Author: bugman
Date: Mon Apr 14 19:37:56 2014
New Revision: 22755
URL: http://svn.gna.org/viewcvs/relax?rev=22755&view=rev
Log:
Created parameter tables with no additional trailing text.
This is used in a few of the user functions.
Modified:
trunk/specific_analyses/consistency_tests/parameter_object.py
trunk/specific_analyses/frame_order/parameter_object.py
trunk/specific_analyses/jw_mapping/parameter_object.py
trunk/specific_analyses/model_free/parameter_object.py
trunk/specific_analyses/n_state_model/parameter_object.py
trunk/specific_analyses/relax_disp/parameter_object.py
trunk/specific_analyses/relax_fit/parameter_object.py
trunk/user_functions/value.py
Modified: trunk/specific_analyses/consistency_tests/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/consistency_tests/parameter_object.py?rev=22755&r1=22754&r2=22755&view=diff
==============================================================================
--- trunk/specific_analyses/consistency_tests/parameter_object.py
(original)
+++ trunk/specific_analyses/consistency_tests/parameter_object.py Mon
Apr 14 19:37:56 2014
@@ -56,8 +56,9 @@
# Set up the user function documentation.
self._set_uf_title("Consistency testing parameters")
self._uf_param_table(label="table: consistency testing parameters",
caption="Consistency testing parameters.")
- self._uf_param_table(label="table: consistency testing parameter
value setting", caption="Consistency testing parameter value setting.",
default=True)
+ self._uf_param_table(label="table: consistency testing parameter
value setting", caption="Consistency testing parameters.")
+ self._uf_param_table(label="table: consistency testing parameter
value setting with defaults", caption="Consistency testing parameter value
setting.", default=True)
# Value setting documentation.
- for doc in self._uf_doc_loop(["table: consistency testing
parameters", "table: consistency testing parameter value setting"]):
+ for doc in self._uf_doc_loop(["table: consistency testing parameter
value setting", "table: consistency testing parameter value setting with
defaults"]):
doc.add_paragraph("In consistency testing, the CSA value, angle
Theta ('orientation') and global correlation time must be set prior to the
calculation of consistency functions.")
Modified: trunk/specific_analyses/frame_order/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/parameter_object.py?rev=22755&r1=22754&r2=22755&view=diff
==============================================================================
--- trunk/specific_analyses/frame_order/parameter_object.py (original)
+++ trunk/specific_analyses/frame_order/parameter_object.py Mon Apr 14
19:37:56 2014
@@ -72,4 +72,4 @@
# Set up the user function documentation.
self._set_uf_title("Frame order parameters")
self._uf_param_table(label="table: frame order parameters",
caption="Frame order parameters.", scope='global')
- self._uf_param_table(label="table: frame order parameter value
setting", caption="Frame order parameter value setting.", scope='global',
default=True)
+ self._uf_param_table(label="table: frame order parameter value
setting with defaults", caption="Frame order parameter value setting.",
scope='global', default=True)
Modified: trunk/specific_analyses/jw_mapping/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/jw_mapping/parameter_object.py?rev=22755&r1=22754&r2=22755&view=diff
==============================================================================
--- trunk/specific_analyses/jw_mapping/parameter_object.py (original)
+++ trunk/specific_analyses/jw_mapping/parameter_object.py Mon Apr 14
19:37:56 2014
@@ -53,8 +53,9 @@
# Set up the user function documentation.
self._set_uf_title("Reduced spectral density mapping parameters")
self._uf_param_table(label="table: J(w) parameters",
caption="Reduced spectral density mapping parameters.")
- self._uf_param_table(label="table: J(w) parameter value setting",
caption="Reduced spectral density mapping parameter value setting.",
default=True)
+ self._uf_param_table(label="table: J(w) parameter value setting",
caption="Reduced spectral density mapping parameters.")
