Author: bugman
Date: Thu Apr 24 17:53:20 2008
New Revision: 5988
URL: http://svn.gna.org/viewcvs/relax?rev=5988&view=rev
Log:
Converted the read function to the new relax design.
Modified:
1.3/generic_fns/intensity.py
Modified: 1.3/generic_fns/intensity.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/intensity.py?rev=5988&r1=5987&r2=5988&view=diff
==============================================================================
--- 1.3/generic_fns/intensity.py (original)
+++ 1.3/generic_fns/intensity.py Thu Apr 24 17:53:20 2008
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004, 2007 Edward d'Auvergne
#
+# Copyright (C) 2004, 2007-2008 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -30,7 +30,9 @@
# relax module imports.
from data import Data as relax_data_store
+from generic_fns.selection import generate_spin_id, return_spin
from relax_errors import RelaxError, RelaxArgNotInListError,
RelaxNoPipeError, RelaxNoSequenceError
+from relax_io import extract_data, strip
from relax_warnings import RelaxWarning
@@ -171,92 +173,97 @@
return header_lines
-def read(run=None, file=None, dir=None, format=None, heteronuc=None,
proton=None, int_col=None, assign_func=None):
- """Function for reading peak intensity data."""
-
- # Arguments.
- self.run = run
- self.format = format
- self.heteronuc = heteronuc
- self.proton = proton
- self.int_col = int_col
- self.assign_func = assign_func
+def read(file=None, dir=None, format=None, heteronuc=None, proton=None,
int_col=None, assign_func=None):
+ """Read the peak intensity data.
+
+ @keyword file: The name of the file containing the peak
intensities.
+ @type file: str
+ @keyword dir: The directory where the file is located.
+ @type dir: str
+ @keyword format: The type of file containing peak intensities.
This can currently be
+ one of 'sparky' or 'xeasy'.
+ @type format: str
+ @keyword heteronuc: The name of the heteronucleus as specified in
the peak intensity
+ file.
+ @type heteronuc: str
+ @keyword proton: The name of the proton as specified in the peak
intensity file.
+ @type proton: str
+ @keyword int_col: The column containing the peak intensity data
(for a non-standard
+ formatted file).
+ @type int_col: int
+ @keyword assign_func: A function used to place the intensity data
within the spin container.
+ @type assign_func: func
+ """
# Format argument.
format_list = ['sparky', 'xeasy']
- if self.format not in format_list:
- raise RelaxArgNotInListError, ('format', self.format, format_list)
+ if format not in format_list:
+ raise RelaxArgNotInListError, ('format', format, format_list)
# Sparky.
- if self.format == 'sparky':
+ if format == 'sparky':
# Print out.
print "Sparky formatted data file.\n"
# Set the intensity reading function.
- self.intensity = self.intensity_sparky
+ intensity = intensity_sparky
# XEasy.
- elif self.format == 'xeasy':
+ elif format == 'xeasy':
# Print out.
print "XEasy formatted data file.\n"
# Set the intensity reading function.
- self.intensity = self.intensity_xeasy
+ intensity = intensity_xeasy
# Set the default proton dimension.
- self.H_dim = 'w1'
-
- # Test if the run exists.
- if not self.run in relax_data_store.run_names:
- raise RelaxNoPipeError, self.run
+ H_dim = 'w1'
+
+ # Test if the current data pipe exists.
+ if not relax_data_store.current_pipe:
+ raise RelaxNoPipeError
# Test if sequence data is loaded.
- if not relax_data_store.res.has_key(self.run):
- raise RelaxNoSequenceError, self.run
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
# Extract the data from the file.
- self.file_data = self.relax.IO.extract_data(file, dir)
+ file_data = extract_data(file, dir)
# Determine the number of header lines.
- num = self.number_of_header_lines()
+ num = number_of_header_lines()
print "Number of header lines found: " + `num`
# Remove the header.
- self.file_data = self.file_data[num:]
+ file_data = file_data[num:]
# Strip the data.
- self.file_data = self.relax.IO.strip(self.file_data)
+ file_data = strip(file_data)
# Determine the proton and heteronucleus dimensions in the XEasy text
file.
- if self.format == 'xeasy':
- self.det_dimensions()
+ if format == 'xeasy':
+ det_dimensions()
# Loop over the peak intensity data.
- for i in xrange(len(self.file_data)):
+ for i in xrange(len(file_data)):
# Extract the data.
- res_num, H_name, X_name, intensity =
self.intensity(self.file_data[i])
+ res_num, H_name, X_name, intensity = intensity(file_data[i])
# Skip data.
- if X_name != self.heteronuc or H_name != self.proton:
- warn(RelaxWarning("Proton and heteronucleus names do not match,
skipping the data %s: " % `self.file_data[i]`))
+ if X_name != heteronuc or H_name != proton:
+ warn(RelaxWarning("Proton and heteronucleus names do not match,
skipping the data %s: " % `file_data[i]`))
continue
- # Find the index of relax_data_store.res[self.run] which corresponds
to res_num.
- index = None
- for j in xrange(len(relax_data_store.res[self.run])):
- if relax_data_store.res[self.run][j].num == res_num:
- index = j
- break
- if index == None:
- warn(RelaxWarning("Cannot find residue number %s within the
sequence." % res_num))
+ # Get the spin container.
+ spin_id = generate_spin_id(res_num=res_num, spin_name=X_name)
+ spin = return_spin(spin_id)
+ if not spin:
+ warn(RelaxWarning("Cannot find the spin %s within the sequence."
% spin_id))
continue
- # Remap the data structure 'relax_data_store.res[self.run][index]'.
- data = relax_data_store.res[self.run][index]
-
- # Skip unselected residues.
- if not data.select:
+ # Skip unselected spins.
+ if not spin.select:
continue
# Assign the data.
- self.assign_func(run=self.run, i=index, intensity=intensity)
+ assign_func(spin=spin, intensity=intensity)
r5988 - /1.3/generic_fns/intensity.py