Hi, I haven't migrated the results.read() user function to the new design yet. This one cannot work. I'll give more details in response to your other post (https://mail.gna.org/public/relax-users/2008-01/msg00017.html, Message-id: <[EMAIL PROTECTED]>).
Regards, Edward On Jan 24, 2008 4:41 PM, Douglas Kojetin <[EMAIL PROTECTED]> wrote: > Hi Edward, > > As an example, can you tell me how the following portion of > diff_tensor_pdb.py would need to be edited to work with the unstable > 1.3 branch? The code below fails on the results.read(...) call. I > have a feeling it has something to do with the pipe.create(...) > function and the what you wrote on how the pipe name is not passed > into each user function. > > > ### start error_output > > % relax1.3 diff_tensor_pdb.py > > ImportError: relaxation curve fitting is unavailible, try compiling > the C modules. > > > > relax repository checkout > > Protein dynamics by NMR relaxation data > analysis > > Copyright (C) 2001-2006 Edward d'Auvergne > Copyright (C) 2006-2008 the relax > development team > > This is free software which you are welcome to modify and > redistribute under the conditions of the > GNU General Public License (GPL). This program, including all > modules, is licensed under the GPL > and comes with absolutely no warranty. For details type 'GPL'. > Assistance in using this program > can be accessed by typing 'help'. > > script = 'diff_tensor_pdb.py' > ------------------------------------------------------------------------ > ---------------------------- > # Script for creating a PDB representation of the Brownian rotational > diffusion tensor. > > # Create the run. > name = 'sims' > pipe.create(name, 'mf') > > # Read the results. > results.read(name, dir='final') > > # Display the diffusion tensor. > diffusion_tensor.display(name) > > # Create the tensor PDB file. > tensor_file = 'tensor.pdb' > structure.create_diff_tensor_pdb(name, file=tensor_file, force=1) > > # PyMOL. > #pymol.view(name) > #pymol.cartoon(name) > #pymol.tensor_pdb(name, file=tensor_file) > ------------------------------------------------------------------------ > ---------------------------- > > relax> pipe.create(pipe_name='sims', pipe_type='mf') > > relax> results.read(run='sims', file='results', dir='final', > format='columnar') > Traceback (most recent call last): > File "/usr/local/bin/relax1.3", line 421, in ? > Relax() > File "/usr/local/bin/relax1.3", line 142, in __init__ > self.interpreter.run(self.script_file) > File "/usr/local/relax/1.3/prompt/interpreter.py", line 241, in run > return run_script(intro=self.__intro_string, local=self.local, > script_file=script_file, quit=self.__quit_flag, > show_script=self.__show_script, > raise_relax_error=self.__raise_relax_error) > File "/usr/local/relax/1.3/prompt/interpreter.py", line 502, in > run_script > return console.interact(intro, local, script_file, quit, > show_script=show_script, raise_relax_error=raise_relax_error) > File "/usr/local/relax/1.3/prompt/interpreter.py", line 398, in > interact_script > execfile(script_file, local) > File "diff_tensor_pdb.py", line 8, in ? > results.read(name, dir='final') > File "/usr/local/relax/1.3/prompt/results.py", line 125, in read > self.__relax__.generic.results.read(run=run, file=file, > directory=dir, format=format) > AttributeError: 'module' object has no attribute 'results' > > > ### end error_output > > > Thanks, > Doug > > > On Jan 24, 2008, at 10:18 AM, Edward d'Auvergne wrote: > > > > Hi, > > > > The problem is simply differences between the stable 1.2 versions and > > the unstable 1.3 line. In the development of relax 1.3, many of the > > user functions have been renamed. There has also been a significant > > redesign of relax. For full details, have a look at the following > > links and the threads that they start: > > > > * The parent message 'Redesign of the relax data model: A HOWTO for > > breaking relax.' located at > > https://mail.gna.org/public/relax-devel/2006-10/msg00053.html > > (Message-id: > > <[EMAIL PROTECTED]>). > > > > * Section 1 'Redesign of the relax data model: 1. Why change?' > > located at https://mail.gna.org/public/relax-devel/2006-10/ > > msg00054.html > > (Message-id: > > <[EMAIL PROTECTED]>). > > > > * Section 2 'Subject: Redesign of the relax data model: 2. A new run > > concept' located at > > https://mail.gna.org/public/relax-devel/2006-10/msg00056.html > > (Message-id: > > <[EMAIL PROTECTED]>). > > > > * Section 3 'Redesign of the relax data model: 3. Molecules, > > residues, and spins' located at > > https://mail.gna.org/public/relax-devel/2006-10/msg00057.html > > (Message-id: > > <[EMAIL PROTECTED]>). > > > > * Section 4 'Redesign of the relax data model: 4. Conclusion' > > located at https://mail.gna.org/public/relax-devel/2006-10/ > > msg00058.html > > (Message-id: > > <[EMAIL PROTECTED]>). > > > > > > Note also that the 1.3 line code is not fully functional yet as this > > redesign has been slow and is still in progress. But if you do want > > to play with the current code, note that the name 'run' has been > > replaced by the name 'pipe' and that the concept of a data pipe has > > been introduced so that the pipe name is not passed into each user > > function. That user functions apply automatically to the 'current' > > data pipe in which you are currently sitting. And that you can switch > > between data pipes, merge them, branch them, etc. > > > > Regards, > > > > Edward > > > > > > > > On Jan 24, 2008 3:14 PM, Douglas Kojetin > > <[EMAIL PROTECTED]> wrote: > >> Hi All, > >> > >> When trying to use relax 1.3 (current svn version), I see the > >> following error when trying to use run.create(): > >> > >> % /usr/local/relax/1.3/relax > >> > >> ImportError: relaxation curve fitting is unavailible, try compiling > >> the C modules. > >> > >> > >> > >> relax repository checkout > >> > >> Protein dynamics by NMR relaxation data > >> analysis > >> > >> Copyright (C) 2001-2006 Edward > >> d'Auvergne > >> Copyright (C) 2006-2008 the relax > >> development team > >> > >> This is free software which you are welcome to modify and > >> redistribute under the conditions of the > >> GNU General Public License (GPL). This program, including all > >> modules, is licensed under the GPL > >> and comes with absolutely no warranty. For details type 'GPL'. > >> Assistance in using this program > >> can be accessed by typing 'help'. > >> > >> relax> run.create('test','mf') > >> Traceback (most recent call last): > >> File "<console>", line 1, in ? > >> NameError: name 'run' is not defined > >> relax> > >> > >> > >> > >> Any ideas about this problem? > >> > >> Thanks, > >> Doug > >> > >> _______________________________________________ > >> relax (http://nmr-relax.com) > >> > >> This is the relax-users mailing list > >> [email protected] > >> > >> To unsubscribe from this list, get a password > >> reminder, or change your subscription options, > >> visit the list information page at > >> https://mail.gna.org/listinfo/relax-users > >> > > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