+ self._uf_param_table(label="table: J(w) parameter value setting with
defaults", caption="Reduced spectral density mapping parameter value
setting.", default=True)
# Value setting documentation.
- for doc in self._uf_doc_loop(["table: J(w) parameters", "table: J(w)
parameter value setting"]):
+ for doc in self._uf_doc_loop(["table: J(w) parameter value setting",
"table: J(w) parameter value setting with defaults"]):
doc.add_paragraph("In reduced spectral density mapping, the CSA
value must be set prior to the calculation of spectral density values.")
Modified: trunk/specific_analyses/model_free/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/model_free/parameter_object.py?rev=22755&r1=22754&r2=22755&view=diff
==============================================================================
--- trunk/specific_analyses/model_free/parameter_object.py (original)
+++ trunk/specific_analyses/model_free/parameter_object.py Mon Apr 14
19:37:56 2014
@@ -74,10 +74,11 @@
self._uf_param_table(label="table: model-free parameter writing",
caption="Model-free parameters.")
self._uf_param_table(label="table: model-free parameters and min
stats", caption="Model-free parameters and minimisation statistics.",
sets=['params', 'fixed', 'min'])
self._uf_param_table(label="table: all model-free parameters",
caption="Model-free parameters.", scope=None)
- self._uf_param_table(label="table: mf parameter value setting",
caption="Model-free parameter value setting.", default=True)
+ self._uf_param_table(label="table: model-free parameter value
setting", caption="Model-free parameters.")
+ self._uf_param_table(label="table: model-free parameter value
setting with defaults", caption="Model-free parameter value setting.",
default=True)
# Parameter setting documentation.
- for doc in self._uf_doc_loop(["table: model-free parameters",
"table: mf parameter value setting"]):
+ for doc in self._uf_doc_loop(["table: model-free parameter value
setting", "table: model-free parameter value setting with defaults"]):
doc.add_paragraph("Setting a parameter value may have no effect
depending on which model-free model is chosen. For example if S2f values and
S2s values are set but the data pipe corresponds to the model-free model 'm4'
then because these data values are not parameters of the model they will have
no effect.")
doc.add_paragraph("Note that the Rex values are scaled
quadratically with field strength and should be supplied as a field strength
independent value. Use the following formula to obtain the correct value:")
doc.add_verbatim(" value = rex / (2.0 * pi * frequency) ** 2")
Modified: trunk/specific_analyses/n_state_model/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/n_state_model/parameter_object.py?rev=22755&r1=22754&r2=22755&view=diff
==============================================================================
--- trunk/specific_analyses/n_state_model/parameter_object.py (original)
+++ trunk/specific_analyses/n_state_model/parameter_object.py Mon Apr 14
19:37:56 2014
@@ -57,8 +57,9 @@
# Set up the user function documentation.
self._set_uf_title("N-state model parameters")
self._uf_param_table(label="table: N-state parameters",
caption="N-state model parameters.", scope='global', type=True)
- self._uf_param_table(label="table: N-state parameter value setting",
caption="N-state model parameter value setting.", scope='global',
default=True, type=True)
+ self._uf_param_table(label="table: N-state parameter value setting",
caption="N-state model parameters.", scope='global', type=True)
+ self._uf_param_table(label="table: N-state parameter value setting
with defaults", caption="N-state model parameter value setting.",
scope='global', default=True, type=True)
# Value setting documentation.
- for doc in self._uf_doc_loop(["table: N-state parameters", "table:
N-state parameter value setting"]):
+ for doc in self._uf_doc_loop(["table: N-state parameter value
setting", "table: N-state parameter value setting with defaults"]):
doc.add_paragraph("Setting parameters for the N-state model is a
little different from the other type of analyses as each state has a set of
parameters with the same names as the other states. To set the parameters
for a specific state c (ranging from 0 for the first to N-1 for the last, the
number c should be given as the index argument. So the Euler angle gamma of
the third state is specified using the parameter name 'gamma' and index of
2.")
