Author: bugman
Date: Tue Oct 21 18:35:59 2008
New Revision: 7897
URL: http://svn.gna.org/viewcvs/relax?rev=7897&view=rev
Log:
Renamed the generic_fns.intensity module to generic_fns/spectrum.
Added:
branches/spectral_errors/generic_fns/spectrum.py
- copied unchanged from r7894,
branches/spectral_errors/generic_fns/intensity.py
Removed:
branches/spectral_errors/generic_fns/intensity.py
Removed: branches/spectral_errors/generic_fns/intensity.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/generic_fns/intensity.py?rev=7896&view=auto
==============================================================================
--- branches/spectral_errors/generic_fns/intensity.py (original)
+++ branches/spectral_errors/generic_fns/intensity.py (removed)
@@ -1,420 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2004, 2007-2008 Edward d'Auvergne
#
-# Copyright (C) 2008 Sebastien Morin
#
-#
#
-# This file is part of the program relax.
#
-#
#
-# relax is free software; you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation; either version 2 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# relax is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with relax; if not, write to the Free Software
#
-# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
-#
#
-###############################################################################
-
-# Module docstring.
-"""Module containing functions for the handling of peak intensities."""
-
-
-# Python module imports.
-from re import split
-from warnings import warn
-import string
-import sys
-
-# relax module imports.
-from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id, return_spin
-from generic_fns import pipes
-from relax_errors import RelaxError, RelaxArgNotInListError,
RelaxNoSequenceError
-from relax_io import extract_data, strip
-from relax_warnings import RelaxWarning, RelaxNoSpinWarning
-
-
-def det_dimensions(file_data, proton, heteronuc, int_col):
- """Determine which are the proton and heteronuclei dimensions of the
XEasy text file.
-
- @return: None
- """
-
- # Loop over the lines of the file until the proton and heteronucleus is
reached.
- for i in xrange(len(file_data)):
- # Extract the data.
- res_num, w1_name, w2_name, intensity = intensity_xeasy(file_data[i],
int_col)
-
- # Proton in w1, heteronucleus in w2.
- if w1_name == proton and w2_name == heteronuc:
- # Set the proton dimension.
- H_dim = 'w1'
-
- # Print out.
- print "The proton dimension is w1"
-
- # Don't continue (waste of time).
- break
-
- # Heteronucleus in w1, proton in w2.
- if w1_name == heteronuc and w2_name == proton:
- # Set the proton dimension.
- H_dim = 'w2'
-
- # Print out.
- print "The proton dimension is w2"
-
- # Don't continue (waste of time).
- break
-
-
-def intensity_generic(line, int_col):
- """Function for returning relevant data from the generic peak intensity
line.
-
- The residue number, heteronucleus and proton names, and peak intensity
will be returned.
-
-
- @param line: The single line of information from the intensity
file.
- @type line: list of str
- @keyword int_col: The column containing the peak intensity data (for a
non-standard formatted
- file).
- @type int_col: int
- @raises RelaxError: When the expected peak intensity is not a float.
- """
-
-
- # Not implemented yet...
-
-
-def intensity_nmrview(line, int_col):
- """Function for returning relevant data from the NMRView peak intensity
line.
-
- The residue number, heteronucleus and proton names, and peak intensity
will be returned.
-
-
- @param line: The single line of information from the intensity
file.
- @type line: list of str
- @keyword int_col: The column containing the peak intensity data. The
default is 16 for
- intensities. Setting the int_col argument to 15 will
use the volumes (or
- evolumes). For a non-standard formatted file, use a
different value.
- @type int_col: int
- @raises RelaxError: When the expected peak intensity is not a float.
- """
-
- # The residue number
- res_num = ''
- try:
- res_num = string.strip(line[1],'{')
- res_num = string.strip(res_num,'}')
- res_num = string.split(res_num,'.')
- res_num = res_num[0]
- except ValueError:
- raise RelaxError, "The peak list is invalid."
