Author: bugman
Date: Wed Mar 13 15:36:39 2013
New Revision: 18816
URL: http://svn.gna.org/viewcvs/relax?rev=18816&view=rev
Log:
Shifted all of the model-free specific analysis class documentation variables
to the top.
This is simply for better organisation of the code.
Modified:
trunk/specific_fns/model_free/main.py
Modified: trunk/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_fns/model_free/main.py?rev=18816&r1=18815&r2=18816&view=diff
==============================================================================
--- trunk/specific_fns/model_free/main.py (original)
+++ trunk/specific_fns/model_free/main.py Wed Mar 13 15:36:39 2013
@@ -44,6 +44,42 @@
class Model_free_main:
"""Class containing functions specific to model-free analysis."""
+
+ default_value_doc = Desc_container("Model-free default values")
+ _table = uf_tables.add_table(label="table: mf default values",
caption="Model-free default values.")
+ _table.add_headings(["Data type", "Object name", "Value"])
+ _table.add_row(["Local tm", "'local_tm'", "10 * 1e-9"])
+ _table.add_row(["Order parameters S2, S2f, and S2s", "'s2', 's2f',
's2s'", "0.8"])
+ _table.add_row(["Correlation time te", "'te'", "100 * 1e-12"])
+ _table.add_row(["Correlation time tf", "'tf'", "10 * 1e-12"])
+ _table.add_row(["Correlation time ts", "'ts'", "1000 * 1e-12"])
+ _table.add_row(["Chemical exchange relaxation", "'rex'", "0.0"])
+ _table.add_row(["CSA", "'csa'", "-172 * 1e-6"])
+ default_value_doc.add_table(_table.label)
+
+ return_data_name_doc = Desc_container("Model-free data type string
matching patterns")
+ _table = uf_tables.add_table(label="table: mf data type patterns",
caption="Model-free data type string matching patterns.")
+ _table.add_headings(["Data type", "Object name"])
+ _table.add_row(["Local tm", "'local_tm'"])
+ _table.add_row(["Order parameter S2", "'s2'"])
+ _table.add_row(["Order parameter S2f", "'s2f'"])
+ _table.add_row(["Order parameter S2s", "'s2s'"])
+ _table.add_row(["Correlation time te", "'te'"])
+ _table.add_row(["Correlation time tf", "'tf'"])
+ _table.add_row(["Correlation time ts", "'ts'"])
+ _table.add_row(["Chemical exchange", "'rex'"])
+ _table.add_row(["CSA", "'csa'"])
+ return_data_name_doc.add_table(_table.label)
+
+ 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.")
+
def _are_mf_params_set(self, spin):
"""Test if the model-free parameter values are set.
@@ -1309,18 +1345,6 @@
return types[param]
- default_value_doc = Desc_container("Model-free default values")
- _table = uf_tables.add_table(label="table: mf default values",
caption="Model-free default values.")
- _table.add_headings(["Data type", "Object name", "Value"])
- _table.add_row(["Local tm", "'local_tm'", "10 * 1e-9"])
- _table.add_row(["Order parameters S2, S2f, and S2s", "'s2', 's2f',
's2s'", "0.8"])
- _table.add_row(["Correlation time te", "'te'", "100 * 1e-12"])
- _table.add_row(["Correlation time tf", "'tf'", "10 * 1e-12"])
- _table.add_row(["Correlation time ts", "'ts'", "1000 * 1e-12"])
- _table.add_row(["Chemical exchange relaxation", "'rex'", "0.0"])
- _table.add_row(["CSA", "'csa'", "-172 * 1e-6"])
- default_value_doc.add_table(_table.label)
-
def default_value(self, param):
"""The default model-free parameter values.
@@ -2053,31 +2077,6 @@
# Final printout.
if verbose and not deselect_flag:
print("No spins have been deselected.")
-
-
- return_data_name_doc = Desc_container("Model-free data type string
matching patterns")
- _table = uf_tables.add_table(label="table: mf data type patterns",
caption="Model-free data type string matching patterns.")
- _table.add_headings(["Data type", "Object name"])
- _table.add_row(["Local tm", "'local_tm'"])
- _table.add_row(["Order parameter S2", "'s2'"])
- _table.add_row(["Order parameter S2f", "'s2f'"])
- _table.add_row(["Order parameter S2s", "'s2s'"])
- _table.add_row(["Correlation time te", "'te'"])
- _table.add_row(["Correlation time tf", "'tf'"])
- _table.add_row(["Correlation time ts", "'ts'"])
- _table.add_row(["Chemical exchange", "'rex'"])
- _table.add_row(["CSA", "'csa'"])
- return_data_name_doc.add_table(_table.label)
-
-
- 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.")
def set_error(self, model_info, index, error):
r18816 - /trunk/specific_fns/model_free/main.py