Modified: trunk/specific_analyses/relax_disp/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_disp/parameter_object.py?rev=22755&r1=22754&r2=22755&view=diff
==============================================================================
--- trunk/specific_analyses/relax_disp/parameter_object.py (original)
+++ trunk/specific_analyses/relax_disp/parameter_object.py Mon Apr 14
19:37:56 2014
@@ -95,8 +95,9 @@
self._set_uf_title("Relaxation dispersion parameters")
self._uf_param_table(label="table: dispersion parameters",
caption="Relaxation dispersion parameters.", type=True)
self._uf_param_table(label="table: dispersion parameters and min
stats", caption="Relaxation dispersion parameters and minimisation
statistics.", sets=['params', 'fixed', 'min'])
- self._uf_param_table(label="table: dispersion parameter value
setting", caption="Relaxation dispersion parameter value setting.",
default=True, type=True)
+ self._uf_param_table(label="table: dispersion parameter value
setting", caption="Relaxation dispersion parameters.", type=True)
+ self._uf_param_table(label="table: dispersion parameter value
setting with defaults", caption="Relaxation dispersion parameter value
setting.", default=True, type=True)
# Value setting documentation.
- for doc in self._uf_doc_loop(["table: dispersion parameters",
"table: dispersion parameter value setting"]):
+ for doc in self._uf_doc_loop(["table: dispersion parameter value
setting", "table: dispersion parameter value setting with defaults"]):
doc.add_paragraph("Any of the relaxation dispersion parameters
which are of the 'float' type can be set. Note that setting values for
parameters which are not part of the model will have no effect.")
Modified: trunk/specific_analyses/relax_fit/parameter_object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/relax_fit/parameter_object.py?rev=22755&r1=22754&r2=22755&view=diff
==============================================================================
--- trunk/specific_analyses/relax_fit/parameter_object.py (original)
+++ trunk/specific_analyses/relax_fit/parameter_object.py Mon Apr 14
19:37:56 2014
@@ -62,4 +62,5 @@
self._set_uf_title("Relaxation curve fitting parameters")
self._uf_param_table(label="table: curve-fit parameters",
caption="Relaxation curve fitting parameters.")
self._uf_param_table(label="table: curve-fit parameters and min
stats", caption="Relaxation curve fitting parameters and minimisation
statistics.", sets=['params', 'fixed', 'min'])
- self._uf_param_table(label="table: curve-fit parameter value
setting", caption="Relaxation curve fitting parameter value setting.",
default=True)
+ self._uf_param_table(label="table: curve-fit parameter value
setting", caption="Relaxation curve fitting parameters.")
+ self._uf_param_table(label="table: curve-fit parameter value setting
with defaults", caption="Relaxation curve fitting parameter value setting.",
default=True)
Modified: trunk/user_functions/value.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/value.py?rev=22755&r1=22754&r2=22755&view=diff
==============================================================================
--- trunk/user_functions/value.py (original)
+++ trunk/user_functions/value.py Mon Apr 14 19:37:56 2014
@@ -88,12 +88,12 @@
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("If this is used to change values of previously
minimised parameters, then the minimisation statistics (chi-squared value,
iteration count, function count, gradient count, and Hessian count) will be
reset.")
# Prompt examples.
-uf.desc.append(relax_fit_params.uf_doc(label="table: curve-fit parameters"))
-uf.desc.append(model_free_params.uf_doc(label="table: model-free
parameters"))
-uf.desc.append(jw_mapping_params.uf_doc(label="table: J(w) parameters"))
-uf.desc.append(consistency_test_params.uf_doc(label="table: consistency
testing parameters"))
-uf.desc.append(n_state_params.uf_doc(label="table: N-state parameters"))
-uf.desc.append(relax_disp_params.uf_doc(label="table: dispersion
parameters"))
+uf.desc.append(relax_fit_params.uf_doc(label="table: curve-fit parameter
value setting"))
+uf.desc.append(model_free_params.uf_doc(label="table: model-free parameter
value setting"))
+uf.desc.append(jw_mapping_params.uf_doc(label="table: J(w) parameter value
setting"))
+uf.desc.append(consistency_test_params.uf_doc(label="table: consistency
testing parameter value setting"))
+uf.desc.append(n_state_params.uf_doc(label="table: N-state parameter value
setting"))
+uf.desc.append(relax_disp_params.uf_doc(label="table: dispersion parameter
value setting"))
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To copy the CSA values from the data pipe 'm1' to
'm2', type:")
uf.desc[-1].add_prompt("relax> value.copy('m1', 'm2', 'csa')")
@@ -270,12 +270,12 @@
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("The spin system can be identified in the file
using two different formats. The first is the spin ID string column which
can include the molecule name, the residue name and number, and the spin name
and number. Alternatively the molecule name, residue number, residue name,
spin number and/or spin name columns can be supplied allowing this
information to be in separate columns. Note that the numbering of columns
starts at one. The spin ID string can be used to restrict the reading to
certain spin types, for example only 15N spins when only residue information
is in the file.")
