Author: tlinnet
Date: Wed Sep 3 22:50:52 2014
New Revision: 25612
URL: http://svn.gna.org/viewcvs/relax?rev=25612&view=rev
Log:
Added initial start for protocol for repeated analysis of dispersion data.
task #7826(https://gna.org/task/index.php?7826): Write an python class for
the repeated analysis of dispersion data.
Added:
trunk/auto_analyses/relax_disp_repeat_cpmg.py
Modified:
trunk/auto_analyses/__init__.py
Modified: trunk/auto_analyses/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/__init__.py?rev=25612&r1=25611&r2=25612&view=diff
==============================================================================
--- trunk/auto_analyses/__init__.py (original)
+++ trunk/auto_analyses/__init__.py Wed Sep 3 22:50:52 2014
@@ -27,6 +27,7 @@
'frame_order',
'noe',
'relax_disp',
+ 'relax_disp_repeat_cpmg',
'relax_fit',
'stereochem_analysis'
]
Added: trunk/auto_analyses/relax_disp_repeat_cpmg.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/relax_disp_repeat_cpmg.py?rev=25612&view=auto
==============================================================================
--- trunk/auto_analyses/relax_disp_repeat_cpmg.py (added)
+++ trunk/auto_analyses/relax_disp_repeat_cpmg.py Wed Sep 3 22:50:52
2014
@@ -0,0 +1,146 @@
+###############################################################################
+#
#
+# Copyright (C) 2014 Troels E. Linnet
#
+#
#
+# This file is part of the program relax (http://www.nmr-relax.com).
#
+#
#
+# This program is free software: you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation, either version 3 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# This program is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
+#
#
+###############################################################################
+
+# Module docstring.
+"""The automatic relaxation dispersion protocol for repeated data for CPMG.
+
+U{task #7826<https://gna.org/task/index.php?78266>}, Write an python class
for the repeated analysis of dispersion data.
+"""
+
+# Python module imports.
+from datetime import datetime
+from glob import glob
+from os import getcwd, sep
+
+# relax module imports.
+from lib.io import sort_filenames
+from prompt.interpreter import Interpreter
+from specific_analyses.relax_disp.variables import MODEL_R2EFF
+from status import Status; status = Status()
+
+
+# Define sfrq key to dic.
+DIC_KEY_FORMAT = "%.8f"
+
+
+class Relax_disp_rep:
+
+ """The relaxation dispersion analysis for repeated data."""
+
+ # Some class variables.
+ opt_func_tol = 1e-25
+ opt_max_iterations = int(1e7)
+
+ def __init__(self, settings):
+ """Perform a repeated dispersion analysis for settings given."""
+
+ # Unpack settings from dictionary to self.
+ for setting, value in settings.iteritems():
+ setattr(self, setting, value)
+
+ # Standard settings.
+ if not hasattr(self, 'pipe_name'):
+ setattr(self, 'pipe_name', 'base_pipe')
+
+ if not hasattr(self, 'pipe_bundle'):
+ setattr(self, 'pipe_bundle', 'repeat')
+
+ if not hasattr(self, 'time'):
+ setattr(self, 'time', datetime.now().strftime('%Y_%m_%d_%H_%M'))
+
+ # No results directory, so default to the current directory.
+ if not hasattr(self, 'results_dir'):
+ setattr(self, 'results_dir', getcwd() + sep + 'results' + sep +
self.time )
+
+ # If no models, then just R2eff
+ if not hasattr(self, 'models'):
+ setattr(self, 'models', [MODEL_R2EFF] )
+
+ # Standard Grid Search.
+ if not hasattr(self, 'grid_inc'):
+ setattr(self, 'grid_inc', 11 )
+
+ # Standard Monte-Carlo simulations.
+ if not hasattr(self, 'mc_sim_num'):
+ setattr(self, 'mc_sim_num', 40 )
+
+ # Standard Monte-Carlo simulations for exponential fit. '-1' is
getting R2eff err from Co-variance.
+ if not hasattr(self, 'exp_mc_sim_num'):
+ setattr(self, 'exp_mc_sim_num', -1 )
+
+ # Standard model selection.
+ if not hasattr(self, 'modsel'):
+ setattr(self, 'modsel', 'AIC' )
+
+ # The R2eff/R1rho value in rad/s by which to judge insignificance.
If the maximum difference between two points on all dispersion curves for a
spin is less than this value, that spin will be deselected.
+ # This does not affect the 'No Rex' model. Set this value to 0.0 to
use all data. The value will be passed on to the relax_disp.insignificance
user function.
+ if not hasattr(self, 'insignificance'):
+ setattr(self, 'insignificance', 1.0 )
+
+ # A flag which if True will set the grid R20 values from the minimum
R2eff values through the r20_from_min_r2eff user function.
+ # This will speed up the grid search with a factor
GRID_INC^(Nr_spec_freq). For a CPMG experiment with two fields and standard
GRID_INC=21, the speed-up is a factor 441.
+ if not hasattr(self, 'set_grid_r20'):
+ setattr(self, 'set_grid_r20', True )
+
+ # Define glop pattern for ser files.
+ glob_pat = '*.ser'
+
+ # Loop over peak files.
+ for sfrq in self.sfrqs:
+ # Access the key in self.
+ key = DIC_KEY_FORMAT % (sfrq)
+ peaks_folder = getattr(self, key)['peaks_folder']
+
+ # Get the file list.
+ file_list = glob(peaks_folder + sep + glob_pat)
+
+ # Sort the file list Alphanumeric, reverted.
+ file_list_sort = sort_filenames(filenames=file_list, rev=True)
+
+ for cur_file in file_list_sort:
+ print(key, cur_file)
+
+ # Define glop pattern for ser files.
+ glob_pat = '*.rmsd'
+
+ # Loop over rmsd files.
+ for sfrq in self.sfrqs:
+ # Access the key in self.
+ key = DIC_KEY_FORMAT % (sfrq)
+ rmsd_folder = getattr(self, key)['rmsd_folder']
+
+ # Get the file list.
+ file_list = glob(rmsd_folder + sep + glob_pat)
+
+ # Sort the file list Alphanumeric, reverted.
+ file_list_sort = sort_filenames(filenames=file_list, rev=True)
+
+ for cur_file in file_list_sort:
+ print(key, cur_file)
+
+
+ # Load the interpreter.
+ #self.interpreter = Interpreter(show_script=False,
raise_relax_error=True)
+ #self.interpreter.populate_self()
+ #self.interpreter.on(verbose=False)
+
+
+
r25612 - in /trunk/auto_analyses: __init__.py relax_disp_repeat_cpmg.py