Author: bugman
Date: Wed Jan 25 15:01:47 2012
New Revision: 15250
URL: http://svn.gna.org/viewcvs/relax?rev=15250&view=rev
Log:
Merged revisions 15236,15238,15245-15249 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r15236 | bugman | 2012-01-24 19:25:14 +0100 (Tue, 24 Jan 2012) | 5 lines
More speed ups for the Selection.__contains_mol_res_spin_containers()
method.
Certain unnecessary tests are now skipped.
........
r15238 | bugman | 2012-01-24 21:04:14 +0100 (Tue, 24 Jan 2012) | 3 lines
Speed up for the generic_fns.relax_re.search() function.
........
r15245 | bugman | 2012-01-25 14:24:25 +0100 (Wed, 25 Jan 2012) | 3 lines
Indentation fix.
........
r15246 | bugman | 2012-01-25 14:32:40 +0100 (Wed, 25 Jan 2012) | 5 lines
Modified the J(w) mapping test data to include relaxation values of None.
This should trigger bug #19329 (https://gna.org/bugs/index.php?19329) in
the test suite.
........
r15247 | bugman | 2012-01-25 14:39:13 +0100 (Wed, 25 Jan 2012) | 6 lines
Fix for bug #19329 (https://gna.org/bugs/index.php?19329).
The spin is now deselected if there is really less than three data points,
excluding data points of
None.
........
r15248 | bugman | 2012-01-25 14:43:54 +0100 (Wed, 25 Jan 2012) | 3 lines
Added some value.write user functions to the J(w) mapping sample script.
........
r15249 | bugman | 2012-01-25 14:50:54 +0100 (Wed, 25 Jan 2012) | 3 lines
Added value.write uf calls to the J(w) mapping system test script.
........
Modified:
branches/cst/ (props changed)
branches/cst/generic_fns/mol_res_spin.py
branches/cst/generic_fns/relax_re.py
branches/cst/sample_scripts/jw_mapping.py
branches/cst/specific_fns/jw_mapping.py
branches/cst/test_suite/shared_data/jw_mapping/R1.dat
branches/cst/test_suite/shared_data/jw_mapping/R2.dat
branches/cst/test_suite/shared_data/jw_mapping/noe.dat
branches/cst/test_suite/system_tests/scripts/jw_mapping.py
Propchange: branches/cst/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Jan 25 15:01:47 2012
@@ -1,1 +1,1 @@
-/1.3:1-15232
+/1.3:1-15249
Modified: branches/cst/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/mol_res_spin.py?rev=15250&r1=15249&r2=15250&view=diff
==============================================================================
--- branches/cst/generic_fns/mol_res_spin.py (original)
+++ branches/cst/generic_fns/mol_res_spin.py Wed Jan 25 15:01:47 2012
@@ -223,6 +223,10 @@
# No molecule container sent in, therefore the molecule is
assumed to match.
select_mol = True
+ # Quick exit.
+ if not select_mol:
+ return False
+
# Residue container.
if res:
# No residues in selection object, therefore default to a match.
@@ -235,6 +239,10 @@
else:
# No residue container sent in, therefore the residue is assumed
to match.
select_res = True
+
+ # Quick exit.
+ if not select_res:
+ return False
# Spin container.
if spin:
Modified: branches/cst/generic_fns/relax_re.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/generic_fns/relax_re.py?rev=15250&r1=15249&r2=15250&view=diff
==============================================================================
--- branches/cst/generic_fns/relax_re.py (original)
+++ branches/cst/generic_fns/relax_re.py Wed Jan 25 15:01:47 2012
@@ -67,6 +67,10 @@
# Force a conversion to str.
pattern = str(pattern)
+ # Quick string check.
+ if id == pattern:
+ return True
+
# First replace any '*' with '.*' (relax to re conversion).
pattern_re = replace(pattern, '*', '.*')
id_re = replace(id, '*', '.*')
Modified: branches/cst/sample_scripts/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/sample_scripts/jw_mapping.py?rev=15250&r1=15249&r2=15250&view=diff
==============================================================================
--- branches/cst/sample_scripts/jw_mapping.py (original)
+++ branches/cst/sample_scripts/jw_mapping.py Wed Jan 25 15:01:47 2012
@@ -64,6 +64,11 @@
grace.view(file='jwx.agr')
grace.view(file='jwh.agr')
+# Write out the values.
