Author: bugman
Date: Wed Mar 17 01:31:41 2010
New Revision: 11017
URL: http://svn.gna.org/viewcvs/relax?rev=11017&view=rev
Log:
Creation of the NOE auto-analysis module.
This is a modified copy of the sample script created by Michael Bieri.
The key references are:
Start: https://mail.gna.org/public/relax-devel/2010-03/msg00051.html,
The file: https://mail.gna.org/public/relax-devel/2010-03/msg00052.html,
Details: https://mail.gna.org/public/relax-devel/2010-03/msg00054.html.
Added:
1.3/auto_analyses/noe.py
- copied, changed from r11016, 1.3/sample_scripts/noe.py
Copied: 1.3/auto_analyses/noe.py (from r11016, 1.3/sample_scripts/noe.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/auto_analyses/noe.py?p2=1.3/auto_analyses/noe.py&p1=1.3/sample_scripts/noe.py&r1=11016&r2=11017&rev=11017&view=diff
==============================================================================
--- 1.3/sample_scripts/noe.py (original)
+++ 1.3/auto_analyses/noe.py Wed Mar 17 01:31:41 2010
@@ -1,6 +1,7 @@
###############################################################################
#
#
# Copyright (C) 2004-2008 Edward d'Auvergne
#
+# Copyright (C) 2010 Michael Bieri
#
#
#
# This file is part of the program relax.
#
#
#
@@ -20,57 +21,145 @@
#
#
###############################################################################
-# Script for calculating NOEs.
-##############################
+# Module docstring.
+"""The automatic relaxation curve fitting protocol."""
+
+#python modules
+import time
+from os import sep
+
+# relax module imports.
+from prompt.interpreter import Interpreter
+import generic_fns.structure.main
-# Create the NOE data pipe.
-pipe.create('NOE', 'noe')
-# Load the backbone amide 15N spins from a PDB file.
-structure.read_pdb('Ap4Aase_new_3.pdb')
-structure.load_spins(spin_id='@N')
+class NOE_calc:
+ def __init__(self, pipe_name='noe', noe_ref = None, noe_ref_rmsd = None,
noe_sat = None, noe_sat_rmsd = None, freq = '', unresolved = None, pdb_file =
None, results_folder = None, int_method='height', mc_num=500):
+ """Perform relaxation curve fitting.
-# Load the reference spectrum and saturated spectrum peak intensities.
-spectrum.read_intensities(file='ref.list', spectrum_id='ref_ave')
-spectrum.read_intensities(file='sat.list', spectrum_id='sat_ave')
+ @keyword pipe_name: The name of the data pipe to create.
+ @type pipe_name: str
+ @keyword noe_ref: The NOE reference peak file.
+ @type noe_ref: file
+ @keyword noe_ref_rmsd: Background RMSD of reference NOE spectrum.
+ @type noe_ref_rmsd: int
+ @keyword sat_ref: The NOE saturated peak file.
+ @type sat_ref: file
+ @keyword noe_sat_rmsd: Background RMSD of saturated NOE spectrum.
+ @type noe_sat_rmsd: int
+ @keyword frq: Frequency of current set up.
+ @type frq: int
+ @keyword unresolved: Residues to exclude.
+ @type unresolved: str
+ @keyword pdb_file: Structure file in pdb format.
+ @type pdb_file: str
+ @keyword results_folder:Folder where results files are placed in.
+ @type results_folder: str
+ @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
+ """
-# Set the spectrum types.
-noe.spectrum_type('ref', 'ref_ave')
-noe.spectrum_type('sat', 'sat_ave')
+ # 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.noe_sat = noe_sat
+ self.noe_sat_rmsd = noe_sat_rmsd
+ self.noe_ref = noe_ref
+ self.noe_ref_rmsd =noe_ref_rmsd
+ self.frq = freq
+ self.unresolved = unresolved
+ self.pdb_file = pdb_file
+ self.results_folder = results_folder
+ self.grace_dir = results_folder + sep + 'grace'
+ self.int_method = int_method
+ self.mc_num = mc_num
-# Set the errors.
