Author: bugman
Date: Thu Apr 24 17:33:56 2008
New Revision: 5987
URL: http://svn.gna.org/viewcvs/relax?rev=5987&view=rev
Log:
Converted all class methods into module functions, and deleted the class.
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=5987&r1=5986&r2=5987&view=diff
==============================================================================
--- 1.3/generic_fns/intensity.py (original)
+++ 1.3/generic_fns/intensity.py Thu Apr 24 17:33:56 2008
@@ -34,239 +34,229 @@
from relax_warnings import RelaxWarning
-
-
-
-class Intensity:
- def __init__(self, relax):
- """Class containing functions for handelling peak intensities."""
-
- self.relax = relax
-
-
- def det_dimensions(self):
- """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(self.file_data)):
- # Extract the data.
- res_num, w1_name, w2_name, intensity =
self.intensity(self.file_data[i])
-
- # Proton in w1, heteronucleus in w2.
- if w1_name == self.proton and w2_name == self.heteronuc:
- # Set the proton dimension.
- self.H_dim = 'w1'
-
- # Print out.
- print "The proton dimension is w1"
-
- # Don't continue (waste of time).
+def det_dimensions():
+ """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(self.file_data)):
+ # Extract the data.
+ res_num, w1_name, w2_name, intensity =
self.intensity(self.file_data[i])
+
+ # Proton in w1, heteronucleus in w2.
+ if w1_name == self.proton and w2_name == self.heteronuc:
+ # Set the proton dimension.
+ self.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 == self.heteronuc and w2_name == self.proton:
+ # Set the proton dimension.
+ self.H_dim = 'w2'
+
+ # Print out.
+ print "The proton dimension is w2"
+
+ # Don't continue (waste of time).
+ break
+
+
+def intensity_sparky(line):
+ """Function for returning relevant data from the Sparky peak intensity
line.
+
+ The residue number, heteronucleus and proton names, and peak intensity
will be returned.
+ """
+
+ # The Sparky assignment.
+ 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 self.int_col == None:
+ self.int_col = 3
+
+ # Intensity.
+ try:
+ intensity = float(line[self.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):
+ """Function for returning relevant data from the XEasy peak intensity
line.
+
+ The residue number, heteronucleus and proton names, and peak intensity
will be returned.
+ """
+
+ # 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 self.H_dim == 'w1':
+ h_name = line[4]
+ x_name = line[7]
+ else:
+ x_name = line[4]
+ h_name = line[7]
+
+ # Intensity (located in column 10).
+ try:
+ intensity = float(line[10])
+ 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():
+ """Function for determining how many header lines are in the intensity
file.
+
+ @return: The number of header lines.
+ @rtype: int
+ """
+
+ # Sparky.
+ #########
+
+ # Assume the Sparky file has two header lines!
+ if self.format == 'sparky':
+ return 2
+
+
+ # XEasy.
+ ########
+
+ # Loop over the lines of the file until a peak intensity value is
reached.
+ header_lines = 0
+ for i in xrange(len(self.file_data)):
+ # Try to see if the intensity can be extracted.
+ try:
+ self.intensity(self.file_data[i])
+ 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(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
+
+ # Format argument.
+ format_list = ['sparky', 'xeasy']
+ if self.format not in format_list:
+ raise RelaxArgNotInListError, ('format', self.format, format_list)
+
+ # Sparky.
+ if self.format == 'sparky':
+ # Print out.
+ print "Sparky formatted data file.\n"
+
+ # Set the intensity reading function.
+ self.intensity = self.intensity_sparky
+
+ # XEasy.
+ elif self.format == 'xeasy':
+ # Print out.
+ print "XEasy formatted data file.\n"
+
+ # Set the intensity reading function.
+ self.intensity = self.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
+
+ # Test if sequence data is loaded.
+ if not relax_data_store.res.has_key(self.run):
+ raise RelaxNoSequenceError, self.run
+
+ # Extract the data from the file.
+ self.file_data = self.relax.IO.extract_data(file, dir)
+
+ # Determine the number of header lines.
