Author: bugman
Date: Wed Mar 26 18:39:06 2014
New Revision: 22545
URL: http://svn.gna.org/viewcvs/relax?rev=22545&view=rev
Log:
Merged revisions 22543-22544 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r22543 | bugman | 2014-03-26 18:32:15 +0100 (Wed, 26 Mar 2014) | 10 lines
Changed the Noe.test_noe_analysis system test to handle the peak
intensities correctly.
This relates to bug #21863 (https://gna.org/bugs/?21863), , the grace.write
user function not being
able to write ref/sat plots as described in sample script noe.py.
Instead of trying to produce the 'ref.agr' and 'sat.agr' files for the
non-existent 'ref' and 'sat'
parameters, instead the 'intensities.agr' file is being produced for the
peak intensity parameter.
The reference and saturated intensities will appear as two graph sets
within that plot.
........
r22544 | bugman | 2014-03-26 18:38:41 +0100 (Wed, 26 Mar 2014) | 11 lines
Changed the Noe analysis sample script to properly handle the peak
intensity Grace plots.
This relates to bug #21863 (https://gna.org/bugs/?21863), the grace.write
user function not being
able to write ref/sat plots as described in sample script noe.py.
Instead of trying to produce the 'ref.agr' and 'sat.agr' files for the
non-existent 'ref' and 'sat'
parameters, instead the 'intensities.agr' file is being produced for the
peak intensity parameter.
The reference and saturated intensities will appear as two graph sets
within that plot. These
changes match those of the test suite.
........
Modified:
branches/double_rotor/ (props changed)
branches/double_rotor/docs/latex/noe.tex
branches/double_rotor/sample_scripts/noe.py
branches/double_rotor/test_suite/system_tests/noe.py
branches/double_rotor/test_suite/system_tests/scripts/noe/noe.py
Propchange: branches/double_rotor/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Mar 26 18:39:06 2014
@@ -1 +1 @@
-/trunk:1-22541
+/trunk:1-22544
Modified: branches/double_rotor/docs/latex/noe.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/docs/latex/noe.tex?rev=22545&r1=22544&r2=22545&view=diff
==============================================================================
--- branches/double_rotor/docs/latex/noe.tex (original)
+++ branches/double_rotor/docs/latex/noe.tex Wed Mar 26 18:39:06 2014
@@ -84,13 +84,11 @@
value.write(param='noe', file='noe.out', force=True)
# Create Grace files.
-grace.write(y_data_type='ref', file='ref.agr', force=True)
-grace.write(y_data_type='sat', file='sat.agr', force=True)
+grace.write(y_data_type='intensities', file='intensities.agr', force=True)
grace.write(y_data_type='noe', file='noe.agr', force=True)
# View the Grace files.
-grace.view(file='ref.agr')
-grace.view(file='sat.agr')
+grace.view(file='intensities.agr')
grace.view(file='noe.agr')
# Write the results.
@@ -317,32 +315,23 @@
Any two dimensional data set can be plotted in relax in conjunction with the
program
\href{http://plasma-gate.weizmann.ac.il/Grace/}{Grace}\index{software!Grace|textbf}.
The program is also known as Xmgrace and was previously known as ACE/gr or
Xmgr.
The highly flexible relax user function \uf{grace\ufsep{}write} is capable
of producing 2D plots of any x-y data sets.
-The three commands
+The two commands
\begin{lstlisting}[firstnumber=41]
# Create Grace files.
-grace.write(y_data_type='ref', file='ref.agr', force=True)
-grace.write(y_data_type='sat', file='sat.agr', force=True)
+grace.write(y_data_type='intensities', file='intensities.agr', force=True)
grace.write(y_data_type='noe', file='noe.agr', force=True)
\end{lstlisting}
-will create three separate plots of the peak intensity of the reference and
saturated spectra as well as the NOE.
+will create one plot of the peak intensity of the reference and saturated
spectra as different graph sets in the same plot as well as one plot for the
NOE and its error.
The x-axis in all three defaults to the residue number.
-As the x and y-axes can be any parameter the command
-
-\begin{lstlisting}[numbers=none]
-grace.write(x_data_type='ref', y_data_type='sat', file='ref_vs_sat.agr',
force=True)
-\end{lstlisting}
-
-would create a plot of the reference verses the saturated intensity with one
point per residue.
-Returning to the sample script three Grace data files are created
\file{ref.agr}, \file{sat.agr}, and \file{noe.agr} and placed in the default
directory \directory{.\ossep{}grace}.
+Returning to the sample script three Grace data files are created
\file{intensities.agr} and \file{noe.agr} and placed in the default directory
\directory{.\ossep{}grace}.
These can be visualised by opening the file within Grace.