-
- # Nuclei names.
- x_name = ''
- if line[8]!='{}':
- x_name = string.strip(line[8],'{')
- x_name = string.strip(x_name,'}')
- x_name = string.split(x_name,'.')
- x_name = x_name[1]
- h_name = ''
- if line[1]!='{}':
- h_name = string.strip(line[1],'{')
- h_name = string.strip(h_name,'}')
- h_name = string.split(h_name,'.')
- h_name = h_name[1]
-
- # The peak intensity column.
- if int_col == None:
- int_col = 16
- if int_col == 16:
- print 'Using peak heights.'
- if int_col == 15:
- print 'Using peak volumes (or evolumes).'
-
- # Intensity.
- try:
- intensity = float(line[int_col])
- except ValueError:
- raise RelaxError, "The peak intensity value " + `intensity` + " from
the line " + `line` + " is invalid."
-
- # Return the data.
- return res_num, h_name, x_name, intensity
-
-
-def intensity_sparky(line, int_col):
- """Function for returning relevant data from the Sparky peak intensity
line.
-
- The residue number, heteronucleus and proton names, and peak intensity
will be returned.
-
-
- @param line: The single line of information from the intensity
file.
- @type line: list of str
- @keyword int_col: The column containing the peak intensity data (for a
non-standard formatted
- file).
- @type int_col: int
- @raises RelaxError: When the expected peak intensity is not a float.
- """
-
-
- # The Sparky assignment.
- assignment = ''
- res_num = ''
- h_name = ''
- x_name = ''
- intensity = ''
- if line[0]!='?-?':
- assignment = split('([A-Z]+)', line[0])
- assignment = assignment[1:-1]
-
- # The residue number.
- try:
- res_num = int(assignment[1])
- except:
- raise RelaxError, "Improperly formatted Sparky file."
-
- # Nuclei names.
- x_name = assignment[2]
- h_name = assignment[4]
-
- # The peak intensity column.
- if int_col == None:
- int_col = 3
-
- # Intensity.
- try:
- intensity = float(line[int_col])
- except ValueError:
- raise RelaxError, "The peak intensity value " + `intensity` + "
from the line " + `line` + " is invalid."
-
- # Return the data.
- return res_num, h_name, x_name, intensity
-
-
-def intensity_xeasy(line, int_col, H_dim='w1'):
- """Function for returning relevant data from the XEasy peak intensity
line.
-
- The residue number, heteronucleus and proton names, and peak intensity
will be returned.
-
-
- @param line: The single line of information from the intensity
file.
- @type line: list of str
- @keyword int_col: The column containing the peak intensity data (for a
non-standard formatted
- file).
- @type int_col: int
- @raises RelaxError: When the expected peak intensity is not a float.
- """
-
- # Test for invalid assignment lines which have the column numbers
changed and return empty data.
- if line[4] == 'inv.':
- return None, None, None, 0.0
-
- # The residue number.
- try:
- res_num = int(line[5])
- except:
- raise RelaxError, "Improperly formatted XEasy file."
-
- # Nuclei names.
- if H_dim == 'w1':
- h_name = line[4]
- x_name = line[7]
- else:
- x_name = line[4]
- h_name = line[7]
-
- # The peak intensity column.
- if int_col == None:
- int_col = 10
-
- # Intensity.
- try:
- intensity = float(line[int_col])
- except ValueError:
- raise RelaxError, "The peak intensity value " + `intensity` + " from
the line " + `line` + " is invalid."
-
- # Return the data.
- return res_num, h_name, x_name, intensity
-
-
-def number_of_header_lines(file_data, format, int_col, intensity):
- """Function for determining how many header lines are in the intensity
file.
-
- @param file_data: The processed results file data.
- @type file_data: list of lists of str
- @param format: The type of file containing peak intensities. This
can currently be one of
- 'generic', 'nmrview', 'sparky' or 'xeasy'.
