Nicely done! Cheers,
Edward On 27 July 2010 05:35, <[email protected]> wrote: > Author: michaelbieri > Date: Tue Jul 27 05:35:59 2010 > New Revision: 11356 > > URL: http://svn.gna.org/viewcvs/relax?rev=11356&view=rev > Log: > Directory to save file can be specified. > > Modified: > branches/bieri_gui/auto_analyses/dauvergne_protocol.py > > Modified: branches/bieri_gui/auto_analyses/dauvergne_protocol.py > URL: > http://svn.gna.org/viewcvs/relax/branches/bieri_gui/auto_analyses/dauvergne_protocol.py?rev=11356&r1=11355&r2=11356&view=diff > ============================================================================== > --- branches/bieri_gui/auto_analyses/dauvergne_protocol.py (original) > +++ branches/bieri_gui/auto_analyses/dauvergne_protocol.py Tue Jul 27 > 05:35:59 2010 > @@ -155,9 +155,11 @@ > > > class dAuvergne_protocol: > - def __init__(self, diff_model=None, mf_models=['m0', 'm1', 'm2', 'm3', > 'm4', 'm5', 'm6', 'm7', 'm8', 'm9'], local_tm_models=['tm0', 'tm1', 'tm2', > 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 'tm9'], pdb_file=None, > seq_args=None, het_name=None, relax_data=None, unres=None, exclude=None, > bond_length=None, csa=None, hetnuc=None, proton='1H', grid_inc=11, > min_algor='newton', mc_num=500, max_iter=None, user_fns=None, conv_loop=True): > + def __init__(self, save_dir=None, diff_model=None, mf_models=['m0', > 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9'], > local_tm_models=['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', > 'tm8', 'tm9'], pdb_file=None, seq_args=None, het_name=None, relax_data=None, > unres=None, exclude=None, bond_length=None, csa=None, hetnuc=None, > proton='1H', grid_inc=11, min_algor='newton', mc_num=500, max_iter=None, > user_fns=None, conv_loop=True): > """Perform the full model-free analysis protocol of d'Auvergne and > Gooley, 2008b. > > + �...@keyword save_dir: The directory, where files are saved > in. > + �...@type save_dir: str > @keyword diff_model: The global diffusion model to optimise. > This can be one of 'local_tm', 'sphere', 'oblate', 'prolate', 'ellipsoid', or > 'final'. > @type diff_model: str > @keyword mf_models: The model-free models. > @@ -218,6 +220,12 @@ > self.max_iter = max_iter > self.conv_loop = conv_loop > > + # Project directory (i.e. directory containing the model-free model > results and the newly generated files) > + if save_dir: > + self.save_dir = save_dir+sep > + else: > + self.save_dir = '' > + > # User variable checks. > self.check_vars() > > @@ -258,7 +266,7 @@ > > if self.diff_model == 'local_tm': > # Base directory to place files into. > - self.base_dir = 'local_tm'+sep > + self.base_dir = self.save_dir+'local_tm'+sep > > # Sequential optimisation of all model-free models (function must > be modified to suit). > self.multi_model(local_tm=True) > @@ -284,7 +292,7 @@ > # Inital round of optimisation for diffusion models MII to MV. > if self.round == 0: > # Base directory to place files into. > - self.base_dir = self.diff_model + sep+'init'+sep > + self.base_dir = > self.save_dir+self.diff_model+sep+'init'+sep > > # Run name. > name = self.diff_model > @@ -293,7 +301,7 @@ > self.interpreter.pipe.create(name, 'mf') > > # Load the local tm diffusion model MI results. > - self.interpreter.results.read(file='results', > dir='local_tm'+sep+'aic') > + self.interpreter.results.read(file='results', > dir=self.save_dir+'local_tm'+sep+'aic') > > # Remove the tm parameter. > self.interpreter.model_free.remove_tm() > @@ -337,7 +345,7 @@ > # Normal round of optimisation for diffusion models MII to MV. > else: > # Base directory to place files into. > - self.base_dir = self.diff_model + > sep+'round_'+repr(self.round)+sep > + self.base_dir = self.save_dir+self.diff_model + > sep+'round_'+repr(self.round)+sep > > # Load the optimised diffusion tensor from either the > previous round. > self.load_tensor() > @@ -383,7 +391,7 @@ > self.interpreter.pipe.create('local_tm', 'mf') > > # Load the local tm diffusion model MI results. > - self.interpreter.results.read(file='results', > dir='local_tm'+sep+'aic') > + self.interpreter.results.read(file='results', > dir=self.save_dir+'local_tm'+sep+'aic') > > # Loop over models MII to MV. > for model in ['sphere', 'prolate', 'oblate', 'ellipsoid']: > @@ -404,7 +412,7 @@ > self.interpreter.pipe.create(model, 'mf') > > # Load the diffusion model results. > - self.interpreter.results.read(file='results', dir=model + > sep+'round_'+repr(self.round)+sep+'opt') > + self.interpreter.results.read(file='results', > dir=self.save_dir+model + sep+'round_'+repr(self.round)+sep+'opt') > > # Model selection between MI to MV. > self.model_selection(modsel_pipe='final', write_flag=False) > @@ -429,7 +437,7 @@ > # Write the final results. > ########################## > > - self.interpreter.results.write(file='results', dir='final', > force=True) > + self.interpreter.results.write(file='results', > dir=self.save_dir+'final', force=True) > > > # Unknown script behaviour. > @@ -699,7 +707,13 @@ > > # Get a list of all files in the directory model. If no directory > exists, set the round to 'init' or 0. > try: > - dir_list = listdir(getcwd()+sep+model) > + # Files are in same directory / no directory specified > + if self.save_dir =='': > + dir_list = listdir(getcwd()+sep+model) > + > + # Directory is specified > + else: > + dir_list = listdir(self.save_dir+model)) > except: > return 0 > > @@ -740,11 +754,11 @@ > > # Load the optimised diffusion tensor from the initial round. > if self.round == 1: > - self.interpreter.results.read('results', self.diff_model + > sep+'init') > + self.interpreter.results.read('results', > self.save_dir+self.diff_model + sep+'init') > > # Load the optimised diffusion tensor from the previous round. > else: > - self.interpreter.results.read('results', self.diff_model + > sep+'round_'+repr(self.round-1)+sep+'opt') > + self.interpreter.results.read('results', > self.save_dir+self.diff_model + sep+'round_'+repr(self.round-1)+sep+'opt') > > > def model_selection(self, modsel_pipe=None, dir=None, write_flag=True): > @@ -824,7 +838,7 @@ > self.interpreter.minimise(self.min_algor) > > # Write the results. > - dir = self.base_dir + name > + dir = self.save_dir+self.base_dir + name > self.interpreter.results.write(file='results', dir=dir, > force=True) > > # Unset the status. > > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-commits 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-commits > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel 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-devel