+value.write(param='j0', file='j0.txt', force=True)
+value.write(param='jwx', file='jwx.txt', force=True)
+value.write(param='jwh', file='jwh.txt', force=True)
+
# Finish.
results.write(file='results', force=True)
state.save('save', force=True)
Modified: branches/cst/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/specific_fns/jw_mapping.py?rev=15250&r1=15249&r2=15250&view=diff
==============================================================================
--- branches/cst/specific_fns/jw_mapping.py (original)
+++ branches/cst/specific_fns/jw_mapping.py Wed Jan 25 15:01:47 2012
@@ -314,9 +314,17 @@
spin.select = False
# Require 3 or more data points.
- elif len(spin.ri_data) < 3:
- warn(RelaxDeselectWarning(spin_id, 'insufficient relaxation
data, 3 or more data points are required'))
- spin.select = False
+ else:
+ # Count the points.
+ data_points = 0
+ for id in cdp.ri_ids:
+ if spin.ri_data.has_key(id) and spin.ri_data[id] != None:
+ data_points += 1
+
+ # Not enough.
+ if data_points < 3:
+ warn(RelaxDeselectWarning(spin_id, 'insufficient
relaxation data, 3 or more data points are required'))
+ spin.select = False
return_data_name_doc = ["Reduced spectral density mapping data type
string matching patterns", """
@@ -391,7 +399,7 @@
# Skip deselected spins.
if not spin.select:
- return
+ return
# Return J(0) sim data.
if index == 0:
Modified: branches/cst/test_suite/shared_data/jw_mapping/R1.dat
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/test_suite/shared_data/jw_mapping/R1.dat?rev=15250&r1=15249&r2=15250&view=diff
==============================================================================
--- branches/cst/test_suite/shared_data/jw_mapping/R1.dat (original)
+++ branches/cst/test_suite/shared_data/jw_mapping/R1.dat Wed Jan 25 15:01:47
2012
@@ -1,2 +1,3 @@
-2 Gly 1.0 0.05
-1 Gly 0.9 0.05
+1 Gly None None
Modified: branches/cst/test_suite/shared_data/jw_mapping/R2.dat
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/test_suite/shared_data/jw_mapping/R2.dat?rev=15250&r1=15249&r2=15250&view=diff
==============================================================================
--- branches/cst/test_suite/shared_data/jw_mapping/R2.dat (original)
+++ branches/cst/test_suite/shared_data/jw_mapping/R2.dat Wed Jan 25 15:01:47
2012
@@ -1,3 +1,4 @@
-2 Gly 15.0 0.5
-1 Gly 13.9 0.8
0 Gly 12.0 0.5
+1 Gly None None
Modified: branches/cst/test_suite/shared_data/jw_mapping/noe.dat
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/test_suite/shared_data/jw_mapping/noe.dat?rev=15250&r1=15249&r2=15250&view=diff
==============================================================================
--- branches/cst/test_suite/shared_data/jw_mapping/noe.dat (original)
+++ branches/cst/test_suite/shared_data/jw_mapping/noe.dat Wed Jan 25
15:01:47 2012
@@ -1,3 +1,4 @@
-2 Gly 0.90 0.05
-1 Gly 0.79 0.05
0 Gly 0.6 0.1
+1 Gly None None
Modified: branches/cst/test_suite/system_tests/scripts/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/test_suite/system_tests/scripts/jw_mapping.py?rev=15250&r1=15249&r2=15250&view=diff
==============================================================================
--- branches/cst/test_suite/system_tests/scripts/jw_mapping.py (original)
+++ branches/cst/test_suite/system_tests/scripts/jw_mapping.py Wed Jan 25
15:01:47 2012
@@ -45,6 +45,11 @@
grace.write(y_data_type='jwx', file='devnull', force=True)
grace.write(y_data_type='jwh', file='devnull', force=True)
+# Value writing.
+value.write(param='j0', file='devnull', force=True)
+value.write(param='jwx', file='devnull', force=True)
+value.write(param='jwh', file='devnull', force=True)
+
# Finish.
results.write(file='devnull', force=True)
state.save('devnull', force=True)
r15250 - in /branches/cst: ./ generic_fns/ sample_scripts/ specific_fns/ test_suite/shared_data/jw_mapping/ test_suite/syste...