Author: bugman
Date: Tue Aug 20 16:47:58 2013
New Revision: 20636
URL: http://svn.gna.org/viewcvs/relax?rev=20636&view=rev
Log:
Merged revisions 20634-20635 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r20634 | bugman | 2013-08-20 16:41:30 +0200 (Tue, 20 Aug 2013) | 6 lines
Changes for the spectrum.read_intensities user function dim argument.
The default is now w1, the indirect dimension in a 2D experiment. The
description has also been
fixed.
........
r20635 | bugman | 2013-08-20 16:47:21 +0200 (Tue, 20 Aug 2013) | 3 lines
Fixes for all of the peak intensity reading functions - the w1 and w2
dimensions were swapped.
........
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/lib/software/nmrpipe.py
branches/relax_disp/lib/software/nmrview.py
branches/relax_disp/lib/software/sparky.py
branches/relax_disp/lib/software/xeasy.py
branches/relax_disp/user_functions/spectrum.py
Propchange: branches/relax_disp/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Aug 20 16:47:58 2013
@@ -1,1 +1,1 @@
-/trunk:1-20626
+/trunk:1-20635
Modified: branches/relax_disp/lib/software/nmrpipe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/software/nmrpipe.py?rev=20636&r1=20635&r2=20636&view=diff
==============================================================================
--- branches/relax_disp/lib/software/nmrpipe.py (original)
+++ branches/relax_disp/lib/software/nmrpipe.py Tue Aug 20 16:47:58 2013
@@ -97,7 +97,7 @@
continue
# First split by the 2D separator.
- assign2, assign1 = re.split('-', line[ass_i])
+ assign1, assign2 = re.split('-', line[ass_i])
# The assignment of the first dimension.
row1 = re.split('([A-Z]+)', assign1)
@@ -109,7 +109,7 @@
# Get the residue number.
try:
- res_num = int(row2[-3])
+ res_num = int(row1[-3])
except:
raise RelaxError("Improperly formatted NMRPipe SeriesTab file.,
cannot process the assignment '%s'." % line[0])
Modified: branches/relax_disp/lib/software/nmrview.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/software/nmrview.py?rev=20636&r1=20635&r2=20636&view=diff
==============================================================================
--- branches/relax_disp/lib/software/nmrview.py (original)
+++ branches/relax_disp/lib/software/nmrview.py Tue Aug 20 16:47:58 2013
@@ -81,18 +81,18 @@
raise RelaxError("The peak list is invalid.")
# Nuclei names.
+ name2 = ''
+ if line[1]!='{}':
+ name2 = line[1].strip('{')
+ name2 = name2.strip('}')
+ name2 = name2.split('.')
+ name2 = name2[1]
name1 = ''
- if line[1]!='{}':
- name1 = line[1].strip('{')
+ if line[8]!='{}':
+ name1 = line[8].strip('{')
name1 = name1.strip('}')
name1 = name1.split('.')
name1 = name1[1]
- name2 = ''
- if line[8]!='{}':
- name2 = line[8].strip('{')
- name2 = name2.strip('}')
- name2 = name2.split('.')
- name2 = name2[1]
# Intensity.
try:
Modified: branches/relax_disp/lib/software/sparky.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/software/sparky.py?rev=20636&r1=20635&r2=20636&view=diff
==============================================================================
--- branches/relax_disp/lib/software/sparky.py (original)
+++ branches/relax_disp/lib/software/sparky.py Tue Aug 20 16:47:58 2013
@@ -69,7 +69,7 @@
continue
# First split by the 2D separator.
- assign2, assign1 = split('-', line[0])
+ assign1, assign2 = split('-', line[0])
# The assignment of the first dimension.
row1 = split('([a-zA-Z]+)', assign1)
@@ -81,7 +81,7 @@
# The residue number.
try:
- res_num = int(row2[-3])
+ res_num = int(row1[-3])
except:
raise RelaxError("Improperly formatted Sparky file, cannot
process the assignment '%s'." % line[0])
Modified: branches/relax_disp/lib/software/xeasy.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/software/xeasy.py?rev=20636&r1=20635&r2=20636&view=diff
==============================================================================
--- branches/relax_disp/lib/software/xeasy.py (original)
+++ branches/relax_disp/lib/software/xeasy.py Tue Aug 20 16:47:58 2013
@@ -41,9 +41,9 @@
@raises RelaxError: When the expected peak intensity is not a float.
"""
- # The hardcoded column positions.
- w1_col = 4
- w2_col = 7
+ # The hardcoded column positions (note that w1 and w2 are swapped!).
+ w1_col = 7
+ w2_col = 4
if int_col == None:
int_col = 10
@@ -70,7 +70,7 @@
# Loop over the file data.
for line in file_data:
# Test for invalid assignment lines which have the column numbers
changed and return empty data.
- if line[w1_col] == 'inv.':
+ if line[w1_col] == 'inv.' or line[w2_col] == 'inv.':
continue
# The residue number.
Modified: branches/relax_disp/user_functions/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/spectrum.py?rev=20636&r1=20635&r2=20636&view=diff
==============================================================================
--- branches/relax_disp/user_functions/spectrum.py (original)
+++ branches/relax_disp/user_functions/spectrum.py Tue Aug 20 16:47:58 2013
@@ -239,11 +239,11 @@
)
uf.add_keyarg(
name = "dim",
- default = 2,
+ default = 1,
py_type = "int",
min = 1,
desc_short = "spectral dimension to read",
- desc = "Associate the data with the spins of any dimension in the peak
list. This defaults to w2, the heteronucleus in HSQC type experiments."
+ desc = "Associate the data with the spins of any dimension in the peak
list. This defaults to w1, the heteronucleus in HSQC type experiments."
)
uf.add_keyarg(
name = "int_method",
@@ -336,7 +336,7 @@
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("The peak intensity can either be from peak
heights or peak volumes.")
uf.desc[-1].add_paragraph("The spectrum ID is a label which is subsequently
utilised by other user functions. If this identifier matches that of a
previously loaded set of intensities, then this indicates a replicated
spectrum.")
-uf.desc[-1].add_paragraph("The spectral dimension is used to specify if the
intensity data should be loaded into the spins identified by the first
dimension, second dimension, etc.")
+uf.desc[-1].add_paragraph("The spectral dimension is used to specify if the
intensity data should be loaded into the spins identified by the first
dimension w1, second dimension w2, etc.")
uf.desc[-1].add_paragraph("The integration method is required for the
subsequent error analysis. When peak heights are measured, this should be
set to 'height'. Volume integration methods are a bit varied and hence two
values are accepted. If the volume integration involves pure point
summation, with no deconvolution algorithms or other methods affecting peak
heights, then the value should be set to 'point sum'. All other volume
integration methods, e.g. line shape fitting, the value should be set to
'other'.")
uf.desc[-1].add_paragraph("If a series of intensities extracted from Bruker
FID files processed in Topspin or XWinNMR are to be compared, the ncproc
parameter may need to be supplied. This is because this FID is stored using
integer representation and is scaled using ncproc to avoid numerical
truncation artifacts. If two spectra have significantly different maximal
intensities, then ncproc will be different for both. The intensity scaling
is binary, i.e. 2**ncproc. Therefore if spectrum A has an ncproc of 6 and and
spectrum B a value of 7, then a reference intensity in B will be double that
of A. Internally, relax stores the intensities scaled by 2**ncproc.")
# File formats.
r20636 - in /branches/relax_disp: ./ lib/software/ user_functions/