- @type format: str
- @param int_col: The column containing the peak intensity data (for a
non-standard
- formatted file).
- @type int_col: int
- @param intensity: The intensity extraction function.
- @type intensity: func
- @return: The number of header lines.
- @rtype: int
- """
-
- # Generic.
- ##########
-
- # Assume the generic file has two header lines!
- if format == 'generic':
- return 2
-
- # NMRView.
- ##########
-
- # Assume the NMRView file has six header lines!
- elif format == 'nmrview':
- return 6
-
-
- # Sparky.
- #########
-
- # Assume the Sparky file has two header lines!
- elif format == 'sparky':
- return 2
-
-
- # XEasy.
- ########
-
- # Loop over the lines of the file until a peak intensity value is
reached.
- elif format == 'xeasy':
- header_lines = 0
- for i in xrange(len(file_data)):
- # Try to see if the intensity can be extracted.
- try:
- if int_col:
- intensity(file_data[i], int_col)
- else:
- intensity(file_data[i], int_col)
- except RelaxError:
- header_lines = header_lines + 1
- except IndexError:
- header_lines = header_lines + 1
- else:
- break
-
- # Return the number of lines.
- return header_lines
-
-
-def read(file=None, dir=None, format=None, heteronuc=None, proton=None,
int_col=None, assign_func=None, spectrum_type=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 'generic', 'nmrview', '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
- @keyword spectrum_type: The optional spectrum type to be sent back into
assign_func().
- @type spectrum_type: str
- """
-
- # Format argument.
- format_list = ['generic', 'nmrview', 'sparky', 'xeasy']
- if format not in format_list:
- raise RelaxArgNotInListError, ('format', format, format_list)
-
- # Generic.
- if format == 'generic':
- # Print out.
- print "Generic formatted data file.\n"
-
- # Set the intensity reading function.
- intensity_fn = intensity_generic
-
- # NMRView.
- elif format == 'nmrview':
- # Print out.
- print "NMRView formatted data file.\n"
-
- # Set the intensity reading function.
- intensity_fn = intensity_nmrview
-
- # Sparky.
- elif format == 'sparky':
- # Print out.
- print "Sparky formatted data file.\n"
-
- # Set the intensity reading function.
- intensity_fn = intensity_sparky
-
- # XEasy.
- elif format == 'xeasy':
- # Print out.
- print "XEasy formatted data file.\n"
-
- # Set the default proton dimension.
- H_dim = 'w1'
-
- # Set the intensity reading function.
- intensity_fn = intensity_xeasy
-
- # Test if the current data pipe exists.
- pipes.test()
-
- # Test if sequence data is loaded.
- if not exists_mol_res_spin_data():
- raise RelaxNoSequenceError
-
- # Extract the data from the file.
- file_data = extract_data(file, dir)
-
- # Determine the number of header lines.
- num = number_of_header_lines(file_data, format, int_col, intensity_fn)
- print "Number of header lines found: " + `num`
-
- # Remove the header.
- file_data = file_data[num:]
-
- # Strip the data.
- file_data = strip(file_data)
-
- # Determine the proton and heteronucleus dimensions in the XEasy text
file.
- if format == 'xeasy':
- det_dimensions(file_data=file_data, proton=proton,
heteronuc=heteronuc, int_col=int_col)
-
- # Loop over the peak intensity data.
- for i in xrange(len(file_data)):
- # Extract the data.
- res_num, H_name, X_name, intensity = intensity_fn(file_data[i],
int_col)
-
- # Skip data.
- 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
-
- # 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(RelaxNoSpinWarning(spin_id))
- continue
-
- # Skip deselected spins.
- if not spin.select:
- continue
-
- # Assign the data.
- assign_func(spin=spin, intensity=intensity,
spectrum_type=spectrum_type)
r7897 - in /branches/spectral_errors/generic_fns: intensity.py spectrum.py