to do is not use the cmd.load() function but use his own file reading procedure. The lines containing coordinates could be extracted from the file (by recognizing them with a regexp) and passed to the cmd.read_pdbstr() function. The CGO commands could be read separately. Then there is no need to worry about where cmd.load() thinks file is. Rob, thanks for the response. I'm currently using a variation of what you wrote above. It's just that the primary use case in my lab is to load multiple structures at once when starting pymol on the command line. $ pymol 1AAA.pdb 1AAB.pdb 1AAC.pdb or, more frequently $ pymol *.pdb I then want the user to be able to click on my plugin in the Plugin menu and have it run without the need for a GUI asking where to find the files (so I can reread them for the extra info I need). In the example above, there's no problem: The files are all located in the current working directory so I know where to find them. I start having problems when users do things as below: $ pymol ../1AAD.pdb ~/jsmith/1AAE.pdb ./structures/1AAF.pdb When PyMOL loads these structures, it drops the path information to create the object name and none of these structures are in the current working directory. Hence, my plugin can't find the files. For the time being, I'm going to instruct users in my lab that the structures they load must be in the same directory as the one from which they execute pymol. At some point I will (hopefully) release the plugin to the public. If I see that it's being used, I'll consider adding some preprocessing step that checks to see if the files can be found and if not, maybe execute a restricted find command up and down one or two directories or pop up a GUI that asks users to specify where to find the files (that couldn't be found). I don't want to beat/flog a dead horse here, but other suggestions are always welcome. Best, -Ron
Re: [PyMOL] Paths to loaded objects
Ron, I'm not sure I fully understand your suggestion. It sounds to me like what you're saying is that I should add code (e.g. a dictionary) to the importing.py load() function which saves the file information of objects as they're loaded. But then instead of just distributing my plugin, I would have to get users to change their PyMOL source, as well (which I'm not willing to do). Am I understanding correctly? Well, I may have been misunderstanding you...I'd though you mentioned you were using a gui to load the pdb files, which would be the natural place to add additional code. I'd assumed the gui you were talking about was specific to your plugin (if this isn't the case, then my suggestion doesn't help that much). Any other ways around this problem? You could try turning on logging, and scan through the logfile looking for load events (on my system, using the standard gui menus to open a pdb, this stores the full path to the input pdb file; although it does not associate it with the object name). Of course then you're stuck with the problem of getting the name/path of the logfile... Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
Re: [PyMOL] Paths to loaded objects
I think he means for you to have a Load button as part of your plugin. That button would first record the path to the file and then call through to cmd.load(). On 8/19/06, Ron Jacak r...@email.unc.edu wrote: Peter, I'm working on a plugin that reads information appended to the end of PDB files to draw CGO objects. Right now, I have the user specify the filesystem path to the currently loaded objects through the plugin GUI so that I know where to go to find the file. For one object, this isn't so bad. But if users load multiple objects that are in different directories, I will have to change the GUI so that the user has to specify the path to each object loaded. This kind of situation would quickly become tedious. Does PyMOL store the paths for objects that are loaded somewhere? I know I can get the current working directory using getcwd(), so I'm hoping there's a way to get the path to the loaded objects as well. I don't know of a way to get file information from a pymol object, but you could work around this by using a python dictionary (when the pdb file is loaded, store the full path to the file in a dictionary using the pymol object name as the key). I'm not sure I fully understand your suggestion. It sounds to me like what you're saying is that I should add code (e.g. a dictionary) to the importing.py load() function which saves the file information of objects as they're loaded. But then instead of just distributing my plugin, I would have to get users to change their PyMOL source, as well (which I'm not willing to do). Am I understanding correctly? Any other ways around this problem? -Ron Ron Jacak Graduate Student University of North Carolina - Chapel Hill - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Paths to loaded objects
Peter, I'm working on a plugin that reads information appended to the end of PDB files to draw CGO objects. Right now, I have the user specify the filesystem path to the currently loaded objects through the plugin GUI so that I know where to go to find the file. For one object, this isn't so bad. But if users load multiple objects that are in different directories, I will have to change the GUI so that the user has to specify the path to each object loaded. This kind of situation would quickly become tedious. Does PyMOL store the paths for objects that are loaded somewhere? I know I can get the current working directory using getcwd(), so I'm hoping there's a way to get the path to the loaded objects as well. I don't know of a way to get file information from a pymol object, but you could work around this by using a python dictionary (when the pdb file is loaded, store the full path to the file in a dictionary using the pymol object name as the key). I'm not sure I fully understand your suggestion. It sounds to me like what you're saying is that I should add code (e.g. a dictionary) to the importing.py load() function which saves the file information of objects as they're loaded. But then instead of just distributing my plugin, I would have to get users to change their PyMOL source, as well (which I'm not willing to do). Am I understanding correctly? Any other ways around this problem? -Ron Ron Jacak Graduate Student University of North Carolina - Chapel Hill
[PyMOL] Paths to loaded objects
Hi all, I'm working on a plugin that reads information appended to the end of PDB files to draw CGO objects. Right now, I have the user specify the filesystem path to the currently loaded objects through the plugin GUI so that I know where to go to find the file. For one object, this isn't so bad. But if users load multiple objects that are in different directories, I will have to change the GUI so that the user has to specify the path to each object loaded. This kind of situation would quickly become tedious. Does PyMOL store the paths for objects that are loaded somewhere? I know I can get the current working directory using getcwd(), so I'm hoping there's a way to get the path to the loaded objects as well. I've searched all over the Wiki and the mailing list archives and I haven't been able to find anything relevant. I also looked through importing.py but all I saw was cmd.exp_path() and it doesn't seem to me like the full path that's returned is being stored anywhere. Perhaps in the C layers it gets saved somewhere? Thanks for any help, -Ron Ron Jacak Graduate Student University of North Carolina - Chapel Hill
Re: [PyMOL] Paths to loaded objects
Hi, I'm working on a plugin that reads information appended to the end of PDB files to draw CGO objects. Right now, I have the user specify the filesystem path to the currently loaded objects through the plugin GUI so that I know where to go to find the file. For one object, this isn't so bad. But if users load multiple objects that are in different directories, I will have to change the GUI so that the user has to specify the path to each object loaded. This kind of situation would quickly become tedious. Does PyMOL store the paths for objects that are loaded somewhere? I know I can get the current working directory using getcwd(), so I'm hoping there's a way to get the path to the loaded objects as well. I don't know of a way to get file information from a pymol object, but you could work around this by using a python dictionary (when the pdb file is loaded, store the full path to the file in a dictionary using the pymol object name as the key). Of course the fact that I don't know how to get the full path from a pymol object doesn't mean that there isn't a way... Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
