Author: bugman
Date: Thu Jan 19 09:48:54 2012
New Revision: 15186
URL: http://svn.gna.org/viewcvs/relax?rev=15186&view=rev
Log:
Converted the NOE specific analysis to use the new SPIN_PARAM list API
structure.
Modified:
branches/spec_api/sample_scripts/noe.py
branches/spec_api/specific_fns/noe/__init__.py
branches/spec_api/specific_fns/noe/main.py
branches/spec_api/test_suite/system_tests/scripts/noe.py
Modified: branches/spec_api/sample_scripts/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/sample_scripts/noe.py?rev=15186&r1=15185&r2=15186&view=diff
==============================================================================
--- branches/spec_api/sample_scripts/noe.py (original)
+++ branches/spec_api/sample_scripts/noe.py Thu Jan 19 09:48:54 2012
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2004-2008 Edward d'Auvergne
#
+# Copyright (C) 2004-2012 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -59,8 +59,8 @@
value.write(param='noe', file='noe.out', force=True)
# Create grace files.
-grace.write(y_data_type='ref_ave', file='ref.agr', force=True)
-grace.write(y_data_type='sat_ave', file='sat.agr', force=True)
+grace.write(y_data_type='ref', file='ref.agr', force=True)
+grace.write(y_data_type='sat', file='sat.agr', force=True)
grace.write(y_data_type='noe', file='noe.agr', force=True)
# View the grace files.
Modified: branches/spec_api/specific_fns/noe/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/specific_fns/noe/__init__.py?rev=15186&r1=15185&r2=15186&view=diff
==============================================================================
--- branches/spec_api/specific_fns/noe/__init__.py (original)
+++ branches/spec_api/specific_fns/noe/__init__.py Thu Jan 19 09:48:54 2012
@@ -42,4 +42,12 @@
# Place methods into the API.
self.return_conversion_factor = self._return_no_conversion_factor
+ self.return_data_desc = self._return_data_desc_spin
+ self.return_data_name = self._return_data_name_spin
+ self.return_grace_string = self._return_grace_string_spin
self.return_value = self._return_value_general
+
+ # Set up the spin parameters.
+ self.SPIN_PARAMS.add('ref', desc='The reference peak intensity',
grace_string='Reference intensity')
+ self.SPIN_PARAMS.add('sat', desc='The saturated peak intensity',
grace_string='Saturated intensity')
+ self.SPIN_PARAMS.add('noe', desc='The NOE', grace_string='\\qNOE\\Q')
Modified: branches/spec_api/specific_fns/noe/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/specific_fns/noe/main.py?rev=15186&r1=15185&r2=15186&view=diff
==============================================================================
--- branches/spec_api/specific_fns/noe/main.py (original)
+++ branches/spec_api/specific_fns/noe/main.py Thu Jan 19 09:48:54 2012
@@ -30,6 +30,7 @@
from generic_fns.mol_res_spin import exists_mol_res_spin_data, spin_loop
from relax_errors import RelaxArgNotInListError, RelaxError,
RelaxNoSequenceError
from relax_warnings import RelaxDeselectWarning
+from specific_fns.api_common import API_common
class Noe_main:
@@ -231,95 +232,20 @@
spin.select = False
- def return_data_desc(self, name, spin=None):
- """Return a description of the spin specific object.
-
- @param name: The name of the spin specific object.
- @type name: str
- @param spin: The spin container.
- @type spin: SpinContainer instance
- @return: The object description, or None.
- @rtype: str or None
- """
-
- # Model-free specific objects.
- if name == 'select':
- return 'The spin selection flag'
- if name == 'fixed':
- return 'The fixed flag'
- if name == 'ref':
- return 'The reference peak intensity'
- if name == 'sat':
- return 'The saturated peak intensity'
- if name == 'noe':
- return 'The NOE'
-
-
return_data_name_doc = ["NOE calculation data type string matching
patterns", """
-
____________________________________________________________________________________________
- | | |
|
- | Data type | Object name | Patterns
|
-
|________________________|______________|__________________________________________________|
- | | |
|
- | Reference intensity | 'ref' | '^[Rr]ef$' or '[Rr]ef[
-_][Ii]nt' |
- | | |
|
- | Saturated intensity | 'sat' | '^[Ss]at$' or '[Ss]at[
-_][Ii]nt' |
- | | |
|
- | NOE | 'noe' | '^[Nn][Oo][Ee]$'
|
-
|________________________|______________|__________________________________________________|
+ _________________________________________
+ | | |
+ | Data type | Object name |
+ |________________________|______________|
+ | | |
+ | Reference intensity | 'ref' |
+ | | |
+ | Saturated intensity | 'sat' |
+ | | |
+ | NOE | 'noe' |
+ |________________________|______________|
"""]
-
- def return_data_name(self, param):
- """Return a unique identifying string for the steady-state NOE
parameter.
-
- @param param: The steady-state NOE parameter.
- @type param: str
- @return: The unique parameter identifying string.
- @rtype: str
- """
-
- # Reference intensity.
- if match('^[Rr]ef$', param) or match('[Rr]ef[ -_][Ii]nt', param):
- return 'ref'
-
- # Saturated intensity.
- if match('^[Ss]at$', param) or match('[Ss]at[ -_][Ii]nt', param):
- return 'sat'
-
- # NOE.
- if match('^[Nn][Oo][Ee]$', param):
- return 'noe'
-
-
- def return_grace_string(self, param):
- """Return the Grace string representation of the parameter.
-
- This is used for axis labelling.
-
- @param param: The specific analysis parameter.
- @type param: str
- @return: The Grace string representation of the parameter.
- @rtype: str
- """
-
- # Get the object name.
- object_name = self.return_data_name(param)
-
- # Reference intensity.
- if object_name == 'ref':
- return 'Reference intensity'
-
- # Saturated intensity.
- if object_name == 'sat':
- return 'Saturated intensity'
-
- # NOE.
- if object_name == 'noe':
- return '\\qNOE\\Q'
-
- # Return the parameter as the Grace string.
- return param
def return_units(self, param):
Modified: branches/spec_api/test_suite/system_tests/scripts/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/system_tests/scripts/noe.py?rev=15186&r1=15185&r2=15186&view=diff
==============================================================================
--- branches/spec_api/test_suite/system_tests/scripts/noe.py (original)
+++ branches/spec_api/test_suite/system_tests/scripts/noe.py Thu Jan 19
09:48:54 2012
@@ -44,8 +44,8 @@
value.write(param='noe', file='devnull', force=True)
# Create grace files.
-grace.write(y_data_type='ref_ave', file='devnull', force=True)
-grace.write(y_data_type='sat_ave', file='devnull', force=True)
+grace.write(y_data_type='ref', file='devnull', force=True)
+grace.write(y_data_type='sat', file='devnull', force=True)
grace.write(y_data_type='noe', file='devnull', force=True)
# Write the results.
r15186 - in /branches/spec_api: sample_scripts/ specific_fns/noe/ test_suite/system_tests/scripts/