Author: michaelbieri
Date: Wed Mar 10 01:57:51 2010
New Revision: 10960
URL: http://svn.gna.org/viewcvs/relax?rev=10960&view=rev
Log:
everted the changes of relax_fit.py to original version of Edward
d'Auvergne.
See
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/auto_analyses/relax_fit.py?rev=10687&view=log
for more informations.
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=10960&r1=10959&r2=10960&view=diff
==============================================================================
--- branches/bieri_gui/auto_analyses/relax_fit.py (original)
+++ branches/bieri_gui/auto_analyses/relax_fit.py Wed Mar 10 01:57:51 2010
@@ -29,25 +29,17 @@
# relax module imports.
from prompt.interpreter import Interpreter
-import generic_fns.structure.main
-
class Relax_fit:
- def __init__(self, pipe_name='rx', rx_type = 'x', freq = '',
seq_args=None, directory = None, file_names=None, relax_times=None,
int_method='height', mc_num=500, pdb_file = None, unresolved = None):
+ 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 freq: Spectrometer frequency.
- @type freq: str
- @keyword rx_type: Type of Rx analysis: R1 or R2
- @type rx_type: 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 directory: Location of the generated results files.
- @type directory: str, directory
@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.
@@ -56,14 +48,10 @@
@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
- @keyword pdb_file: The structure file.
- @type pdb_file: str, file
- @keyword unresolved: Unresolved residues.
- @type unresolved: str
"""
# Store the args.
- self.pipe_name = pipe_name + ' ' +
str(time.asctime(time.localtime())) # add date and time to allow multiple
executions of relax_fit
+ self.pipe_name = pipe_name
self.seq_args = seq_args
self.file_names = file_names
self.relax_times = relax_times
@@ -95,37 +83,112 @@
self.interpreter.pipe.create(self.pipe_name, 'relax_fit')
# Load the sequence.
- if self.pdb_file == '!!! Sequence file selected !!!': # load
sequence of file
- print 'Sequence file' # FIXME
- #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])
-
- else: # load PDB File
- self.interpreter.structure.read_pdb(self.pdb_file)
- generic_fns.structure.main.load_spins(spin_id='@N')
+ 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, heteronuc='N',
proton='H')
+
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=float(self.relax_times[i]),
spectrum_id=self.file_names[i])
+
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()
+
+ # 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])
# Specify the duplicated spectra.
for i in range(len(self.file_names)):
for j in range(i+1, len(self.file_names)):
# Relax times match, so this is a replicate.
if self.relax_times[i] == self.relax_times[j]:
-
self.interpreter.spectrum.replicated(spectrum_ids=[self.file_names[i],
self.file_names[j]])
+
self.interpreter.spectrum.replicated(spectrum_ids=[self.file_names[i],
self.file_names[i]])
# Peak intensity error analysis.
self.interpreter.spectrum.error_analysis()
# Deselect unresolved spins.
- if self.unresolved == '':
- print ''
- else:
- self.interpreter.deselect.read(file='unresolved') # FIXME.
relax should read the list without creating a file
+ self.interpreter.deselect.read(file='unresolved')
# Set the relaxation curve type.
self.interpreter.relax_fit.select_model('exp')
@@ -144,20 +207,27 @@
self.interpreter.monte_carlo.error_analysis()
# Save the relaxation rates.
- self.interpreter.value.write(param='rx',
file='r'+self.rx_type+'_'+self.freq+'.out', dir = self.directory,
force=True)
+ self.interpreter.value.write(param='rx', file='rx.out', force=True)
# Save the results.
- self.interpreter.results.write(file='results', dir =
self.directory, force=True)
+ self.interpreter.results.write(file='results', force=True)
# Create Grace plots of the data.
- self.interpreter.grace.write(y_data_type='chi2', file='chi2.agr',
dir = self.grace_dir, force=True) # Minimised chi-squared value.
- self.interpreter.grace.write(y_data_type='i0', file='i0.agr', dir
= self.grace_dir, force=True) # Initial peak intensity.
- self.interpreter.grace.write(y_data_type='rx',
file='r'+self.rx_type+'_'+self.freq+'.agr', dir = self.grace_dir,
force=True) # Relaxation rate.
- self.interpreter.grace.write(x_data_type='relax_times',
y_data_type='int', file='intensities.agr', dir = self.grace_dir,
force=True) # Average peak intensities.
- self.interpreter.grace.write(x_data_type='relax_times',
y_data_type='int', norm=True, file='intensities_norm.agr', dir =
self.grace_dir, force=True) # Average peak intensities (normalised).
+ self.interpreter.grace.write(y_data_type='chi2', file='chi2.agr',
force=True) # Minimised chi-squared value.
