r25605 - /trunk/lib/spectrum/nmrpipe.py -- September 03, 2014 - 22:50

Author: tlinnet
Date: Wed Sep  3 22:50:37 2014
New Revision: 25605

URL: http://svn.gna.org/viewcvs/relax?rev=25605&view=rev
Log:
Added function to extract the 'Noise Std Dev' from NMRPipe showApod.

Modified:
    trunk/lib/spectrum/nmrpipe.py

Modified: trunk/lib/spectrum/nmrpipe.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/spectrum/nmrpipe.py?rev=25605&r1=25604&r2=25605&view=diff
==============================================================================
--- trunk/lib/spectrum/nmrpipe.py       (original)
+++ trunk/lib/spectrum/nmrpipe.py       Wed Sep  3 22:50:37 2014
@@ -223,3 +223,33 @@
 
     else:
         raise RelaxError("python module 'subprocess' not found.  Cannot call 
showApod.")
+
+
+def show_apod_rmsd(file_name=None, dir=None, path_to_command='showApod'):
+    """Extract showApod 'Noise Std Dev' for spectrum fourier transformed 
with NMRPipe.
+
+    @keyword file:              The filename of the NMRPipe fourier 
transformed file.
+    @type file:                 str
+    @keyword dir:               The directory where the file is located.
+    @type dir:                  str
+    @keyword path_to_command:   If showApod not in PATH, then specify 
absolute path as: /path/to/showApod
+    @type dir:                  str
+    @return:                    The Noise Std Dev from line: 'REMARK 
Automated Noise Std Dev in Processed Data'
+    @rtype:                     float
+    """
+
+    # Call extract function.
+    show_apod_lines = show_apod_extract(file_name=file_name, dir=dir, 
path_to_command=path_to_command)
+
+    # Loop over the lines
+    found = False
+    for line in show_apod_lines:
+        # Look for line with this remark.
+        if line[:49] == 'REMARK Automated Noise Std Dev in Processed Data:':
+            # The rest of the line is the rmsd.
+            rmsd = float(line[49:].split()[0])
+            return rmsd
+
+    if not found:
+        raise RelaxError("Could not find the line: 'REMARK Automated Noise 
Std Dev in Processed Data:', from the output of showApod.")
+