Author: bugman
Date: Fri Nov 10 08:21:56 2006
New Revision: 2800
URL: http://svn.gna.org/viewcvs/relax?rev=2800&view=rev
Log:
Ported r2798 and r2799 from the 1.3 line (fix for bug #7676).
The command used was:
svn merge -r2797:2799 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
These changes fix bug #7676 (https://gna.org/bugs/?7676) reported by Stephen
Headey <s dot j dot
headey at massey dot ac dot nz>.
Modified:
1.2/generic_fns/intensity.py
Modified: 1.2/generic_fns/intensity.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/generic_fns/intensity.py?rev=2800&r1=2799&r2=2800&view=diff
==============================================================================
--- 1.2/generic_fns/intensity.py (original)
+++ 1.2/generic_fns/intensity.py Fri Nov 10 08:21:56 2006
@@ -29,6 +29,40 @@
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).
+ 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.
@@ -80,8 +114,12 @@
raise RelaxError, "Improperly formatted XEasy file."
# Nuclei names.
- x_name = line[7]
- h_name = line[4]
+ 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:
@@ -90,7 +128,42 @@
raise RelaxError, "The peak intensity value " + `intensity` + "
from the line " + `line` + " is invalid."
# Return the data.
- return res_num, x_name, h_name, intensity
+ 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):
@@ -111,13 +184,22 @@
# 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 self.relax.data.run_names:
@@ -128,22 +210,30 @@
raise RelaxNoSequenceError, self.run
# Extract the data from the file.
- file_data = self.relax.IO.extract_data(file, dir)
+ 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.
- file_data = file_data[2:]
+ self.file_data = self.file_data[num:]
# Strip the data.
- file_data = self.relax.IO.strip(file_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(file_data)):
+ for i in xrange(len(self.file_data)):
# Extract the data.
- res_num, X_name, H_name, intensity = self.intensity(file_data[i])
+ 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:
- print "Skipping the data: " + `file_data[i]`
+ warn(RelaxWarning("Proton and heteronucleus names do not
match, skipping the data %s: " % `self.file_data[i]`))
continue
# Find the index of self.relax.data.res[self.run] which
corresponds to res_num.
@@ -153,7 +243,7 @@
index = j
break
if index == None:
- print "Skipping the data: " + `file_data[i]`
+ warn(RelaxWarning("Cannot find residue number %s within the
sequence." % res_num))
continue
# Remap the data structure
'self.relax.data.res[self.run][index]'.
r2800 - /1.2/generic_fns/intensity.py