Author: bugman
Date: Tue Jul 13 13:28:44 2010
New Revision: 11298
URL: http://svn.gna.org/viewcvs/relax?rev=11298&view=rev
Log:
Major patch for integrating the GUI into the noe calculation.
This patch is from Michael Bieri (https://gna.org/users/michaelbieri) and is
from file #9490
(https://gna.org/support/download.php?file_id=9490) attached to task #6847
(https://gna.org/task/?6847).
Changes include:
- output filename can be specified
- folder, where results files will be placed, can be specified
- label of hetero nucleus and proton of peak lists and pdb file can be
selected
- sequence is read either by sequence file or pdb file
- removed white spaces and progress output.
Modified:
1.3/auto_analyses/noe.py
Modified: 1.3/auto_analyses/noe.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/auto_analyses/noe.py?rev=11298&r1=11297&r2=11298&view=diff
==============================================================================
--- 1.3/auto_analyses/noe.py (original)
+++ 1.3/auto_analyses/noe.py Tue Jul 13 13:28:44 2010
@@ -35,9 +35,13 @@
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):
+ def __init__(self, output_file='noe.out', seq_args=None,
pipe_name='noe', noe_ref=None, noe_ref_rmsd=None, noe_sat=None,
noe_sat_rmsd=None, unresolved=None, pdb_file=None, results_folder=None,
int_method='height', heteronuc='N', proton='H', heteronuc_pdb='N'):
"""Perform relaxation curve fitting.
+ @keyword output_file: Name of the output file.
+ @type output_file: 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 pipe_name: The name of the data pipe to create.
@type pipe_name: str
@keyword noe_ref: The NOE reference peak file.
@@ -48,8 +52,6 @@
@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.
@@ -58,23 +60,29 @@
@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
+ @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
"""
# 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.output_file = output_file
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.grace_dir = results_folder+sep+'grace'
self.int_method = int_method
- self.mc_num = mc_num
+ self.heteronuc = heteronuc
+ self.proton = proton
+ self.heteronuc_pdb = heteronuc_pdb
# User variable checks.
self.check_vars()
@@ -95,66 +103,47 @@
self.interpreter.pipe.create(self.pipe_name, 'noe')
# 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
+ if self.pdb_file: # 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%'
-
+ generic_fns.structure.main.load_spins(spin_id=heteronuc_pdb)
+
+ 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])
+
# 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')
+ 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')
-
- # 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
+ self.interpreter.deselect.read(file=self.unresolved)
# Calculate the NOEs.
self.interpreter.calc()
- # 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)
+ self.interpreter.value.write(param='noe', file=self.output_file, 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%'
+ 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)
# 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):
r11298 - /1.3/auto_analyses/noe.py