Author: bugman
Date: Mon Apr 14 17:08:35 2014
New Revision: 22740
URL: http://svn.gna.org/viewcvs/relax?rev=22740&view=rev
Log:
The model-free parameter setting documentation has been shifted into the
parameter list object.
As the text was quite out of date, it has been updated to the current relax
design.
Modified:
trunk/specific_analyses/model_free/parameter_object.py
trunk/specific_analyses/model_free/uf.py
trunk/user_functions/value.py
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=22740&r1=22739&r2=22740&view=diff
==============================================================================
--- trunk/specific_analyses/model_free/parameter_object.py (original)
+++ trunk/specific_analyses/model_free/parameter_object.py Mon Apr 14
17:08:35 2014
@@ -74,3 +74,12 @@
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)
+
+ # Parameter setting documentation.
+ for doc in self._uf_doc_loop(["table: model-free parameters",
"table: mf parameter value setting"]):
+ 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")
+ doc.add_paragraph("where:")
+ doc.add_list_element("rex is the chemical exchange value for the
current frequency.")
+ doc.add_list_element("frequency is the proton frequency
corresponding to the data.")
Modified: trunk/specific_analyses/model_free/uf.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/model_free/uf.py?rev=22740&r1=22739&r2=22740&view=diff
==============================================================================
--- trunk/specific_analyses/model_free/uf.py (original)
+++ trunk/specific_analyses/model_free/uf.py Mon Apr 14 17:08:35 2014
@@ -73,16 +73,6 @@
eliminate_doc.append(Desc_container("Arguments"))
eliminate_doc[-1].add_paragraph("The 'args' argument must be a tuple of
length 2, the elements of which must be numbers. For example, to eliminate
models which have a local tm value greater than 25 ns and models with
internal correlation times greater than 1.5 times tm, set 'args' to (25 *
1e-9, 1.5).")
-# Parameter setting documentation.
-set_doc = Desc_container("Model-free set details")
-set_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 run corresponds to model-free model 'm4' then,
because these data values are not parameters of the model, they will have no
effect.")
-set_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 get the correct value:")
-set_doc.add_verbatim(" value = rex / (2.0 * pi * frequency) ** 2")
-set_doc.add_paragraph("where:")
-set_doc.add_list_element("rex is the chemical exchange value for the current
frequency.")
-set_doc.add_list_element("pi is in the namespace of relax, ie just type
'pi'.")
-set_doc.add_list_element("frequency is the proton frequency corresponding to
the data.")
-
# Parameter writing documentation.
write_doc = Desc_container("Model-free parameter writing details")
write_doc.add_paragraph("For the model-free theory, it is assumed that Rex
values are scaled quadratically with field strength. The values will seem
quite small as they will be written out as a field strength independent
value. Hence please use the following formula to convert the value to that
expected for a given magnetic field strength:")
Modified: trunk/user_functions/value.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/value.py?rev=22740&r1=22739&r2=22740&view=diff
==============================================================================
--- trunk/user_functions/value.py (original)
+++ trunk/user_functions/value.py Mon Apr 14 17:08:35 2014
@@ -97,7 +97,6 @@
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(regexp_doc)
-uf.desc.append(model_free_uf.set_doc)
uf.desc.append(model_free_params.uf_doc(label="table: model-free
parameters"))
uf.desc.append(jw_mapping_uf.set_doc)
uf.desc.append(jw_mapping_params.uf_doc(label="table: J(w) parameters"))
@@ -288,7 +287,6 @@
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(regexp_doc)
-uf.desc.append(model_free_uf.set_doc)
uf.desc.append(model_free_params.uf_doc(label="table: model-free
parameters"))
uf.desc.append(jw_mapping_uf.set_doc)
uf.desc.append(jw_mapping_params.uf_doc(label="table: J(w) parameters"))
@@ -379,7 +377,6 @@
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(regexp_doc)
-uf.desc.append(model_free_uf.set_doc)
uf.desc.append(diffusion_tensor.__set_doc__)
uf.desc.append(model_free_params.uf_doc(label="table: mf parameter value
setting"))
uf.desc.append(jw_mapping_uf.set_doc)
r22740 - in /trunk: specific_analyses/model_free/parameter_object.py specific_analyses/model_free/uf.py user_functions/value.py