Author: bugman
Date: Fri Jun 22 18:32:57 2012
New Revision: 17041
URL: http://svn.gna.org/viewcvs/relax?rev=17041&view=rev
Log:
Merged revisions 17039-17040 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r17039 | bugman | 2012-06-22 18:21:16 +0200 (Fri, 22 Jun 2012) | 5 lines
Converted the consistency testing documentation strings to the Uf_tables
and Desc_container design.
This is needed to use the consistency testing documentation within the user
function help system.
........
r17040 | bugman | 2012-06-22 18:23:31 +0200 (Fri, 22 Jun 2012) | 3 lines
Added the consistency testing documentation to the grace.write and value.*
user functions.
........
Modified:
branches/interatomic/ (props changed)
branches/interatomic/specific_fns/consistency_tests.py
branches/interatomic/user_functions/grace.py
branches/interatomic/user_functions/value.py
Propchange: branches/interatomic/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Jun 22 18:32:57 2012
@@ -1,1 +1,1 @@
-/trunk:1-17030
+/trunk:1-17040
Modified: branches/interatomic/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/specific_fns/consistency_tests.py?rev=17041&r1=17040&r2=17041&view=diff
==============================================================================
--- branches/interatomic/specific_fns/consistency_tests.py (original)
+++ branches/interatomic/specific_fns/consistency_tests.py Fri Jun 22
18:32:57 2012
@@ -36,6 +36,8 @@
from relax_errors import RelaxError, RelaxFuncSetupError,
RelaxNoSequenceError, RelaxNoValueError, RelaxSpinTypeError
from relax_warnings import RelaxDeselectWarning
import specific_fns
+from user_functions.data import Uf_tables; uf_tables = Uf_tables()
+from user_functions.objects import Desc_container
class Consistency_tests(API_base, API_common):
@@ -272,30 +274,17 @@
setattr(data_cont, name, None)
- default_value_doc = """
- Consistency testing default values
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- These default values are found in the file 'physical_constants.py'.
-
-
______________________________________________________________________________________
- | | |
|
- | Data type | Object name | Value
|
-
|_______________________________________|____________________|_________________________|
- | | |
|
- | Bond length | 'r' | 1.02
* 1e-10 |
- | | |
|
- | CSA | 'csa' | -172
* 1e-6 |
- | | |
|
- | Heteronucleus type | 'heteronuc_type' | '15N'
|
- | | |
|
- | Proton type | 'proton_type' | '1H'
|
- | | |
|
- | Angle Theta | 'orientation' | 15.7
|
- | | |
|
- | Correlation time | 'tc' | 13 *
1e-9 |
-
|_______________________________________|____________________|_________________________|
-
- """
+ default_value_doc = Desc_container("Consistency testing default values")
+ default_value_doc.add_paragraph("These default values are found in the
file 'physical_constants.py'.")
+ _table = uf_tables.add_table(label="table: consistency testing default
values", caption="Consistency testing default values.")
+ _table.add_headings(["Data type", "Object name", "Value"])
+ _table.add_row(["Bond length", "'r'", "1.02 * 1e-10"])
+ _table.add_row(["CSA", "'csa'", "-172 * 1e-6"])
+ _table.add_row(["Heteronucleus type", "'heteronuc_type'", "'15N'"])
+ _table.add_row(["Angle theta", "'proton_type'", "'1H'"])
+ _table.add_row(["Proton type", "'orientation'", "15.7"])
+ _table.add_row(["Correlation time", "'tc'", "13 * 1e-9"])
+ default_value_doc.add_table(_table.label)
def overfit_deselect(self):
@@ -333,45 +322,23 @@
spin.select = False
- return_data_name_doc = """
- Consistency testing data type string matching patterns
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- ___________________________________________
- | | |
- | Data type | Object name |
- |_______________________|__________________|
- | | |
- | J(0) | 'j0' |
- | | |
- | F_eta | 'f_eta' |
- | | |
- | F_R2 | 'f_r2' |
- | | |
- | Bond length | 'r' |
- | | |
- | CSA | 'csa' |
- | | |
- | Heteronucleus type | 'heteronuc_type' |
- | | |
- | Proton type | 'proton_type' |
- | | |
- | Angle Theta | 'orientation' |
- | | |
- | Correlation time | 'tc' |
- |_______________________|__________________|
- """
-
-
- set_doc = """
- Consistency testing set details
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- In consistency testing, only four values can be set, the bond
length, CSA, angle
- Theta ('orientation') and correlation time values. These must be set
prior to the
- calculation of consistency functions.
-
- """
+ return_data_name_doc = Desc_container("Consistency testing data type
string matching patterns")
+ _table = uf_tables.add_table(label="table: Consistency testing data
types", caption="Consistency testing data type string matching patterns.")
