r12542 - /branches/bruker_import/generic_fns/pdc.py -- February 17, 2011 - 17:30

Author: bugman
Date: Thu Feb 17 17:30:24 2011
New Revision: 12542

URL: http://svn.gna.org/viewcvs/relax?rev=12542&view=rev
Log:
Implemented the reading of relaxation data from the PDC file.


Modified:
    branches/bruker_import/generic_fns/pdc.py

Modified: branches/bruker_import/generic_fns/pdc.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/bruker_import/generic_fns/pdc.py?rev=12542&r1=12541&r2=12542&view=diff
==============================================================================
--- branches/bruker_import/generic_fns/pdc.py (original)
+++ branches/bruker_import/generic_fns/pdc.py Thu Feb 17 17:30:24 2011
@@ -23,10 +23,61 @@
 # Module docstring.
 """Module for the reading of Bruker Protein Dynamics Centre (PDC) files."""
 
+# Python module imports.
+from re import search, split
+
 # relax module imports.
 from generic_fns import pipes
 from generic_fns.mol_res_spin import exists_mol_res_spin_data, spin_loop
+from generic_fns.relax_data import pack_data
 from relax_errors import RelaxError
+from relax_io import extract_data
+
+
+def get_relax_data(data):
+    """Determine the relaxation data from the given PDC data.
+
+    @param data:    The list of Tx, Tx error, and scaling factor for a given 
residue from the PDC file.
+    @type data:     list of str
+    """
+
+    # Convert the value from Tx to Rx.
+    rx = 1.0 / float(data[0])
+
+    # Remove the scaling.
+    rx_err = float(data[1]) / float(data[2])
+
+    # Convert the Tx error to an Rx error.
+    rx_err = rx**2 * rx_err
+
+    # Return the value and error.
+    return rx, rx_err
+
+
+def get_res_num(data):
+    """Determine the residue number from the given PDC data.
+
+    @param data:    The list of residue info, split by whitespace, from the 
PDC file.
+    @type data:     list of str
+    """
+
+    # Init.
+    res_num = None
+
+    # Loop over the list.
+    for i in range(len(data)):
+        # Split the data.
+        row = split('([0-9]+)', data[i])
+
+        # Loop over the new list.
+        for j in range(len(row)):
+            try:
+                res_num = int(row[j])
+            except ValueError:
+                pass
+
+    # Return the value.
+    return ":%s" % res_num
 
 
 def read(file=None, dir=None):
@@ -44,3 +95,43 @@
     # Test if sequence data is loaded.
     if not exists_mol_res_spin_data():
         raise RelaxNoSequenceError
+
+    # Extract the data from the file.
+    file_data = extract_data(file, dir)
+
+    # Init.
+    values = []
+    errors = []
+    res_nums = []
+
+    # Loop over the data.
+    in_ri_data = False
+    for line in file_data:
+        # The data type.
+        if len(line) == 3 and search('T1', line[2]):
+            ri_label = 'R1'
+            continue
+
+        # Get the frequency.
+        if len(line) == 3 and line[0] == 'Proton' and line[1] == 
'frequency[MHz]:':
+            frq = float(line[2])
+            frq_label = str(int(round(float(line[2])/10)*10))
+            continue
+
+        # Inside the relaxation data section.
+        if len(line) == 2 and line[0] == 'SECTION:' and line[1] == 'results':
+            in_ri_data = True
+            continue
+
+        # The relaxation data.
+        if in_ri_data and line[0] != 'Peak':
+            # The residue info.
+            res_nums.append(get_res_num(line[:-5]))
+
+            # Get the relaxation data.
+            rx, rx_err = get_relax_data(line[-3:])
+            values.append(rx)
+            errors.append(rx_err)
+
+    # Pack the data.
+    pack_data(ri_label, frq_label, frq, values, errors, ids=res_nums)