Author: bugman
Date: Fri Jul 8 11:59:52 2011
New Revision: 13528
URL: http://svn.gna.org/viewcvs/relax?rev=13528&view=rev
Log:
Converted all of the model-free documentation used in the user functions to
the new design.
Modified:
branches/gui_testing/specific_fns/model_free/main.py
Modified: branches/gui_testing/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/gui_testing/specific_fns/model_free/main.py?rev=13528&r1=13527&r2=13528&view=diff
==============================================================================
--- branches/gui_testing/specific_fns/model_free/main.py (original)
+++ branches/gui_testing/specific_fns/model_free/main.py Fri Jul 8 11:59:52
2011
@@ -1345,10 +1345,7 @@
return names
- default_value_doc = """
- Model-free default values
- ~~~~~~~~~~~~~~~~~~~~~~~~~
-
+ default_value_doc = ["Model-free default values", """
_______________________________________________________________________________________
| | |
|
| Data type | Object name | Value
|
@@ -1375,7 +1372,7 @@
| Proton type | 'proton_type' | '1H'
|
|_______________________________________|____________________|________________________|
- """
+ """]
def default_value(self, param):
"""The default model-free parameter values.
@@ -1611,42 +1608,23 @@
dp_to.mol = deepcopy(dp_from.mol)
- eliminate_doc = """
- Local tm model elimination rule
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- The local tm, in some cases, may exceed the value expected for a
global correlation time.
- Generally the tm value will be stuck at the upper limit defined for
the parameter. These
- models are eliminated using the rule:
+ eliminate_doc = [["Local tm model elimination rule", """
+ The local tm, in some cases, may exceed the value expected for a
global correlation time. Generally the tm value will be stuck at the upper
limit defined for the parameter. These models are eliminated using the rule:
tm >= c
- The default value of c is 50 ns, although this can be overridden by
supplying the value (in
- seconds) as the first element of the args tuple.
-
-
- Internal correlation times {te, tf, ts} model elimination rules
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- These parameters may experience the same problem as the local tm in
that the model fails and
- the parameter value is stuck at the upper limit. These parameters
are constrained using the
- formula (te, tf, ts <= 2tm). These failed models are eliminated
using the rule:
+ The default value of c is 50 ns, although this can be overridden by
supplying the value (in seconds) as the first element of the args tuple.
+ """],
+ ["Internal correlation times {te, tf, ts} model elimination rules",
"""
+ These parameters may experience the same problem as the local tm in
that the model fails and the parameter value is stuck at the upper limit.
These parameters are constrained using the formula (te, tf, ts <= 2tm).
These failed models are eliminated using the rule:
te, tf, ts >= c . tm
- The default value of c is 1.5. Because of round-off errors and the
constraint algorithm,
- setting c to 2 will result in no models being eliminated as the
minimised parameters will
- always be less than 2tm. The value can be changed by supplying the
value as the second
- element of the tuple.
-
-
- Arguments
- ~~~~~~~~~
-
- 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).
- """
+ The default value of c is 1.5. Because of round-off errors and the
constraint algorithm, setting c to 2 will result in no models being
eliminated as the minimised parameters will always be less than 2tm. The
value can be changed by supplying the value as the second element of the
tuple.
+ """],
+ ["Arguments", """
+ 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).
+ """]]
def eliminate(self, name, value, model_info, args, sim=None):
"""Model-free model elimination, parameter by parameter.
@@ -2191,10 +2169,7 @@
return relax_data.return_data_desc(name)
- return_data_name_doc = """
- Model-free data type string matching patterns
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
+ return_data_name_doc = ["Model-free data type string matching patterns",
"""
____________________________________________________________________________________________
| | |
|
| Data type | Object name | Patterns
|
@@ -2225,7 +2200,7 @@
| Proton type | 'proton_type' | '^[Pp]roton$'
|
|________________________|__________________|______________________________________________|
- """
+ """]
def return_data_name(self, param):
"""Return a unique identifying string for the model-free parameter.
@@ -2395,17 +2370,10 @@
return 'ppm'
- set_doc = """
- Model-free set details
- ~~~~~~~~~~~~~~~~~~~~~~
-
- 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.
-
- 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 = ["Model-free set details", """
+ 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.
+
+ 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:
value = Rex / (2.0 * pi * frequency) ** 2
@@ -2413,7 +2381,7 @@
Rex is the chemical exchange value for the current frequency.
pi is in the namespace of relax, ie just type 'pi'.
frequency is the proton frequency corresponding to the data.
- """
+ """]
def set_error(self, model_info, index, error):
r13528 - /branches/gui_testing/specific_fns/model_free/main.py