Author: bugman
Date: Mon Mar 11 13:41:23 2013
New Revision: 18765
URL: http://svn.gna.org/viewcvs/relax?rev=18765&view=rev
Log:
Modified the dauvergne_protocol model-free auto-analysis to aid in debugging.
The write_results_dir argument has been added to allow the test suite to read
from one directory in
test suite shared data directories and redirect output to a temporary
directory.
Modified:
trunk/auto_analyses/dauvergne_protocol.py
Modified: trunk/auto_analyses/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/dauvergne_protocol.py?rev=18765&r1=18764&r2=18765&view=diff
==============================================================================
--- trunk/auto_analyses/dauvergne_protocol.py (original)
+++ trunk/auto_analyses/dauvergne_protocol.py Mon Mar 11 13:41:23 2013
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2012 Edward d'Auvergne
#
+# Copyright (C) 2004-2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -119,15 +119,17 @@
opt_func_tol = 1e-25
opt_max_iterations = int(1e7)
- def __init__(self, pipe_name=None, pipe_bundle=None, results_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'], grid_inc=11, diff_tensor_grid_inc={'sphere': 11,
'prolate': 11, 'oblate': 11, 'ellipsoid': 6}, min_algor='newton',
mc_sim_num=500, max_iter=None, user_fns=None, conv_loop=True):
+ def __init__(self, pipe_name=None, pipe_bundle=None, results_dir=None,
write_results_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'], grid_inc=11,
diff_tensor_grid_inc={'sphere': 11, 'prolate': 11, 'oblate': 11, 'ellipsoid':
6}, min_algor='newton', mc_sim_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 pipe_name: The name of the data pipe containing
the sequence info. This data pipe should have all values set including the
CSA value, the bond length, the heteronucleus name and proton name. It
should also have all relaxation data loaded.
@type pipe_name: str
@keyword pipe_bundle: The data pipe bundle to associate
all spawned data pipes with.
@type pipe_bundle: str
- @keyword results_dir: The directory, where files are saved
in.
+ @keyword results_dir: The directory where optimisation
results will read from. Results will also be saved to this directory if the
write_results_dir argument is not given.
@type results_dir: str
+ @keyword write_results_dir: The directory where optimisation
results will be saved in. If None, it will default to the value of the
results_dir argument. This is mainly used for debugging.
+ @type write_results_dir: str or None
@keyword diff_model: The global diffusion model to
optimise. This can be one of 'local_tm', 'sphere', 'oblate', 'prolate',
'ellipsoid', or 'final'. If all or a subset of these are supplied as a list,
then these will be automatically looped over and calculated.
@type diff_model: str or list of str
@keyword mf_models: The model-free models.
@@ -184,6 +186,10 @@
self.results_dir = results_dir + sep
else:
self.results_dir = getcwd() + sep
+ if write_results_dir:
+ self.write_results_dir = write_results_dir + sep
+ else:
+ self.write_results_dir = self.results_dir
# Data checks.
self.check_vars()
@@ -876,11 +882,11 @@
"""Create Grace plots of the final model-free results."""
# Save the results file.
- dir = self.results_dir + 'final'
+ dir = self.write_results_dir + 'final'
self.interpreter.results.write(file='results', dir=dir, force=True)
# The Grace plots.
- dir = self.results_dir + 'final' + sep + 'grace'
+ dir = self.write_results_dir + 'final' + sep + 'grace'
self.interpreter.grace.write(x_data_type='spin', y_data_type='s2',
file='s2.agr', dir=dir, force=True)
self.interpreter.grace.write(x_data_type='spin', y_data_type='s2f',
file='s2f.agr', dir=dir, force=True)
self.interpreter.grace.write(x_data_type='spin', y_data_type='s2s',
file='s2s.agr', dir=dir, force=True)
@@ -893,7 +899,7 @@
self.interpreter.grace.write(x_data_type='te', y_data_type='rex',
file='te_vs_rex.agr', dir=dir, force=True)
# Write the values to text files.
- dir = self.results_dir + 'final'
+ dir = self.write_results_dir + 'final'
self.interpreter.value.write(param='s2', file='s2.txt',
dir=dir, force=True)
self.interpreter.value.write(param='s2f', file='s2f.txt',
dir=dir, force=True)
self.interpreter.value.write(param='s2s', file='s2s.txt',
dir=dir, force=True)
@@ -904,7 +910,7 @@
self.interpreter.value.write(param='local_tm', file='local_tm.txt',
dir=dir, force=True)
# Create the PyMOL macros.
- dir = self.results_dir + 'final' + sep + 'pymol'
+ dir = self.write_results_dir + 'final' + sep + 'pymol'
self.interpreter.pymol.macro_write(data_type='s2', dir=dir,
force=True)
self.interpreter.pymol.macro_write(data_type='s2f', dir=dir,
force=True)
self.interpreter.pymol.macro_write(data_type='s2s', dir=dir,
force=True)
@@ -918,7 +924,7 @@
self.interpreter.pymol.macro_write(data_type='rex', dir=dir,
force=True)
# Create the Molmol macros.
- dir = self.results_dir + 'final' + sep + 'molmol'
+ dir = self.write_results_dir + 'final' + sep + 'molmol'
self.interpreter.molmol.macro_write(data_type='s2', dir=dir,
force=True)
self.interpreter.molmol.macro_write(data_type='s2f', dir=dir,
force=True)
self.interpreter.molmol.macro_write(data_type='s2s', dir=dir,
force=True)
@@ -933,7 +939,7 @@
# Create a diffusion tensor representation of the tensor, if a PDB
file is present.
if hasattr(cdp, 'structure'):
- dir = self.results_dir + 'final'
+ dir = self.write_results_dir + 'final'
self.interpreter.structure.create_diff_tensor_pdb(file="tensor.pdb", dir=dir,
force=True)
r18765 - /trunk/auto_analyses/dauvergne_protocol.py