+ _table.add_headings(["Data type", "Object name"])
+ _table.add_row(["J(0)", "'j0'"])
+ _table.add_row(["F_eta", "'f_eta'"])
+ _table.add_row(["F_R2", "'f_r2'"])
+ _table.add_row(["Bond length", "'r'"])
+ _table.add_row(["CSA", "'csa'"])
+ _table.add_row(["Heteronucleus type", "'heteronuc_type'"])
+ _table.add_row(["Proton type", "'proton_type'"])
+ _table.add_row(["Angle theta", "'orientation'"])
+ _table.add_row(["Correlation time", "'tc'"])
+ return_data_name_doc.add_table(_table.label)
+
+
+ set_doc = Desc_container("Consistency testing set details")
+ set_doc.add_paragraph("In consistency testing, only four values can be
set, the bond length, CSA, angle Theta ('orientation') and correlation time
values. These must be set prior to the calculation of consistency functions.")
def set_error(self, model_info, index, error):
Modified: branches/interatomic/user_functions/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/user_functions/grace.py?rev=17041&r1=17040&r2=17041&view=diff
==============================================================================
--- branches/interatomic/user_functions/grace.py (original)
+++ branches/interatomic/user_functions/grace.py Fri Jun 22 18:32:57 2012
@@ -30,8 +30,9 @@
from generic_fns import grace, minimise
from graphics import WIZARD_IMAGE_PATH
from prompt.doc_string import regexp_doc
+from specific_fns.consistency_tests import Consistency_tests
+from specific_fns.jw_mapping import Jw_mapping
from specific_fns.model_free import Model_free
-from specific_fns.jw_mapping import Jw_mapping
from specific_fns.noe import Noe
from specific_fns.relax_fit import Relax_fit
from user_functions.data import Uf_info; uf_info = Uf_info()
@@ -183,6 +184,7 @@
uf.desc.append(Noe.return_data_name_doc)
uf.desc.append(Relax_fit.return_data_name_doc)
uf.desc.append(Jw_mapping.return_data_name_doc)
+uf.desc.append(Consistency_tests.return_data_name_doc)
uf.desc.append(Model_free.return_data_name_doc)
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
Modified: branches/interatomic/user_functions/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/user_functions/value.py?rev=17041&r1=17040&r2=17041&view=diff
==============================================================================
--- branches/interatomic/user_functions/value.py (original)
+++ branches/interatomic/user_functions/value.py Fri Jun 22 18:32:57 2012
@@ -32,6 +32,7 @@
from generic_fns import diffusion_tensor, pipes, value
from graphics import WIZARD_IMAGE_PATH
from relax_errors import RelaxError
+from specific_fns.consistency_tests import Consistency_tests
from specific_fns.jw_mapping import Jw_mapping
from specific_fns.model_free import Model_free
from specific_fns.relax_fit import Relax_fit
@@ -89,6 +90,8 @@
uf.desc.append(Model_free.return_data_name_doc)
uf.desc.append(Jw_mapping.set_doc)
uf.desc.append(Jw_mapping.return_data_name_doc)
+uf.desc.append(Consistency_tests.set_doc)
+uf.desc.append(Consistency_tests.return_data_name_doc)
uf.desc.append(Relax_fit.set_doc)
uf.desc.append(Relax_fit.return_data_name_doc)
uf.desc.append(N_state_model.set_doc)
@@ -121,6 +124,7 @@
uf.desc.append(regexp_doc)
uf.desc.append(Model_free.return_data_name_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)
uf.desc.append(Relax_fit.return_data_name_doc)
uf.desc.append(N_state_model.return_data_name_doc)
@@ -260,6 +264,8 @@
uf.desc.append(Model_free.return_data_name_doc)
uf.desc.append(Jw_mapping.set_doc)
uf.desc.append(Jw_mapping.return_data_name_doc)
+uf.desc.append(Consistency_tests.set_doc)
+uf.desc.append(Consistency_tests.return_data_name_doc)
uf.desc.append(Relax_fit.set_doc)
uf.desc.append(Relax_fit.return_data_name_doc)
uf.desc.append(N_state_model.set_doc)
@@ -330,12 +336,15 @@
uf.desc.append(Model_free.set_doc)
uf.desc.append(Model_free.return_data_name_doc)
uf.desc.append(Model_free.default_value_doc)
+uf.desc.append(diffusion_tensor.__set_doc__)
+uf.desc.append(diffusion_tensor.__return_data_name_doc__)
+uf.desc.append(diffusion_tensor.__default_value_doc__)
uf.desc.append(Jw_mapping.set_doc)
uf.desc.append(Jw_mapping.return_data_name_doc)
uf.desc.append(Jw_mapping.default_value_doc)
-uf.desc.append(diffusion_tensor.__set_doc__)
-uf.desc.append(diffusion_tensor.__return_data_name_doc__)
-uf.desc.append(diffusion_tensor.__default_value_doc__)
+uf.desc.append(Consistency_tests.set_doc)
+uf.desc.append(Consistency_tests.return_data_name_doc)
+uf.desc.append(Consistency_tests.default_value_doc)
uf.desc.append(Relax_fit.set_doc)
uf.desc.append(Relax_fit.return_data_name_doc)
uf.desc.append(Relax_fit.default_value_doc)
@@ -422,6 +431,7 @@
uf.desc.append(regexp_doc)
uf.desc.append(Model_free.return_data_name_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)
uf.desc.append(Relax_fit.return_data_name_doc)
uf.desc.append(N_state_model.return_data_name_doc)
r17041 - in /branches/interatomic: ./ specific_fns/consistency_tests.py user_functions/grace.py user_functions/value.py