On Thu, Oct 16, 2008 at 10:07 PM, <sebastien.morin.1@xxxxxxxxx> wrote:
Author: semor
Date: Thu Oct 16 22:07:30 2008
New Revision: 7787
URL: http://svn.gna.org/viewcvs/relax?rev=7787&view=rev
Log:
Set the peak intensity as the default for the reading of NMRView peak list.
The volume was being used. Now, the volume can be used with the use of the
'int_col' variable.
Moreover, the docstrings are now more complete for the of NMRView peak
lists.
Modified:
1.3/generic_fns/intensity.py
1.3/prompt/noe.py
1.3/prompt/relax_fit.py
1.3/test_suite/system_tests/peak_lists.py
Modified: 1.3/generic_fns/intensity.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/intensity.py?rev=7787&r1=7786&r2=7787&view=diff
==============================================================================
--- 1.3/generic_fns/intensity.py (original)
+++ 1.3/generic_fns/intensity.py Thu Oct 16 22:07:30 2008
@@ -176,8 +176,9 @@
@param line: The single line of information from the intensity
file.
@type line: list of str
- @keyword int_col: The column containing the peak intensity data (for
a non-standard formatted
- file).
+ @keyword int_col: The column containing the peak intensity data. The
default is 16 for
+ intensities. 'int_col = 15' will use the volumes
(or evolumes). For a
+ non-standard formatted file, use a different value.
@type int_col: int
@raises RelaxError: When the expected peak intensity is not a float.
"""
@@ -208,7 +209,11 @@
# The peak intensity column.
if int_col == None:
- int_col = 15
+ int_col = 16
+ if int_col == 16:
+ print 'Using intensities.'
Here I would say 'Using peak heights' as intensities includes both the
heights and the volumes.
+ if int_col == 15:
+ print 'Using volumes (or evolumes).'
# Intensity.
try:
Modified: 1.3/prompt/noe.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/noe.py?rev=7787&r1=7786&r2=7787&view=diff
==============================================================================
--- 1.3/prompt/noe.py (original)
+++ 1.3/prompt/noe.py Thu Oct 16 22:07:30 2008
@@ -144,7 +144,9 @@
the peak height or peak volume data. Because the columns are
fixed, the 'int_col' argument
will be ignored.
- If the format argument is set to 'nmrview', the file should be a
NMRView peak list.
+ If the 'format' argument is set to 'nmrview', the file should be a
NMRView peak list. The
+ default is to use column 16 (which contains peak intensities) for
peak amplitudes. To use
+ use peak volumes (or evolumes), 'int_col = 15' must be used.
It may be better not to use quotes around 'int_col = 15'. This may be
a little confusing for a new user who is struggling to understand what
a string verses integer is. Maybe something like "setting the int_col
argument to 15 ..." or "setting to 15 ...", etc. would be less
confusing for certain users. This appears elsewhere in this commit.
I've tried to only use quotes for strings in the user function
docstrings, but there are exceptions because of antiquity of the text.
Cheers,
Edward
Re: r7787 - in /1.3: generic_fns/intensity.py prompt/noe.py prompt/relax_fit.py test_suite/system_tests/peak_lists.py