Author: bugman
Date: Tue Aug 19 16:52:47 2014
New Revision: 25081
URL: http://svn.gna.org/viewcvs/relax?rev=25081&view=rev
Log:
Merged revisions
24873-24875,24880-24883,24890,24892-24893,24895-24915,25019-25080 via
svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
................
r24873 | bugman | 2014-07-31 14:32:47 +0200 (Thu, 31 Jul 2014) | 7 lines
Added Andy Baldwin's 2013 R1rho relaxation dispersion model to the manual.
The model has been added to the table of dispersion models and to the
dispersion software comparison
table of the dispersion chapter of the manual. The citation has also been
added to the
bibliography.
................
r24874 | bugman | 2014-07-31 14:36:10 +0200 (Thu, 31 Jul 2014) | 3 lines
The B13 dispersion model is now properly added to the software comparison
table.
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r24875 | bugman | 2014-07-31 14:36:31 +0200 (Thu, 31 Jul 2014) | 3 lines
Added the 'B13' and 'B13 full' dispersion models to the to do section of
the manual.
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r24880 | bugman | 2014-07-31 15:13:18 +0200 (Thu, 31 Jul 2014) | 3 lines
Standardisation of the author names in the bibliography of the relax manual.
................
r24881 | bugman | 2014-07-31 15:36:28 +0200 (Thu, 31 Jul 2014) | 3 lines
Added links for the B13 model to https://gna.org/support/?3155 in the
manual.
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r24882 | bugman | 2014-07-31 15:47:01 +0200 (Thu, 31 Jul 2014) | 3 lines
Expansion of the 'to do' section of the dispersion chapter of the manual.
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r24883 | bugman | 2014-07-31 15:50:03 +0200 (Thu, 31 Jul 2014) | 3 lines
Editing of the 'to do' section of the dispersion chapter of the manual.
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r24890 | bugman | 2014-07-31 18:07:43 +0200 (Thu, 31 Jul 2014) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-24672" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/r1rho_plotting
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r24892 | bugman | 2014-07-31 18:14:28 +0200 (Thu, 31 Jul 2014) | 733 lines
Merged revisions
24744-24750,24758-24777,24780-24782,24785-24786,24789-24795,24811-24813,24824-24831,24844-24849,24851-24856,24858-24865,24868-24872,24876-24879,24884-24887,24889,24891
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/r1rho_plotting
........
r24744 | tlinnet | 2014-07-25 13:59:22 +0200 (Fri, 25 Jul 2014) | 6 lines
Split out the interpolating in
specific_analyses.relax_disp.data.plot_disp_curves() into separate function.
This is to prepare for a interpolating function for spin-lock offset
rather than spin-lock field strength for R1rho models.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24745 | tlinnet | 2014-07-25 13:59:24 +0200 (Fri, 25 Jul 2014) | 4 lines
Split out the looping over frequency and offset into its own function, in
function of specific_analysis.relax_disp.data.plot_disp_curves().
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24746 | tlinnet | 2014-07-25 13:59:26 +0200 (Fri, 25 Jul 2014) | 6 lines
Split out the writing of dispersion graph files in
specific_analyses.relax_disp.data.plot_disp_curves().
This is to prepare for a stand-alone function to plot R1rho graphs,
interpolating theta through spin-lock offset rather than spin-lock field
strength.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24747 | tlinnet | 2014-07-25 13:59:28 +0200 (Fri, 25 Jul 2014) | 4 lines
Fix for function calling and default values of None in sup-plotting
functions.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24748 | tlinnet | 2014-07-25 13:59:30 +0200 (Fri, 25 Jul 2014) | 7 lines
Large extension of specific_analyses.relax_disp.data(), by adding several
helper plotting functions.
This is to prepare for plotting R1rho R2 as function of effective field
in rotating frame: w_eff.