uf.desc[-1].add_paragraph("If this is used to change values of previously
minimised parameters, then the minimisation statistics (chi-squared value,
iteration count, function count, gradient count, and Hessian count) will be
reset.")
-uf.desc.append(relax_fit_params.uf_doc(label="table: curve-fit parameters"))
-uf.desc.append(model_free_params.uf_doc(label="table: model-free
parameters"))
-uf.desc.append(jw_mapping_params.uf_doc(label="table: J(w) parameters"))
-uf.desc.append(consistency_test_params.uf_doc(label="table: consistency
testing parameters"))
-uf.desc.append(n_state_params.uf_doc(label="table: N-state parameters"))
-uf.desc.append(relax_disp_params.uf_doc(label="table: dispersion
parameters"))
+uf.desc.append(relax_fit_params.uf_doc(label="table: curve-fit parameter
value setting"))
+uf.desc.append(model_free_params.uf_doc(label="table: model-free parameter
value setting"))
+uf.desc.append(jw_mapping_params.uf_doc(label="table: J(w) parameter value
setting"))
+uf.desc.append(consistency_test_params.uf_doc(label="table: consistency
testing parameter value setting"))
+uf.desc.append(n_state_params.uf_doc(label="table: N-state parameter value
setting"))
+uf.desc.append(relax_disp_params.uf_doc(label="table: dispersion parameter
value setting"))
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To load 15N CSA values from the file 'csa_values'
in the directory 'data', where spins are only identified by residue name and
number, type one of the following:")
@@ -354,12 +354,12 @@
# Spin identification.
uf.desc.append(Desc_container("Spin identification"))
uf.desc[-1].add_paragraph("If the spin ID is left unset, then this will be
applied to all spins. If the data is global non-spin specific data, such as
diffusion tensor parameters, supplying the spin identifier will terminate the
program with an error.")
-uf.desc.append(relax_fit_params.uf_doc(label="table: curve-fit parameter
value setting"))
-uf.desc.append(model_free_params.uf_doc(label="table: mf parameter value
setting"))
-uf.desc.append(jw_mapping_params.uf_doc(label="table: J(w) parameter value
setting"))
-uf.desc.append(consistency_test_params.uf_doc(label="table: consistency
testing parameter value setting"))
-uf.desc.append(n_state_params.uf_doc(label="table: N-state parameter value
setting"))
-uf.desc.append(relax_disp_params.uf_doc(label="table: dispersion parameter
value setting"))
+uf.desc.append(relax_fit_params.uf_doc(label="table: curve-fit parameter
value setting with defaults"))
+uf.desc.append(model_free_params.uf_doc(label="table: model-free parameter
value setting with defaults"))
+uf.desc.append(jw_mapping_params.uf_doc(label="table: J(w) parameter value
setting with defaults"))
+uf.desc.append(consistency_test_params.uf_doc(label="table: consistency
testing parameter value setting with defaults"))
+uf.desc.append(n_state_params.uf_doc(label="table: N-state parameter value
setting with defaults"))
+uf.desc.append(relax_disp_params.uf_doc(label="table: dispersion parameter
value setting with defaults"))
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
uf.desc[-1].add_paragraph("To set the parameter values for the current data
pipe to the default values, for all spins, type:")
r22755 - in /trunk: specific_analyses/consistency_tests/ specific_analyses/frame_order/ specific_analyses/jw_mapping/ specif...