Author: bugman
Date: Wed Mar 13 15:52:43 2013
New Revision: 18818
URL: http://svn.gna.org/viewcvs/relax?rev=18818&view=rev
Log:
Merged revisions 18816-18817 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r18816 | bugman | 2013-03-13 15:36:39 +0100 (Wed, 13 Mar 2013) | 5 lines
Shifted all of the model-free specific analysis class documentation
variables to the top.
This is simply for better organisation of the code.
........
r18817 | bugman | 2013-03-13 15:51:47 +0100 (Wed, 13 Mar 2013) | 6 lines
Created the model-free write_doc class variable talking about the field
strength independent Rex value.
This has been added to the value.display and value.write user functions to
explain that Rex values
are very small and that the user needs to scale them up.
........
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/specific_fns/model_free/main.py
branches/frame_order_testing/user_functions/value.py
Propchange: branches/frame_order_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Mar 13 15:52:43 2013
@@ -1,1 +1,1 @@
-/trunk:1-18814
+/trunk:1-18817
Modified: branches/frame_order_testing/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/model_free/main.py?rev=18818&r1=18817&r2=18818&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/model_free/main.py (original)
+++ branches/frame_order_testing/specific_fns/model_free/main.py Wed Mar 13
15:52:43 2013
@@ -44,6 +44,47 @@
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.")
+
+ 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:")
+ write_doc.add_verbatim(" Rex = value * (2.0 * pi * frequency) ** 2")
+ write_doc.add_paragraph("The frequency is that of the proton in Hertz.")
+
def _are_mf_params_set(self, spin):
"""Test if the model-free parameter values are set.
@@ -1309,18 +1350,6 @@
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 +2082,6 @@
# 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):
Modified: branches/frame_order_testing/user_functions/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/user_functions/value.py?rev=18818&r1=18817&r2=18818&view=diff
==============================================================================
--- branches/frame_order_testing/user_functions/value.py (original)
+++ branches/frame_order_testing/user_functions/value.py Wed Mar 13 15:52:43
2013
@@ -127,6 +127,7 @@
)
uf.desc.append(regexp_doc)
uf.desc.append(Model_free.return_data_name_doc)
+uf.desc.append(Model_free.write_doc)
uf.desc.append(Jw_mapping.return_data_name_doc)
uf.desc.append(Consistency_tests.return_data_name_doc)
uf.desc.append(Noe.return_data_name_doc)
@@ -434,6 +435,7 @@
uf.desc[-1].add_paragraph("The values corresponding to the given parameter
will be written to file.")
uf.desc.append(regexp_doc)
uf.desc.append(Model_free.return_data_name_doc)
+uf.desc.append(Model_free.write_doc)
uf.desc.append(Jw_mapping.return_data_name_doc)
uf.desc.append(Consistency_tests.return_data_name_doc)
uf.desc.append(Noe.return_data_name_doc)
r18818 - in /branches/frame_order_testing: ./ specific_fns/model_free/main.py user_functions/value.py