R_2 = R1rho / sin^2(theta) - R_1 / tan^2(theta) = (R1rho - R_1 *
cos^2(theta) ) / sin^2(theta)
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24749 | tlinnet | 2014-07-25 13:59:32 +0200 (Fri, 25 Jul 2014) | 4 lines
Extended specific_analyses.relax_disp.optimisation.back_calc_r2eff() to
handle interpolated spin-lock offset values.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24750 | tlinnet | 2014-07-25 13:59:33 +0200 (Fri, 25 Jul 2014) | 4 lines
Removed a wrong adding of empty offset dimension in the get_back_calc()
function of target_functions.relax_disp().
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24758 | tlinnet | 2014-07-25 17:50:24 +0200 (Fri, 25 Jul 2014) | 10 lines
Added the the back_calculated R_2 as function of effective field in
rotating frame: w_eff.
R1rho R_2 is defined as:
R_2 = R1rho / sin^2(theta) - R_1 / tan^2(theta) = (R1rho - R_1 *
cos^2(theta) ) / sin^2(theta)
This is described more at:
http://wiki.nmr-relax.com/DPL94#Equation_-_re-writed_forms
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24759 | tlinnet | 2014-07-25 17:50:27 +0200 (Fri, 25 Jul 2014) | 16 lines
Added an intermediate attempt to show the back_calculated data in the
graph for R1rho R2 as function of the effective field in rotating frame:
w_eff.
The graph is aiming for the representation of Figure 2 in Kjaergaard et
al 2013. (http://dx.doi.org/10.1021/bi4001062).
The figure can be seen at
https://gna.org/support/download.php?file_id=20208.
It becomes clear, that it is not neccessary interpolate through the
spin-lock offset, but it is suffucient to interpolate through the spin-lock
field strengths.
The necessary step was the extraction of the effective effective field in
rotating frame, w_eff.
In earlier attempt is shown at:
http://wiki.nmr-relax.com/File:Matplotlib_52_N_R1_rho_R2eff_w_eff.png
This though show lines for 6 offset values.
The question is how to show the single line of interpolation.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24760 | tlinnet | 2014-07-25 17:50:28 +0200 (Fri, 25 Jul 2014) | 4 lines
Added NMR library function to convert the given frequency from rad/s to
ppm units.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24761 | tlinnet | 2014-07-25 17:50:30 +0200 (Fri, 25 Jul 2014) | 4 lines
Hard-coded restriction of R1rho extra plotting to model DPL94, TP02,
TAP03, MP05, NS_R1RHO_2SITE.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24762 | tlinnet | 2014-07-25 17:50:33 +0200 (Fri, 25 Jul 2014) | 4 lines
Fix for sending the correct data structures to target function, and fix
for the spin index which is always zero in graph production.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24763 | tlinnet | 2014-07-25 18:23:24 +0200 (Fri, 25 Jul 2014) | 4 lines
Moved the file_name creation out of the interpolate function, to make it
a general function for interpolating.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24764 | tlinnet | 2014-07-25 18:23:27 +0200 (Fri, 25 Jul 2014) | 12 lines
Made both interploation functions of the spin-lock field strength and
spin-Ãlock offset return the offset data.
This is make it possible to switch between the interpolating functions,
when plotting R1rho graphs.
This is necessary to produce the R2 as function of effective field in
rotating frame w_eff, and to produce
R1rho as function of theta, when ramping the spin-lock offset.
These graphs can be seen at:
http://wiki.nmr-relax.com/Matplotlib_DPL94_R1rho_R2eff
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24765 | tlinnet | 2014-07-25 20:56:37 +0200 (Fri, 25 Jul 2014) | 4 lines
Changed interpolation function from offset to spin lock field strength,
to plot R1rho R2 as function of effective field.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24766 | tlinnet | 2014-07-25 20:56:40 +0200 (Fri, 25 Jul 2014) | 6 lines
Inverted the input to atan2() function in
specific_analyses/relax_disp/data.py.
This has no influence on the system tests.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24767 | tlinnet | 2014-07-25 20:56:42 +0200 (Fri, 25 Jul 2014) | 4 lines
Changes to the writing out of theta, and its corresponding systemtest
after swithching the input to atan2().
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24768 | tlinnet | 2014-07-25 21:01:47 +0200 (Fri, 25 Jul 2014) | 25 lines
Reverted r24767 and 24766 as this was fatal systemtest
Relax_disp.test_r1rho_kjaergaard_man().
