Author: bugman
Date: Tue Jul 19 08:52:56 2011
New Revision: 13708
URL: http://svn.gna.org/viewcvs/relax?rev=13708&view=rev
Log:
Converted the NOE auto-analysis to operate on a pre setup data pipe.
The previous behaviour was to accept a series of arguments and then all the
user functions were
executed within the auto-analysis. However this eliminates a lot of the
flexibility of relax. So
now the user can set up their sequence data and peak height data as they see
fit, and the
auto-analysis will take that as the starting point.
Modified:
branches/gui_testing/auto_analyses/noe.py
Modified: branches/gui_testing/auto_analyses/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/gui_testing/auto_analyses/noe.py?rev=13708&r1=13707&r2=13708&view=diff
==============================================================================
--- branches/gui_testing/auto_analyses/noe.py (original)
+++ branches/gui_testing/auto_analyses/noe.py Tue Jul 19 08:52:56 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2008 Edward d'Auvergne
#
+# Copyright (C) 2004-2011 Edward d'Auvergne
#
# Copyright (C) 2010 Michael Bieri
#
#
#
# This file is part of the program relax.
#
@@ -30,43 +30,26 @@
# relax module imports.
from prompt.interpreter import Interpreter
+from generic_fns.pipes import cdp_name, has_pipe, switch
import generic_fns.structure.main
from status import Status; status = Status()
class NOE_calc:
- def __init__(self, pipe_name='noe', noe_ref=None, noe_ref_rmsd=None,
noe_sat=None, noe_sat_rmsd=None, seq_args=None, unresolved=None,
pdb_file=None, output_file='noe.out', results_dir=None, int_method='height',
heteronuc='N', proton='H', heteronuc_pdb='N'):
+ def __init__(self, pipe_name=None, output_file='noe.out',
results_dir=None):
"""Perform relaxation curve fitting.
- @keyword pipe_name: The name of the data pipe to create.
+ To use this auto-analysis, a data pipe with all the required data
needs to be set up. This data pipe should contain the NOE peak intensities
from the saturated and reference spectra, peak intensity errors either from
the baseplane noise or replicated spectra, all of the spins loaded and
unresolved spins deselected,
+
+ @keyword pipe_name: The name of the data pipe containing all of
the data for the analysis.
@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 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 unresolved: Residues to exclude.
- @type unresolved: str
- @keyword pdb_file: Structure file in pdb format.
- @type pdb_file: str
@keyword output_file: Name of the output file.
@type output_file: str
@keyword results_dir: Folder where results files are placed in.
@type results_dir: str
@keyword int_method: The integration method, one of 'height',
'point sum' or 'other'.
@type int_method: str
- @keyword heteronuc: Name of heteronucleus of peak list.
- @type heteronuc: str
- @keyword proton: Name of proton of peak list.
- @type proton: str
- @keyword heteronuc_pdb: Name of heteronucleus of PDB file.
- @type heteronuc_pdb: str
"""
# Execution lock.
@@ -74,26 +57,19 @@
# Store the args.
self.pipe_name = pipe_name
- 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.seq_args = seq_args
- self.unresolved = unresolved
- self.pdb_file = pdb_file
self.output_file = output_file
self.results_dir = results_dir
if self.results_dir:
self.grace_dir = results_dir + sep + 'grace'
else:
self.grace_dir = 'grace'
- self.int_method = int_method
- self.heteronuc = heteronuc
- self.proton = proton
- self.heteronuc_pdb = heteronuc_pdb
- # 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)
@@ -110,41 +86,8 @@
def run(self):
"""Set up and run the NOE analysis."""
- # Create the data pipe.
- self.interpreter.pipe.create(self.pipe_name, 'noe')
-
- # Load the sequence.
- if self.pdb_file:
- # Load the PDB file.
- self.interpreter.structure.read_pdb(self.pdb_file)
-
- # Read the spin information.
- generic_fns.structure.main.load_spins(spin_id=self.heteronuc_pdb)
-
- else:
- # Read the sequence file.
- 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])
-
- # Name the spins.
- self.interpreter.spin.name(name=self.heteronuc)
-
- # 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=self.heteronuc,
proton=self.proton)
- self.interpreter.spectrum.read_intensities(file=self.noe_sat,
spectrum_id='sat', int_method=self.int_method, heteronuc=self.heteronuc,
proton=self.proton)
-
- # 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')
-
# Peak intensity error analysis.
self.interpreter.spectrum.error_analysis()
-
- # Deselect unresolved spins.
- self.interpreter.deselect.read(file=self.unresolved, res_num_col=1)
# Calculate the NOEs.
self.interpreter.calc()
@@ -167,6 +110,6 @@
def check_vars(self):
"""Check that the user has set the variables correctly."""
- # Sequence data.
-
-
+ # The pipe name.
+ if not has_pipe(self.pipe_name):
+ raise RelaxNoPipeError(self.pipe_name)
r13708 - /branches/gui_testing/auto_analyses/noe.py