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.'
+ 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.
The 'heteronuc' and 'proton' arguments should be set respectively to
the name of the
Modified: 1.3/prompt/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/relax_fit.py?rev=7787&r1=7786&r2=7787&view=diff
==============================================================================
--- 1.3/prompt/relax_fit.py (original)
+++ 1.3/prompt/relax_fit.py Thu Oct 16 22:07:30 2008
@@ -128,7 +128,7 @@
'xeasy'
'nmrview'
- If the format argument is set to 'sparky', the file should be a
Sparky peak list saved after
+ If the 'format' argument is set to 'sparky', the file should be a
Sparky peak list saved after
typing the command 'lt'. The default is to assume that columns 0,
1, 2, and 3 (1st, 2nd,
3rd, and 4th) contain the Sparky assignment, w1, w2, and peak
intensity data respectively.
The frequency data w1 and w2 are ignored while the peak intensity
data can either be the
@@ -136,13 +136,15 @@
is not within column 3, set the argument int_col to the appropriate
value (column numbering
starts from 0 rather than 1).
- If the format argument is set to 'xeasy', the file should be the
saved XEasy text window
+ If the 'format' argument is set to 'xeasy', the file should be the
saved XEasy text window
output of the list peak entries command, 'tw' followed by 'le'. As
the columns are fixed,
the peak intensity column is hardwired to number 10 (the 11th
column) which contains either
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.
The heteronuc and proton arguments should be set respectively to the
name of the
Modified: 1.3/test_suite/system_tests/peak_lists.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/peak_lists.py?rev=7787&r1=7786&r2=7787&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/peak_lists.py (original)
+++ 1.3/test_suite/system_tests/peak_lists.py Thu Oct 16 22:07:30 2008
@@ -61,8 +61,8 @@
self.relax.interpreter._Relax_fit.read(file="cNTnC.xpk",
dir=sys.path[-1] + "/test_suite/shared_data/peak_lists", relax_time=0.0176,
format='nmrview')
# Test the data.
- self.assertEqual(cdp.mol[0].res[0].spin[0].intensities[0][0],
-6.88333129883)
- self.assertEqual(cdp.mol[0].res[1].spin[0].intensities[0][0],
-5.49038267136)
+ self.assertEqual(cdp.mol[0].res[0].spin[0].intensities[0][0],
-0.1694)
+ self.assertEqual(cdp.mol[0].res[1].spin[0].intensities[0][0],
-0.1142)
class Sparky(TestCase):
r7787 - in /1.3: generic_fns/intensity.py prompt/noe.py prompt/relax_fit.py test_suite/system_tests/peak_lists.py