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.
r11356 - /branches/bieri_gui/auto_analyses/dauvergne_protocol.py