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.")
+
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