Author: semor
Date: Thu Oct 9 19:37:20 2008
New Revision: 7592
URL: http://svn.gna.org/viewcvs/relax?rev=7592&view=rev
Log:
Continued the implementation for the reading of a Nmrview peak list.
Modified:
1.3/generic_fns/intensity.py
1.3/prompt/noe.py
1.3/prompt/relax_fit.py
1.3/specific_fns/noe.py
1.3/specific_fns/relax_fit.py
1.3/test_suite/system_tests/nmrview.py
Modified: 1.3/generic_fns/intensity.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/intensity.py?rev=7592&r1=7591&r2=7592&view=diff
==============================================================================
--- 1.3/generic_fns/intensity.py (original)
+++ 1.3/generic_fns/intensity.py Thu Oct 9 19:37:20 2008
@@ -27,6 +27,7 @@
# Python module imports.
from re import split
from warnings import warn
+import sys
# relax module imports.
from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id, return_spin
@@ -158,13 +159,32 @@
return res_num, h_name, x_name, intensity
+def intensity_nmrview(line, int_col=None):
+ """Function for returning relevant data from the Nmrview peak intensity
line.
+
+ The residue number, heteronucleus and proton names, and peak intensity
will be returned.
+
+
+ @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).
+ @type int_col: int
+ @raises RelaxError: When the expected peak intensity is not a float.
+ """
+
+ # Print some texte indicating the unavailability of this function...
+ print "This function is still unavailable.\n"
+ sys.exit()
+
+
def number_of_header_lines(file_data, format, int_col, intensity):
"""Function for determining how many header lines are in the intensity
file.
@param file_data: The processed results file data.
@type file_data: list of lists of str
@param format: The type of file containing peak intensities. This
can currently be one of
- 'sparky' or 'xeasy'.
+ 'sparky', 'xeasy' or 'nmrview'.
@type format: str
@param int_col: The column containing the peak intensity data (for a
non-standard
formatted file).
@@ -214,7 +234,7 @@
@keyword dir: The directory where the file is located.
@type dir: str
@keyword format: The type of file containing peak intensities.
This can currently be
- one of 'sparky' or 'xeasy'.
+ one of 'sparky', 'xeasy' or 'nmrview'.
@type format: str
@keyword heteronuc: The name of the heteronucleus as specified in
the peak intensity
file.
@@ -231,7 +251,7 @@
"""
# Format argument.
- format_list = ['sparky', 'xeasy']
+ format_list = ['sparky', 'xeasy', 'nmrview']
if format not in format_list:
raise RelaxArgNotInListError, ('format', format, format_list)
@@ -253,6 +273,14 @@
# Set the default proton dimension.
H_dim = 'w1'
+
+ # Nmrview.
+ elif format == 'nmrview':
+ # Print out.
+ print "Nmrview formatted data file.\n"
+
+ # Set the intensity reading function.
+ intensity_fn = intensity_nmrview
# Test if the current data pipe exists.
pipes.test()
Modified: 1.3/prompt/noe.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/noe.py?rev=7592&r1=7591&r2=7592&view=diff
==============================================================================
--- 1.3/prompt/noe.py (original)
+++ 1.3/prompt/noe.py Thu Oct 9 19:37:20 2008
@@ -128,6 +128,7 @@
The 'format' argument can currently be set to:
'sparky'
'xeasy'
+ 'nmrview'
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,
@@ -142,6 +143,8 @@
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.
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=7592&r1=7591&r2=7592&view=diff
==============================================================================
--- 1.3/prompt/relax_fit.py (original)
+++ 1.3/prompt/relax_fit.py Thu Oct 9 19:37:20 2008
@@ -126,6 +126,7 @@
The format argument can currently be set to:
'sparky'
'xeasy'
+ 'nmrview'
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,
@@ -140,6 +141,8 @@
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.
The heteronuc and proton arguments should be set respectively to the
name of the
Modified: 1.3/specific_fns/noe.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/noe.py?rev=7592&r1=7591&r2=7592&view=diff
==============================================================================
--- 1.3/specific_fns/noe.py (original)
+++ 1.3/specific_fns/noe.py Thu Oct 9 19:37:20 2008
@@ -113,7 +113,7 @@
@keyword spectrum_type: The type of spectrum, one of 'ref' or 'sat'.
@type spectrum_type: str
@keyword format: The type of file containing peak
intensities. This can currently be
- one of 'sparky' or 'xeasy'.
+ one of 'sparky', 'xeasy' or 'nmrview'.
@type format: str
@keyword heteronuc: The name of the heteronucleus as specified
in the peak intensity
file.
Modified: 1.3/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/relax_fit.py?rev=7592&r1=7591&r2=7592&view=diff
==============================================================================
--- 1.3/specific_fns/relax_fit.py (original)
+++ 1.3/specific_fns/relax_fit.py Thu Oct 9 19:37:20 2008
@@ -986,7 +986,7 @@
@keyword relax_time: The time, in seconds, of the relaxation
period.
@type relax_time: float
@keyword format: The type of file containing peak
intensities. This can currently be
- one of 'sparky' or 'xeasy'.
+ one of 'sparky', 'xeasy' or 'nmrview'.
@type format: str
@keyword heteronuc: The name of the heteronucleus as specified
in the peak intensity
file.
Modified: 1.3/test_suite/system_tests/nmrview.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/nmrview.py?rev=7592&r1=7591&r2=7592&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/nmrview.py (original)
+++ 1.3/test_suite/system_tests/nmrview.py Thu Oct 9 19:37:20 2008
@@ -57,7 +57,7 @@
self.relax.interpreter._Spin.name(name='N')
# Read the peak list.
- self.relax.interpreter._Relax_fit.read(file="cNTnC.xpk",
dir=sys.path[-1] + "/test_suite/shared_data/peak_lists", relax_time=0.0176)
+ 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],
-6.88333129883)
r7592 - in /1.3: generic_fns/ prompt/ specific_fns/ test_suite/system_tests/