Author: bugman
Date: Thu May 22 15:23:58 2014
New Revision: 23335
URL: http://svn.gna.org/viewcvs/relax?rev=23335&view=rev
Log:
Merged revisions 23327-23329,23331 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r23327 | bugman | 2014-05-22 14:05:01 +0200 (Thu, 22 May 2014) | 17 lines
Added 7 unit tests demonstrating edge case 'no Rex' failures of the 'NS
CPMG 2-site expanded' model.
This follows from the ideas in the post
http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
These tests cover all parameter value combinations which result in no
exchange:
- dw = 0.0,
- pA = 1.0,
- kex = 0.0,
- dw = 0.0 and pA = 1.0,
- dw = 0.0 and kex = 0.0,
- pA = 1.0 and kex = 0.0,
- dw = 0.0, pA = 1.0, and kex = 0.0.
Such tests should be replicated for all dispersion models.
........
r23328 | bugman | 2014-05-22 14:30:58 +0200 (Thu, 22 May 2014) | 6 lines
Created the Structure.test_bug_22069_structure_delete_helix_attribute
system test.
This is to catch bug #22069 (https://gna.org/bugs/index.php?22069), the
failure of the
structure.delete user function with "AttributeError: Internal instance has
no attribute 'helices'".
........
r23329 | bugman | 2014-05-22 14:37:09 +0200 (Thu, 22 May 2014) | 6 lines
Fix for bug #22069 by only deleting helix and sheet data with
structure.delete when it exists.
This is bug #22069 (https://gna.org/bugs/index.php?22069), the failure of
the structure.delete user
function with "AttributeError: Internal instance has no attribute
'helices'".
........
r23331 | bugman | 2014-05-22 14:52:08 +0200 (Thu, 22 May 2014) | 10 lines
Fix for all edge case 'no Rex' failures of the 'NS CPMG 2-site expanded'
model.
This uses the no exchange checking idea, modified to function in the relax
trunk, from
http://article.gmane.org/gmane.science.nmr.relax.devel/5847. This is
importantly on line 1 of the
function.
The recently introduced set of 7 unit tests (r23327) comprehensively
showing these failures now all
pass. This commit is mainly for demonstration purposes.
........
Added:
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_expanded.py
- copied unchanged from r23331,
trunk/test_suite/unit_tests/_lib/_dispersion/test_ns_cpmg_2site_expanded.py
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/lib/dispersion/ns_cpmg_2site_expanded.py
branches/frame_order_cleanup/lib/structure/internal/object.py
branches/frame_order_cleanup/test_suite/system_tests/structure.py
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_dispersion/__init__.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu May 22 15:23:58 2014
@@ -1 +1 @@
-/trunk:1-23324
+/trunk:1-23334
Modified:
branches/frame_order_cleanup/lib/dispersion/ns_cpmg_2site_expanded.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/dispersion/ns_cpmg_2site_expanded.py?rev=23335&r1=23334&r2=23335&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/dispersion/ns_cpmg_2site_expanded.py
(original)
+++ branches/frame_order_cleanup/lib/dispersion/ns_cpmg_2site_expanded.py
Thu May 22 15:23:58 2014
@@ -272,6 +272,12 @@
@type num_cpmg: numpy int16, rank-1 array
"""
+ # Catch parameter values that will result in no exchange, returning flat
R2eff = R20 lines (when kex = 0.0, k_AB = 0.0).
+ if dw == 0.0 or pA == 1.0 or k_AB == 0.0:
+ for i in range(num_points):
+ back_calc[i] = r20
+ return
+
# Repeditive calculations.
half_tcp = 0.5 * tcp
k_AB_plus_k_BA = k_AB + k_BA
Modified: branches/frame_order_cleanup/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/internal/object.py?rev=23335&r1=23334&r2=23335&view=diff
==============================================================================
--- branches/frame_order_cleanup/lib/structure/internal/object.py
(original)
+++ branches/frame_order_cleanup/lib/structure/internal/object.py Thu
May 22 15:23:58 2014
@@ -1579,42 +1579,44 @@
del_res_nums.reverse()
# Handle the helix metadata.
- del_helix_indices = []
- for i in range(len(self.helices)):
- # Trim the helix.
