Author: bugman
Date: Tue Jul 19 16:32:08 2011
New Revision: 13738
URL: http://svn.gna.org/viewcvs/relax?rev=13738&view=rev
Log:
Modified the Rx auto-analysis to now accept a fully loaded data pipe.
The calculations are now performed on a pre-created data pipe containing the
sequence info,
selection state, peak intensities, and replicated spectra or baseplane RMSDs.
Modified:
branches/gui_testing/auto_analyses/relax_fit.py
Modified: branches/gui_testing/auto_analyses/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/gui_testing/auto_analyses/relax_fit.py?rev=13738&r1=13737&r2=13738&view=diff
==============================================================================
--- branches/gui_testing/auto_analyses/relax_fit.py (original)
+++ branches/gui_testing/auto_analyses/relax_fit.py Tue Jul 19 16:32:08 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2010 Edward d'Auvergne
#
+# Copyright (C) 2004-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -27,75 +27,59 @@
from os import sep
# relax module imports.
+from generic_fns.pipes import cdp_name, has_pipe, switch
import generic_fns.structure.main
from prompt.interpreter import Interpreter
-from relax_errors import RelaxError
from status import Status; status = Status()
class Relax_fit:
- def __init__(self, file_root='rx', pipe_name='rx',
results_directory=None, seq_args=None, file_names=None, relax_times=None,
pdb_file=None, unresolved='unresolved', int_method='height', heteronuc='N',
proton='H', load_spin_ids=None, mc_num=500, inc='11', view_plots=True):
+ def __init__(self, pipe_name=None, file_root='rx', results_dir=None,
grid_inc='11', mc_sim_num=500, view_plots=True):
"""Perform relaxation curve fitting.
+ To use this auto-analysis, a data pipe with all the required data
needs to be set up. This data pipe should contain the following:
+
+ - All the spins loaded.
+ - Unresolved spins deselected.
+ - All the peak intensities loaded and relaxation delay times set.
+ - Either the baseplane noise RMDS values should be set or
replicated spectra loaded.
+
+ @keyword pipe_name: The name of the data pipe containing all of
the data for the analysis.
+ @type pipe_name: str
@keyword file_root: File root of the output filea.
@type file_root: str
- @keyword pipe_name: The name of the data pipe to create.
- @type pipe_name: str
- @keyword results_directory: The directory, where results files
are saved.
- @type results_directory: 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 pdb_file: Name of the PDB file.
- @type pdb_file: str
- @keyword unresolved: Filename of the unresolved spin list.
- @type unresolved: str
- @keyword int_method: The integration method, one of 'height',
'point sum' or 'other'.
- @type int_method: str
- @keyword heteronuc: Label of hetero nucleus in the peak
intensity file.
- @type heteronuc: str
- @keyword proton: Label of proton in the peak intensity file.
- @type proton: str
- @keyword load_spin_ids: Id of spin to extract in PDB file.
- @type load_spin_ids: 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 inc: Number of grid search increments.
- @type inc: int
+ @keyword results_dir: The directory where results files are saved.
+ @type results_dir: str
+ @keyword grid_inc: Number of grid search increments.
+ @type grid_inc: int
+ @keyword mc_sim_num: The number of Monte Carlo simulations to be
used for error analysis at the end of the analysis.
+ @type mc_sim_num: int
@keyword view_plots: Flag to automatically view grace plots after
calculation.
- @type view_plots: boolean
+ @type view_plots: bool
"""
# Execution lock.
status.exec_lock.acquire('auto relax fit')
# Store the args.
+ self.pipe_name = pipe_name
self.file_root = file_root
- self.pipe_name = pipe_name
- self.results_directory = results_directory
- if results_directory:
- self.grace_dir = results_directory+sep+'grace'
+ self.results_dir = results_dir
+ if self.results_dir:
+ self.grace_dir = results_dir + sep + 'grace'
else:
- self.grace_dir = None
- self.seq_args = seq_args
- self.file_names = file_names
- self.relax_times = relax_times
- self.pdb_file = pdb_file
- self.unresolved = unresolved
+ self.grace_dir = 'grace'
+ self.mc_sim_num = mc_sim_num
+ self.grid_inc = grid_inc
self.view_plots = view_plots
- self.int_method = int_method
- self.heteronuc = heteronuc
- self.proton = proton
- self.load_spin_ids = load_spin_ids
- self.mc_num = mc_num
- self.inc = inc
- # User variable checks.
+ # Data checks.
self.check_vars()
+
+ # Set the data pipe to the current data pipe.
+ if self.pipe_name != cdp_name():
+ switch(self.pipe_name)
# Load the interpreter.
self.interpreter = Interpreter(show_script=False, quit=False,
raise_relax_error=True)
@@ -112,59 +96,30 @@
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.
- if self.pdb_file: # load PDB File
- self.interpreter.structure.read_pdb(self.pdb_file)
- generic_fns.structure.main.load_spins(spin_id=self.load_spin_ids)
-
- else:
- 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=self.heteronuc, proton=self.proton)
-
- # 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]])
-
# Peak intensity error analysis.
self.interpreter.spectrum.error_analysis()
-
- # Deselect unresolved spins.
- self.interpreter.deselect.read(file=self.unresolved)
# Set the relaxation curve type.
self.interpreter.relax_fit.select_model('exp')
# Grid search.
- self.interpreter.grid_search(inc=self.inc)
+ self.interpreter.grid_search(inc=self.grid_inc)
# 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.setup(number=self.mc_sim_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=self.file_root+'.out',
dir=self.results_directory, force=True)
+ self.interpreter.value.write(param='rx', file=self.file_root+'.out',
dir=self.results_dir, force=True)
# Save the results.
- self.interpreter.results.write(file='results',
dir=self.results_directory, force=True)
+ self.interpreter.results.write(file='results', dir=self.results_dir,
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.
@@ -182,22 +137,12 @@
self.interpreter.grace.view(file='intensities_norm.agr',
dir=self.grace_dir)
# Save the program state.
- self.interpreter.state.save(self.file_root+'.save',
dir=self.results_directory, force=True)
+ self.interpreter.state.save(state=self.file_root+'.save',
dir=self.results_dir, force=True)
def check_vars(self):
"""Check that the user has set the variables correctly."""
- # Sequence data.
- if not self.pdb_file:
- if not isinstance(self.seq_args, list):
- raise RelaxError("The seq_args user variable '%s' must be a
list if a PDB file is not specified." % 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)
-
-
+ # The pipe name.
+ if not has_pipe(self.pipe_name):
+ raise RelaxNoPipeError(self.pipe_name)
r13738 - /branches/gui_testing/auto_analyses/relax_fit.py