+ self.interpreter.grace.write(y_data_type='i0', file='i0.agr',
force=True) # Initial peak intensity.
+ self.interpreter.grace.write(y_data_type='rx', file='rx.agr',
force=True) # Relaxation rate.
+ self.interpreter.grace.write(x_data_type='relax_times',
y_data_type='int', file='intensities.agr', force=True) # Average peak
intensities.
+ self.interpreter.grace.write(x_data_type='relax_times',
y_data_type='int', norm=True, file='intensities_norm.agr', force=True) #
Average peak intensities (normalised).
+
+ # Display the Grace plots.
+ self.interpreter.grace.view(file='chi2.agr')
+ self.interpreter.grace.view(file='i0.agr')
+ self.interpreter.grace.view(file='rx.agr')
+ self.interpreter.grace.view(file='intensities.agr')
+ self.interpreter.grace.view(file='intensities_norm.agr')
# Save the program state.
- self.interpreter.state.save(state =
'r'+self.rx_type+'_'+self.freq+'.save', dir = self.directory, force=True)
+ self.interpreter.state.save('rx.save', force=True)
def check_vars(self):
@@ -175,3 +245,65 @@
raise RelaxError("The column components of the seq_args
user variable '%s' must be either None or integers." % self.seq_args)
+
+ # Specify the duplicated spectra.
+ for i in range(len(self.file_names)):
+ for j in range(i+1, len(self.file_names)):
+ # Relax times match, so this is a replicate.
+ if self.relax_times[i] == self.relax_times[j]:
+
self.interpreter.spectrum.replicated(spectrum_ids=[self.file_names[i],
self.file_names[i]])
+
+ # Peak intensity error analysis.
+ self.interpreter.spectrum.error_analysis()
+
+ # Deselect unresolved spins.
+ self.interpreter.deselect.read(file='unresolved')
+
+ # Set the relaxation curve type.
+ self.interpreter.relax_fit.select_model('exp')
+
+ # Grid search.
+ self.interpreter.grid_search(inc=11)
+
+ # Minimise.
+ self.interpreter.minimise('simplex', scaling=False,
constraints=False)
+
+ # Monte Carlo simulations.
+ self.interpreter.monte_carlo.setup(number=self.mc_num)
+ self.interpreter.monte_carlo.create_data()
+ self.interpreter.monte_carlo.initial_values()
+ self.interpreter.minimise('simplex', scaling=False,
constraints=False)
+ self.interpreter.monte_carlo.error_analysis()
+
+ # Save the relaxation rates.
+ self.interpreter.value.write(param='rx',
file='r'+self.rx_type+'_'+self.freq+'.out', dir = self.directory,
force=True)
+
+ # Save the results.
+ self.interpreter.results.write(file='results', dir =
self.directory, force=True)
+
+ # Create Grace plots of the data.
+ self.interpreter.grace.write(y_data_type='chi2', file='chi2.agr',
dir = self.grace_dir, force=True) # Minimised chi-squared value.
+ self.interpreter.grace.write(y_data_type='i0', file='i0.agr', dir
= self.grace_dir, force=True) # Initial peak intensity.
+ self.interpreter.grace.write(y_data_type='rx',
file='r'+self.rx_type+'_'+self.freq+'.agr', dir = self.grace_dir,
force=True) # Relaxation rate.
+ self.interpreter.grace.write(x_data_type='relax_times',
y_data_type='int', file='intensities.agr', dir = self.grace_dir,
force=True) # Average peak intensities.
+ self.interpreter.grace.write(x_data_type='relax_times',
y_data_type='int', norm=True, file='intensities_norm.agr', dir =
self.grace_dir, force=True) # Average peak intensities (normalised).
+
+ # Save the program state.
+ self.interpreter.state.save(state =
'r'+self.rx_type+'_'+self.freq+'.save', dir = self.directory, force=True)
+
+
+ def check_vars(self):
+ """Check that the user has set the variables correctly."""
+
+ # Sequence data.
+ if not isinstance(self.seq_args, list):
+ raise RelaxError("The seq_args user variable '%s' must be a
list." % self.seq_args)
+ if len(self.seq_args) != 8:
+ raise RelaxError("The seq_args user variable '%s' must be a
list with eight elements." % self.seq_args)
+ if not isinstance(self.seq_args[0], str):
+ raise RelaxError("The file name component of the seq_args user
variable '%s' must be a string." % self.seq_args)
+ for i in range(1, 8):
+ if self.seq_args[i] != None and not
isinstance(self.seq_args[i], int):
+ raise RelaxError("The column components of the seq_args
user variable '%s' must be either None or integers." % self.seq_args)
+
+
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Re: r10960 - /branches/bieri_gui/auto_analyses/relax_fit.py