+ num = self.number_of_header_lines()
+ print "Number of header lines found: " + `num`
+
+ # Remove the header.
+ self.file_data = self.file_data[num:]
+
+ # Strip the data.
+ self.file_data = self.relax.IO.strip(self.file_data)
+
+ # Determine the proton and heteronucleus dimensions in the XEasy text
file.
+ if self.format == 'xeasy':
+ self.det_dimensions()
+
+ # Loop over the peak intensity data.
+ for i in xrange(len(self.file_data)):
+ # Extract the data.
+ res_num, H_name, X_name, intensity =
self.intensity(self.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]`))
+ 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
-
- # Heteronucleus in w1, proton in w2.
- if w1_name == self.heteronuc and w2_name == self.proton:
- # Set the proton dimension.
- self.H_dim = 'w2'
-
- # Print out.
- print "The proton dimension is w2"
-
- # Don't continue (waste of time).
- break
-
-
- def intensity_sparky(self, line):
- """Function for returning relevant data from the Sparky peak
intensity line.
-
- The residue number, heteronucleus and proton names, and peak
intensity will be returned.
- """
-
- # The Sparky assignment.
- 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 self.int_col == None:
- self.int_col = 3
-
- # Intensity.
- try:
- intensity = float(line[self.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(self, line):
- """Function for returning relevant data from the XEasy peak
intensity line.
-
- The residue number, heteronucleus and proton names, and peak
intensity will be returned.
- """
-
- # 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 self.H_dim == 'w1':
- h_name = line[4]
- x_name = line[7]
- else:
- x_name = line[4]
- h_name = line[7]
-
- # Intensity (located in column 10).
- try:
- intensity = float(line[10])
- 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(self):
- """Function for determining how many header lines are in the
intensity file.
-
- @return: The number of header lines.
- @rtype: int
- """
-
- # Sparky.
- #########
-
- # Assume the Sparky file has two header lines!
- if self.format == 'sparky':
- return 2
-
-
- # XEasy.
- ########
-
- # Loop over the lines of the file until a peak intensity value is
reached.
- header_lines = 0
- for i in xrange(len(self.file_data)):
- # Try to see if the intensity can be extracted.
- try:
- self.intensity(self.file_data[i])
- 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(self, 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
-
- # Format argument.
- format_list = ['sparky', 'xeasy']
- if self.format not in format_list:
- raise RelaxArgNotInListError, ('format', self.format,
format_list)
-
- # Sparky.
- if self.format == 'sparky':
- # Print out.
- print "Sparky formatted data file.\n"
-
- # Set the intensity reading function.
- self.intensity = self.intensity_sparky
-
- # XEasy.
- elif self.format == 'xeasy':
- # Print out.
- print "XEasy formatted data file.\n"
-
- # Set the intensity reading function.
- self.intensity = self.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
-
- # Test if sequence data is loaded.
- if not relax_data_store.res.has_key(self.run):
- raise RelaxNoSequenceError, self.run
-
- # Extract the data from the file.
- self.file_data = self.relax.IO.extract_data(file, dir)
-
- # Determine the number of header lines.
- num = self.number_of_header_lines()
- print "Number of header lines found: " + `num`
-
- # Remove the header.
- self.file_data = self.file_data[num:]
-
- # Strip the data.
- self.file_data = self.relax.IO.strip(self.file_data)
-
- # Determine the proton and heteronucleus dimensions in the XEasy
text file.
- if self.format == 'xeasy':
- self.det_dimensions()
-
- # Loop over the peak intensity data.
- for i in xrange(len(self.file_data)):
- # Extract the data.
- res_num, H_name, X_name, intensity =
self.intensity(self.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]`))
- 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))
- 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:
- continue
-
- # Assign the data.
- self.assign_func(run=self.run, i=index, intensity=intensity)
+ if index == None:
+ warn(RelaxWarning("Cannot find residue number %s within the
sequence." % res_num))
+ 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:
+ continue
+
+ # Assign the data.
+ self.assign_func(run=self.run, i=index, intensity=intensity)
r5987 - /1.3/generic_fns/intensity.py