- helix = self._trim_helix(helix=self.helices[i],
trim_res_list=del_res_nums, res_data=res_data)
-
- # Trimmed helix.
- if helix != None:
- self.helices[i] = helix
-
- # No helix left.
- else:
- del_helix_indices.append(i)
-
- # Loop over the reverse helix indices and pop out the data.
- del_helix_indices.reverse()
- for i in del_helix_indices:
- self.helices.pop(i)
+ if hasattr(self, 'helices'):
+ del_helix_indices = []
+ for i in range(len(self.helices)):
+ # Trim the helix.
+ helix = self._trim_helix(helix=self.helices[i],
trim_res_list=del_res_nums, res_data=res_data)
+
+ # Trimmed helix.
+ if helix != None:
+ self.helices[i] = helix
+
+ # No helix left.
+ else:
+ del_helix_indices.append(i)
+
+ # Loop over the reverse helix indices and pop out the data.
+ del_helix_indices.reverse()
+ for i in del_helix_indices:
+ self.helices.pop(i)
# Handle the sheet metadata.
- del_sheet_indices = []
- for i in range(len(self.sheets)):
- # Trim the sheet.
- sheet = self._trim_sheet(sheet=self.sheets[i],
trim_res_list=del_res_nums, res_data=res_data)
-
- # Trimmed sheet.
- if sheet != None:
- self.sheets[i] = sheet
-
- # No sheet left.
- else:
- del_sheet_indices.append(i)
-
- # Loop over the reverse sheet indices and pop out the data.
- del_sheet_indices.reverse()
- for i in del_sheet_indices:
- self.sheets.pop(i)
+ if hasattr(self, 'sheets'):
+ del_sheet_indices = []
+ for i in range(len(self.sheets)):
+ # Trim the sheet.
+ sheet = self._trim_sheet(sheet=self.sheets[i],
trim_res_list=del_res_nums, res_data=res_data)
+
+ # Trimmed sheet.
+ if sheet != None:
+ self.sheets[i] = sheet
+
+ # No sheet left.
+ else:
+ del_sheet_indices.append(i)
+
+ # Loop over the reverse sheet indices and pop out the data.
+ del_sheet_indices.reverse()
+ for i in del_sheet_indices:
+ self.sheets.pop(i)
def empty(self):
Modified: branches/frame_order_cleanup/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/structure.py?rev=23335&r1=23334&r2=23335&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/system_tests/structure.py
(original)
+++ branches/frame_order_cleanup/test_suite/system_tests/structure.py Thu
May 22 15:23:58 2014
@@ -194,6 +194,19 @@
lines = file.readlines()
for i in range(len(lines)):
self.assertEqual(contents[i], lines[i])
+
+
+ def test_bug_22069_structure_delete_helix_attribute(self):
+ """Catch U{bug #22069<https://gna.org/bugs/?22069>}, the failure of
the structure.delete user function with helix attribute errors."""
+
+ # Path of the structure file.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'frame_order'+sep+'cam'
+
+ # Load the structure.
+ self.interpreter.structure.read_pdb('1J7P_1st_NH_rot.pdb', dir=path)
+
+ # Delete the calciums.
+ self.interpreter.structure.delete(atom_id='@CA')
def test_delete_empty(self):
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_dispersion/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/_lib/_dispersion/__init__.py?rev=23335&r1=23334&r2=23335&view=diff
==============================================================================
---
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_dispersion/__init__.py
(original)
+++
branches/frame_order_cleanup/test_suite/unit_tests/_lib/_dispersion/__init__.py
Thu May 22 15:23:58 2014
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2013 Edward d'Auvergne
#
+# Copyright (C) 2013-2014 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -21,5 +21,6 @@
__all__ = [
- 'test___init__'
+ 'test___init__',
+ 'test_ns_cpmg_2site_expanded'
]
r23335 - in /branches/frame_order_cleanup: ./ lib/dispersion/ lib/structure/internal/ test_suite/system_tests/ test_suite/un...