r20503 - /trunk/lib/software/nmrpipe.py -- August 02, 2013 - 13:51

Author: bugman
Date: Fri Aug  2 13:51:50 2013
New Revision: 20503

URL: http://svn.gna.org/viewcvs/relax?rev=20503&view=rev
Log:
Modfied the intensity list to handle intensities for all spectra per spin.

Progress sr #3043: (https://gna.org/support/index.php?3043) - support for 
NMRPipe seriesTab format *.ser.

Troels E. Linnet provided this patch. Commit by: tlinset _aaattt_ 
gmail_dot_com

Signed-off-by: Edward d'Auvergne <edward _att_ nmr-relax _dott_ com>

Modified:
    trunk/lib/software/nmrpipe.py

Modified: trunk/lib/software/nmrpipe.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/software/nmrpipe.py?rev=20503&r1=20502&r2=20503&view=diff
==============================================================================
--- trunk/lib/software/nmrpipe.py (original)
+++ trunk/lib/software/nmrpipe.py Fri Aug  2 13:51:50 2013
@@ -46,13 +46,13 @@
     @rtype:             list of lists of str, str, int, float, str
     """
 
-    # Set start variables
+    # Set start variables.
     modeline = False
     mode = False
     varsline = False
     header = False
 
-    # Loop over lines, to extract variables and find header size
+    # Loop over lines, to extract variables and find header size.
     line_nr = 0
     for line in file_data:
         if len(line) > 0:
@@ -66,44 +66,53 @@
                 break
         line_nr += 1
 
-    # Raise RelaxError, if the MODE is not found
+    # Raise RelaxError, if the MODE is not found.
     if not (modeline and mode):
         raise RelaxError("MODE not detected. Expecting line 2:\nREMARK Mode: 
Summation")
 
-    # Raise RelaxError, if the VARS line is not found
+    # Raise RelaxError, if the VARS line is not found.
     if not (varsline):
         raise RelaxError("VARS not detected. Expecting line 8:\nVARS INDEX 
X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS Z_A0")
 
-    # Raise RelaxError, if the header size is not found
+    # Raise RelaxError, if the header size is not found.
     if not header:
         raise RelaxError("'1' not detected in start of line. Cannot 
determine header size.")
 
-    # Find index of assignment ASS
+    # Find index of assignment ASS.
     ass_i = varsline.index('ASS')
 
-    # Make a regular search for Z_A entries
+    # Make a regular search for Z_A entries.
     Z_A = re.compile("Z_A*")
     spectra = filter(Z_A.search, varsline)
 
-    # Find index of Z_A entries
-    spectra_i = [[x for x in varsline].index(y) for y in spectra]
+    # Find index of Z_A entries.
+    spectra_i = []
+    for y in spectra:
+        spectra_i.append(varsline.index(y))
 
     # Remove the header.
     file_data = file_data[header:]
 
-    # Define a list, for storing all the data
-    data_all = []
+    # Create an empty intensity list.
+    intensity_list = [None]*len(spectra)
 
-    # Define a current counter
+    # Create an empty data list.
+    # Format: H_name, X_name, spin_id, intensity, line.
+    data = [None, None, None, intensity_list, None]
+
+    # Create the whole data_all list, where entries will be replaced later.
+    data_all = [data]*len(file_data)
+
+    # Define a current spectrum counter.
     i = 0
 
-    # Loop over the spectra
+    # Loop over the spectra.
     for spectrum in spectra:
-        # Define a list, for storing the current spectrum data
-        data = []
+        # Current intensity index.
+        int_i = spectra_i[i]
 
-        # Current intensity index
-        int_i = spectra_i[i]
+        # Define a current line counter.
+        j = 0
 
         for line in file_data:
             # Skip non-assigned peaks.
@@ -121,25 +130,35 @@
             x_row = re.split('([A-Z]+)', x_assign)
             x_name = x_row[-2] + x_row[-1]
 
-            # The residue number.
+            # Get the residue number.
             try:
                 res_num = int(x_row[-3])
             except:
                 raise RelaxError("Improperly formatted NMRPipe SeriesTab 
file.")
 
-            # Intensity.
+            # Get the intensity.
             try:
+                # The intensity is given by column multiplication.
                 intensity = float(line[int_i])*float(line[5])
+
+                # Extract the intensity_list
+                intensity_list = data_all[j][3]
+
+                # Replace the intensity.
+                intensity_list[i] = intensity
+
             except ValueError:
                 raise RelaxError("The peak intensity value %s from the line 
%s is invalid."%(intensity,line))
 
-            # Append the data.
-            data.append([h_name, x_name, res_num, intensity])
+            # Replace the data.
+            # Format: H_name, X_name, spin_id, intensity, line.
+            data_all[j] = [h_name, x_name, res_num, list(intensity_list), 
line]
 
-        # Append to all data
-        data_all.append([data,spectrum])
+            # Add 1 to current line counter.
+            j += 1
 
-        # Add 1 to counter
+        # Add 1 to current spectrum counter.
         i += 1
+
     # Return the data.
     return data_all