Author: bugman
Date: Thu Oct 17 09:24:20 2013
New Revision: 21152
URL: http://svn.gna.org/viewcvs/relax?rev=21152&view=rev
Log:
Epydoc docstring fixes to allow the API documentation to be properly compiled.
Modified:
branches/relax_disp/specific_analyses/relax_disp/optimisation.py
branches/relax_disp/test_suite/system_tests/relax_disp.py
Modified: branches/relax_disp/specific_analyses/relax_disp/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/optimisation.py?rev=21152&r1=21151&r2=21152&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/optimisation.py
(original)
+++ branches/relax_disp/specific_analyses/relax_disp/optimisation.py Thu Oct
17 09:24:20 2013
@@ -229,8 +229,8 @@
@type spins: list of SpinContainer instances
@keyword spin_ids: The list of spin ID strings
corresponding to the spins argument.
@type spin_ids: list of str
- @keyword sim_index: The optional MC simulation index.
- @type sim_index: int
+ @keyword sim_index: The index of the simulation to optimise.
This should be None if normal optimisation is desired.
+ @type sim_index: None or int
@keyword scaling_matrix: The diagonal, square scaling matrix.
@type scaling_matrix: numpy diagonal matrix
@keyword min_algor: The minimisation algorithm to use.
@@ -247,8 +247,6 @@
@type constraints: bool
@keyword verbosity: The amount of information to print. The
higher the value, the greater the verbosity.
@type verbosity: int
- @keyword sim_index: The index of the simulation to optimise.
This should be None if normal optimisation is desired.
- @type sim_index: None or int
@keyword lower: The lower bounds of the grid search
which must be equal to the number of parameters in the model. This optional
argument is only used when doing a grid search.
@type lower: array of numbers
@keyword upper: The upper bounds of the grid search
which must be equal to the number of parameters in the model. This optional
argument is only used when doing a grid search.
Modified: branches/relax_disp/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/relax_disp.py?rev=21152&r1=21151&r2=21152&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Thu Oct 17
09:24:20 2013
@@ -1278,22 +1278,25 @@
This uses the data from paper at
U{http://dx.doi.org/10.1073/pnas.0509100103}. This is CPMG data with a fixed
relaxation time period. Experiment in 1.01 M GuHCl (guanidine hydrochloride).
- The comparison is to Figure 2, which is for dataset with 1 M GuHCl.
The reported results are expected to be in rad.s^-1. Conversion into relax
stored values is preferably.
-
- {Representative 15N CPMG relaxation dispersion curve measured on the
cross peaks from residue L61 in folded ACBP at pH 5.3, 1 M GuHCl, and 40C.}
- 1. The dotted line represents a residue-specific fit of all
parameters in Eq. 1.
- - k_AB = 11.3 +/- 0.7 s^{-1}
- - dw = (2.45 +/- 0.09) * 10^3 s^{-1}
- - R2 = 8.0 +/- 0.5 s^{-1}.
- 2. The solid line represents a global fit of k_AB to all protein
residues and a residue-specific fit of dw and R2.}
- - k_AB = 10.55 +/- 0.08 s^{-1}
- - dw = (2.44 +/- 0.08) * 10^3 s^{-1}
- - R2 = 8.4 +/- 0.3 s^{-1}.
-
- Conversion of paper results to relax results is performed by
+ The comparison is to Figure 2, which is for dataset with 1 M GuHCl.
The reported results are expected to be in rad.s^-1. Conversion into relax
stored values is preferably.
+
+ Representative 15N CPMG relaxation dispersion curve measured on the
cross peaks from residue L61 in folded ACBP at pH 5.3, 1 M GuHCl, and 40C:
+
+ 1. The dotted line represents a residue-specific fit of all
parameters in Eq. 1:
+ - k_AB = 11.3 +/- 0.7 s^-1,
+ - dw = (2.45 +/- 0.09) * 10^3 s^-1,
+ - R2 = 8.0 +/- 0.5 s^-1.
+
+ 2. The solid line represents a global fit of k_AB to all protein
residues and a residue-specific fit of dw and R2.:
+ - k_AB = 10.55 +/- 0.08 s^-1,
+ - dw = (2.44 +/- 0.08) * 10^3 s^-1,
+ - R2 = 8.4 +/- 0.3 s^-1.
+
+ Conversion of paper results to relax results is performed by:
+
- dw(ppm) = dw(rad.s^-1) * 10^6 * 1/(2*pi) *
(gyro1H/(gyro15N*spectrometer_freq)) = 2.45E3 * 1E6 / (2 * math.pi) *
(26.7522212E7/(-2.7126E7 * 599.8908622E6)) = -6.41 ppm.
- Figure 3 shows the ln( k_a [s^-1]) for different concentrations of
GuHCl. The precise values are:
+ Figure 3 shows the ln( k_a [s^-1]) for different concentrations of
GuHCl. The precise values are:
- [GuHCL][M] ln(k_a[s^-1]) k_a[s^-1]
- 0.483 0.89623903 2.4503699912708878
r21152 - in /branches/relax_disp: specific_analyses/relax_disp/optimisation.py test_suite/system_tests/relax_disp.py