The model "No Rex" would be selected instead of "DPL94", after the change.
The command used was:
svn merge -r24767:r24765 .
.....
r24767 | tlinnet | 2014-07-25 20:56:42 +0200 (Fri, 25 Jul 2014) | 4
lines
Changes to the writing out of theta, and its corresponding systemtest
after swithching the input to atan2().
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
------------------------------------------------------------------------
r24766 | tlinnet | 2014-07-25 20:56:40 +0200 (Fri, 25 Jul 2014) | 6
lines
Inverted the input to atan2() function in
specific_analyses/relax_disp/data.py.
This has no influence on the system tests.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
.....
........
r24769 | tlinnet | 2014-07-26 13:33:52 +0200 (Sat, 26 Jul 2014) | 4 lines
Improved axis label for plotting R1rho R2 as function of effective field
w_eff.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24770 | tlinnet | 2014-07-26 13:33:58 +0200 (Sat, 26 Jul 2014) | 6 lines
Added sub-title to the plot of R1rho R2 as function of effective field.
This is to add information about how the effective field has been
interpolated.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24771 | tlinnet | 2014-07-26 13:34:03 +0200 (Sat, 26 Jul 2014) | 9 lines
Added functionality to plot R1rho R2 as function of effective field
w_eff, for the R2eff model.
Also renamed a function, to better reflect is functionality.
The hard-coding of which models to plot, has been removed.
If the exp-type is R1rho, then the plotting will commence.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24772 | tlinnet | 2014-07-26 13:34:09 +0200 (Sat, 26 Jul 2014) | 6 lines
Added the spin specific residue name and spin_id to the title of the
dispersion plots.
This is handy, since it is often of interest to have this information at
hand, when looking through many graphs.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24773 | tlinnet | 2014-07-26 13:34:13 +0200 (Sat, 26 Jul 2014) | 4 lines
Renamed and improved epydoc information for interpolating fucntion for
dispersion values.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24774 | tlinnet | 2014-07-26 13:34:18 +0200 (Sat, 26 Jul 2014) | 4 lines
Renamed the interpolating function for offset, and improved the epydoc
information.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24775 | tlinnet | 2014-07-26 13:34:24 +0200 (Sat, 26 Jul 2014) | 6 lines
Corrected the epydoc information for the return_offset_data() function in
specific_analyses.relax_disp.data.
The function has been extended to return more data.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24776 | tlinnet | 2014-07-26 13:34:29 +0200 (Sat, 26 Jul 2014) | 6 lines
Renamed function to represent the functionality of returning data in
correct xmgrace form.
Also improved the epydoc information, for the return of values.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24777 | tlinnet | 2014-07-26 13:34:35 +0200 (Sat, 26 Jul 2014) | 6 lines
Renamed the other function to represent the functionality of returning
data in correct xmgrace form.
Also improved the epydoc information, for the return of values.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24780 | tlinnet | 2014-07-28 12:56:51 +0200 (Mon, 28 Jul 2014) | 6 lines
Added function to calculate rotating frame paramters for lib/nmr.py.
This function is called several times in
specific_analyses/relax_disp/data.py by plotting functions.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24781 | tlinnet | 2014-07-28 12:56:55 +0200 (Mon, 28 Jul 2014) | 4 lines
Replaced repeated calculation of rotating frame parameters to use
function in lib/nmr.py.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
sr #3138(https://gna.org/support/?3138): Interpolating theta through
spin-lock offset [Omega], rather than spin-lock field strength [w1].
........
r24782 | tlinnet | 2014-07-28 12:56:56 +0200 (Mon, 28 Jul 2014) | 6 lines
Skip production of plotting r1rho r2 as function of effective field
w_eff, when spin.isotope is not present.
This can happen when it is 'exp_fit' model curve fitting.
sr #3124(https://gna.org/support/?3124): Grace graphs production for
R1rho analysis with R2_eff as function of Omega_eff.
[... 1964 lines stripped ...]
r25081 - in /branches/frame_order_cleanup: ./ auto_analyses/ docs/latex/ gui/analyses/ lib/ lib/dispersion/ lib/software/ li...