r11896 - /1.3/generic_fns/spectrum.py -- December 17, 2010 - 23:37

Author: bugman
Date: Fri Dec 17 23:37:16 2010
New Revision: 11896

URL: http://svn.gna.org/viewcvs/relax?rev=11896&view=rev
Log:
Added support for CCPN Analysis 2.1 peak lists (exported in Sparky format).

This is a fix for bug #17341 (https://gna.org/bugs/index.php?17341) reported 
by Madeleine Strickland
<M dott Strickland att bristol dot ac dot uk>.


Modified:
    1.3/generic_fns/spectrum.py

Modified: 1.3/generic_fns/spectrum.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/spectrum.py?rev=11896&r1=11895&r2=11896&view=diff
==============================================================================
--- 1.3/generic_fns/spectrum.py (original)
+++ 1.3/generic_fns/spectrum.py Fri Dec 17 23:37:16 2010
@@ -576,9 +576,13 @@
     @rtype:             list of lists of str, str, str, float
     """
 
-    # Assume the Sparky file has two header lines!
-    num = 2
-    print(("Number of header lines found: " + repr(num)))
+    # The number of header lines.
+    num = 0
+    if file_data[0][0] == 'Assignment':
+        num = num + 1
+    if file_data[1] == '':
+        num = num + 1
+    print("Number of header lines found: %s" % num)
 
     # Remove the header.
     file_data = file_data[num:]
@@ -595,36 +599,36 @@
         h_name = ''
         x_name = ''
         intensity = ''
-        if line[0]!='?-?':
-            assignment = split('([A-Z]+)', line[0])
-            if assignment[0] == '':
-                assignment = assignment[1:]
-            if assignment[-1] == '':
-                assignment = assignment[:-1]
-            try:
-                int(assignment[0])
-            except ValueError:
-                assignment = assignment[1:]
-
-            # The residue number.
-            try:
-                res_num = int(assignment[0])
-            except:
-                raise RelaxError("Improperly formatted Sparky file.")
-
-            # Nuclei names.
-            x_name = assignment[1]
-            h_name = assignment[3]
-
-            # 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 " + 
repr(intensity) + " from the line " + repr(line) + " is invalid.")
+
+        # Skip non-assigned peaks.
+        if line[0] == '?-?':
+            continue
+
+        # First split by the 2D separator.
+        x_assign, h_assign = split('-', line[0])
+
+        # The proton info.
+        h_name = split('([A-Z]+)', h_assign)[-2]
+
+        # The heteronucleus info.
+        x_row = split('([A-Z]+)', x_assign)
+        x_name = x_row[-2]
+
+        # The residue number.
+        try:
+            res_num = int(x_row[-3])
+        except:
+            raise RelaxError("Improperly formatted Sparky file.")
+
+        # 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 " + repr(intensity) + 
" from the line " + repr(line) + " is invalid.")
 
         # Generate the spin_id.
         spin_id = generate_spin_id(res_num=res_num, spin_name=x_name)