Author: michaelbieri
Date: Sun Mar 14 23:19:55 2010
New Revision: 10993
URL: http://svn.gna.org/viewcvs/relax?rev=10993&view=rev
Log:
Cleaned up relax_fit.py code, which was broken after revision
http://svn.gna.org/viewcvs/relax?rev=10960&view=rev.
Modified:
branches/bieri_gui/auto_analyses/relax_fit.py
Modified: branches/bieri_gui/auto_analyses/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/auto_analyses/relax_fit.py?rev=10993&r1=10992&r2=10993&view=diff
==============================================================================
--- branches/bieri_gui/auto_analyses/relax_fit.py (original)
+++ branches/bieri_gui/auto_analyses/relax_fit.py Sun Mar 14 23:19:55 2010
@@ -22,10 +22,6 @@
# Module docstring.
"""The automatic relaxation curve fitting protocol."""
-
-#python modules
-import time
-from os import sep
# relax module imports.
from prompt.interpreter import Interpreter
@@ -57,96 +53,6 @@
self.relax_times = relax_times
self.int_method = int_method
self.mc_num = mc_num
- self.pdb_file = pdb_file
- self.unresolved = unresolved
- self.directory = directory
- self.grace_dir = self.directory + sep + 'grace'
- self.rx_type = rx_type
- self.freq = str(freq)
-
- # User variable checks.
- self.check_vars()
-
- # Load the interpreter.
- self.interpreter = Interpreter(show_script=False, quit=False,
raise_relax_error=True)
- self.interpreter.populate_self()
- self.interpreter.on(verbose=False)
-
- # Execute.
- self.run()
-
-
- def run(self):
- """Set up and run the curve-fitting."""
-
- # Create the data pipe.
- self.interpreter.pipe.create(self.pipe_name, 'relax_fit')
-
- # Load the sequence.
- self.interpreter.sequence.read(file=self.seq_args[0],
dir=self.seq_args[1], mol_name_col=self.seq_args[2],
res_num_col=self.seq_args[3], res_name_col=self.seq_args[4],
spin_num_col=self.seq_args[5], spin_name_col=self.seq_args[6],
sep=self.seq_args[7])
-
- # Loop over the spectra.
- for i in xrange(len(self.file_names)):
- # Load the peak intensities.
-
self.interpreter.spectrum.read_intensities(file=self.file_names[i],
spectrum_id=self.file_names[i], int_method=self.int_method)
-
- # Set the relaxation times.
- self.interpreter.relax_fit.relax_time(time=self.relax_times[i]),
spectrum_id=self.file_names[i])
-###############################################################################
-#
#
-# Copyright (C) 2004-2010 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax.
#
-#
#
-# relax 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 2 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# relax 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 relax; if not, write to the Free Software
#
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
-#
#
-###############################################################################
-
-# Module docstring.
-"""The automatic relaxation curve fitting protocol."""
-
-# relax module imports.
-from prompt.interpreter import Interpreter
-
-
-
-class Relax_fit:
- def __init__(self, pipe_name='rx', seq_args=None, file_names=None,
relax_times=None, int_method='height', mc_num=500):
- """Perform relaxation curve fitting.
-
- @keyword pipe_name: The name of the data pipe to create.
- @type pipe_name: str
- @keyword seq_args: The sequence data (file name, dir,
mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col, sep).
These are the arguments to the sequence.read() user function, for more
information please see the documentation for that function.
- @type seq_args: list of lists of [str, None or str, None or
int, None or int, None or int, None or int, None or int, None or int, None or
int, None or str]
- @keyword file_names: A list of all the peak list file names.
- @type file_names: list of str
- @keyword relax_times: The list of relaxation times corresponding
to file_names. These two lists must be of the same size.
- @type relax_times: list of float
- @keyword int_method: The integration method, one of 'height',
'point sum' or 'other'.
- @type int_method: str
- @keyword mc_num: The number of Monte Carlo simulations to be
used for error analysis at the end of the analysis.
- @type mc_num: int
- """
-
- # Store the args.
- self.pipe_name = pipe_name
- self.seq_args = seq_args
- self.file_names = file_names
- self.relax_times = relax_times
- self.int_method = int_method
- self.mc_num = mc_num
# User variable checks.
self.check_vars()
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Re: r10993 - /branches/bieri_gui/auto_analyses/relax_fit.py