However relax will do that for you with the commands
-\begin{lstlisting}[firstnumber=46]
+\begin{lstlisting}[firstnumber=45]
# View the Grace files.
-grace.view(file='ref.agr')
-grace.view(file='sat.agr')
+grace.view(file='intensities.agr')
grace.view(file='noe.agr')
\end{lstlisting}
Modified: branches/double_rotor/sample_scripts/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/sample_scripts/noe.py?rev=22545&r1=22544&r2=22545&view=diff
==============================================================================
--- branches/double_rotor/sample_scripts/noe.py (original)
+++ branches/double_rotor/sample_scripts/noe.py Wed Mar 26 18:39:06 2014
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2013 Edward d'Auvergne
#
+# Copyright (C) 2004-2014 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -59,13 +59,11 @@
value.write(param='noe', file='noe.out', force=True)
# Create grace files.
-grace.write(y_data_type='ref', file='ref.agr', force=True)
-grace.write(y_data_type='sat', file='sat.agr', force=True)
+grace.write(y_data_type='intensities', file='intensities.agr', force=True)
grace.write(y_data_type='noe', file='noe.agr', force=True)
# View the grace files.
-grace.view(file='ref.agr')
-grace.view(file='sat.agr')
+grace.view(file='intensities.agr')
grace.view(file='noe.agr')
# Write the results.
Modified: branches/double_rotor/test_suite/system_tests/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/test_suite/system_tests/noe.py?rev=22545&r1=22544&r2=22545&view=diff
==============================================================================
--- branches/double_rotor/test_suite/system_tests/noe.py (original)
+++ branches/double_rotor/test_suite/system_tests/noe.py Wed Mar 26
18:39:06 2014
@@ -171,7 +171,64 @@
i += 1
# The real Grace file data.
- data = [[], [], [
+ data = [[
+ '@version 50121\n',
+ '@page size 842, 595\n',
+ '@with g0\n',
+ '@ view 0.15, 0.15, 1.28, 0.85\n',
+ '@ xaxis label "Residue number"\n',
+ '@ xaxis label char size 1.00\n',
+ '@ xaxis tick major size 0.50\n',
+ '@ xaxis tick major linewidth 0.5\n',
+ '@ xaxis tick minor linewidth 0.5\n',
+ '@ xaxis tick minor size 0.25\n',
+ '@ xaxis ticklabel char size 0.70\n',
+ '@ yaxis label "Peak intensity"\n',
+ '@ yaxis label char size 1.00\n',
+ '@ yaxis tick major size 0.50\n',
+ '@ yaxis tick major linewidth 0.5\n',
+ '@ yaxis tick minor linewidth 0.5\n',
+ '@ yaxis tick minor size 0.25\n',
+ '@ yaxis ticklabel char size 0.70\n',
+ '@ legend off\n',
+ '@ legend box fill pattern 1\n',
+ '@ legend char size 1.0\n',
+ '@ frame linewidth 0.5\n',
+ '@ s0 symbol 1\n',
+ '@ s0 symbol size 0.45\n',
+ '@ s0 symbol linewidth 0.5\n',
+ '@ s0 errorbar size 0.5\n',
+ '@ s0 errorbar linewidth 0.5\n',
+ '@ s0 errorbar riser linewidth 0.5\n',
+ '@ s0 legend "ref_ave"\n',
+ '@ s1 symbol 2\n',
+ '@ s1 symbol size 0.45\n',
+ '@ s1 symbol linewidth 0.5\n',
+ '@ s1 errorbar size 0.5\n',
+ '@ s1 errorbar linewidth 0.5\n',
+ '@ s1 errorbar riser linewidth 0.5\n',
+ '@ s1 legend "sat_ave"\n',
+ '@target G0.S0\n',
+ '@type xy\n',
+ '4 148614.000000000000000
\n',
+ '5 166842.000000000000000
\n',
+ '6 128690.000000000000000
\n',
+ '40 99566.000000000000000
\n',
+ '40 270047.000000000000000
\n',
+ '55 130959.000000000000000
\n',
+ '&\n',
+ '@target G0.S1\n',
+ '@type xy\n',
+ '4 5050.000000000000000
\n',
+ '5 51643.000000000000000
\n',
+ '6 53663.000000000000000
\n',
+ '40 -65111.000000000000000
\n',
+ '40 -181131.000000000000000
\n',
+ '55 -105322.000000000000000
\n',
+ '&\n',
+ '@with g0\n',
+ '@autoscale\n'
+ ], [
'@version 50121\n',
'@page size 842, 595\n',
'@with g0\n',
@@ -225,7 +282,7 @@
]]
# Check the Grace files.
- ids = ['ref', 'sat', 'noe']
+ ids = ['intensities', 'noe']
for i in range(len(ids)):
# The file name.
file_name = "%s.agr" % ids[i]
Modified: branches/double_rotor/test_suite/system_tests/scripts/noe/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/test_suite/system_tests/scripts/noe/noe.py?rev=22545&r1=22544&r2=22545&view=diff
==============================================================================
--- branches/double_rotor/test_suite/system_tests/scripts/noe/noe.py
(original)
+++ branches/double_rotor/test_suite/system_tests/scripts/noe/noe.py Wed
Mar 26 18:39:06 2014
@@ -47,8 +47,7 @@
value.write(param='noe', file='devnull', force=True)
# Create grace files.
-grace.write(y_data_type='ref', file='ref.agr', dir=ds.tmpdir, force=True)
-grace.write(y_data_type='sat', file='sat.agr', dir=ds.tmpdir, force=True)
+grace.write(y_data_type='intensities', file='intensities.agr',
dir=ds.tmpdir, force=True)
grace.write(y_data_type='noe', file='noe.agr', dir=ds.tmpdir, force=True)
# Write the results.
r22545 - in /branches/double_rotor: ./ docs/latex/ sample_scripts/ test_suite/system_tests/ test_suite/system_tests/scripts/...