r20611 - /branches/peak_intensities/lib/software/nmrview.py -- August 16, 2013 - 19:02

Author: bugman
Date: Fri Aug 16 19:02:03 2013
New Revision: 20611

URL: http://svn.gna.org/viewcvs/relax?rev=20611&view=rev
Log:
The lib.software.nmrview.read_list_intensity() function now operates on the 
Peak_list object.


Modified:
    branches/peak_intensities/lib/software/nmrview.py

Modified: branches/peak_intensities/lib/software/nmrview.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/peak_intensities/lib/software/nmrview.py?rev=20611&r1=20610&r2=20611&view=diff
==============================================================================
--- branches/peak_intensities/lib/software/nmrview.py (original)
+++ branches/peak_intensities/lib/software/nmrview.py Fri Aug 16 19:02:03 2013
@@ -33,24 +33,21 @@
 from lib.warnings import RelaxWarning
 
 
-def read_list_intensity(file_data=None, int_col=None):
-    """Return the peak intensity information from the NMRView peak intensity 
file.
+def read_list_intensity(peak_list=None, file_data=None, int_col=None):
+    """Extract the peak intensity information from the NMRView peak 
intensity file.
 
-    The residue number, heteronucleus and proton names, and peak intensity 
will be returned.
-
-
+    @keyword peak_list: The peak list object to place all data into.
+    @type peak_list:    lib.spectrum.objects.Peak_list instance
     @keyword file_data: The data extracted from the file converted into a 
list of lists.
     @type file_data:    list of lists 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.
-    @return:            The extracted data as a list of lists.  The first 
dimension corresponds to the spin.  The second dimension consists of the 
proton name, heteronucleus name, residue number, the intensity value, and the 
original line of text
-    @rtype:             list of lists of str, str, int, float, str
     """
 
     # Assume the NMRView file has six header lines!
     num = 6
-    print("Number of header lines: " + repr(num))
+    print("Number of header lines: %s" % num)
 
     # Remove the header.
     file_data = file_data[num:]
@@ -85,18 +82,18 @@
             raise RelaxError("The peak list is invalid.")
 
         # Nuclei names.
-        x_name = ''
+        name1 = ''
+        if line[1]!='{}':
+            name1 = line[1].strip('{')
+            name1 = name1.strip('}')
+            name1 = name1.split('.')
+            name1 = name1[1]
+        name2 = ''
         if line[8]!='{}':
-            x_name = line[8].strip('{')
-            x_name = x_name.strip('}')
-            x_name = x_name.split('.')
-            x_name = x_name[1]
-        h_name = ''
-        if line[1]!='{}':
-            h_name = line[1].strip('{')
-            h_name = h_name.strip('}')
-            h_name = h_name.split('.')
-            h_name = h_name[1]
+            name2 = line[8].strip('{')
+            name2 = name2.strip('}')
+            name2 = name2.split('.')
+            name2 = name2[1]
 
         # Intensity.
         try:
@@ -104,8 +101,5 @@
         except ValueError:
             raise RelaxError("The peak intensity value " + repr(intensity) + 
" from the line " + repr(line) + " is invalid.")
 
-        # Append the data.
-        data.append([h_name, x_name, res_num, intensity, line])
-
-    # Return the data.
-    return data
+        # Add the assignment to the peak list object.
+        peak_list.add(res_nums=[res_num, res_num], spin_names=[name1, 
name2], intensity=intensity)