-spectrum.baseplane_rmsd(error=3600, spectrum_id='ref_ave')
-spectrum.baseplane_rmsd(error=3000, spectrum_id='sat_ave')
+ # User variable checks.
+ self.check_vars()
-# Individual residue errors.
-spectrum.baseplane_rmsd(error=122000, spectrum_id='ref_ave', spin_id=":114")
-spectrum.baseplane_rmsd(error=8500, spectrum_id='sat_ave', spin_id=":114")
+ # Load the interpreter.
+ self.interpreter = Interpreter(show_script=False, quit=False,
raise_relax_error=True)
+ self.interpreter.populate_self()
+ self.interpreter.on(verbose=False)
-# Peak intensity error analysis.
-spectrum.error_analysis()
+ # Execute.
+ self.run()
-# Deselect unresolved residues.
-deselect.read(file='unresolved')
-# Calculate the NOEs.
-calc()
+ def run(self):
+ """Set up and run the NOE analysis."""
-# Save the NOEs.
-value.write(param='noe', file='noe.out', force=True)
+ # Create the data pipe.
+ self.interpreter.pipe.create(self.pipe_name, 'noe')
-# Create grace files.
-grace.write(y_data_type='ref_ave', file='ref.agr', force=True)
-grace.write(y_data_type='sat_ave', file='sat.agr', force=True)
-grace.write(y_data_type='noe', file='noe.agr', force=True)
+ # 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')
+
+ # Update Progress bar
+ print 'Progress: 20%'
+
+ # Load the reference spectrum and saturated spectrum peak
intensities.
+ self.interpreter.spectrum.read_intensities(file=self.noe_ref,
spectrum_id='ref', int_method=self.int_method, heteronuc='N', proton='H')
+ self.interpreter.spectrum.read_intensities(file=self.noe_sat,
spectrum_id='sat', int_method=self.int_method, heteronuc='N', proton='H')
-# View the grace files.
-grace.view(file='ref.agr')
-grace.view(file='sat.agr')
-grace.view(file='noe.agr')
+ # Set the spectrum types.
+ self.interpreter.noe.spectrum_type('ref', 'ref')
+ self.interpreter.noe.spectrum_type('sat', 'sat')
+
+ # Set the errors.
+ self.interpreter.spectrum.baseplane_rmsd(error=self.noe_ref_rmsd,
spectrum_id='ref')
+ self.interpreter.spectrum.baseplane_rmsd(error=self.noe_sat_rmsd,
spectrum_id='sat')
+
+ # Update Progress bar
+ print 'Progress: 40%'
+
+ # 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
-# Write the results.
-results.write(file='results', dir=None, force=True)
+ # Calculate the NOEs.
+ self.interpreter.calc()
-# Save the program state.
-state.save('save', force=True)
+ # Update Progress bar
+ print 'Progress: 60%'
+
+ # Save the NOEs.
+ self.interpreter.value.write(param='noe',
file='noe_'+str(self.frq)+'.out', dir = self.results_folder, force=True)
+
+ # Create grace files.
+ self.interpreter.grace.write(y_data_type='ref', file='ref.agr', dir
= self.grace_dir, force=True)
+ self.interpreter.grace.write(y_data_type='sat', file='sat.agr', dir
= self.grace_dir, force=True)
+ self.interpreter.grace.write(y_data_type='noe', file='noe.agr', dir
= self.grace_dir, force=True)
+
+ # Update Progress bar
+ print 'Progress: 80%'
+
+ # Write the results.
+ self.interpreter.results.write(file='results',
dir=self.results_folder, force=True)
+
+ # Save the program state.
+ self.interpreter.state.save(state = 'save', dir=self.results_folder,
force=True)
+
+ # Update Progress bar
+ print 'Progress: 100%'
+
+
+ def check_vars(self):
+ """Check that the user has set the variables correctly."""
+
+ # Sequence data.
+
+
r11017 - /1.3/auto_analyses/noe.py