Author: semor
Date: Thu Jan 10 16:32:48 2008
New Revision: 4598
URL: http://svn.gna.org/viewcvs/relax?rev=4598&view=rev
Log:
Merged revisions 4585-4586 via svnmerge from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.3
........
r4585 | bugman | 2008-01-10 08:35:02 -0500 (Thu, 10 Jan 2008) | 22 lines
Manually ported r4584 from the 1.2 line - the fix to bug #8997
(https://gna.org/bugs/?8997).
The command used was:
svn merge -r4583:4584 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2
.....
r4584 | bugman | 2008-01-10 14:30:10 +0100 (Thu, 10 Jan 2008) | 11 lines
Changed paths:
M /1.2/generic_fns/palmer.py
Fix for bug #8997 (https://gna.org/bugs/index.php?8997).
This bug was reported by Carl Diehl (carl dot diehl at bpc dot lu dot se).
The problem was because of a change between relax versions 1.0 and 1.2.
Previously the residue
number was being searched for, but the changes used the absolute position
to significantly speed up
the code. But the absolute positions are different in a Modelfree
'mfout' file if simulations are
run. The absolute position in this situation is now properly calculated
and the test data attached
to the bug report by Seb now works.
.....
........
r4586 | bugman | 2008-01-10 09:54:12 -0500 (Thu, 10 Jan 2008) | 3 lines
Removed a few empty __init__() class methods and shifted their docstrings
to the class docstring.
........
Modified:
branches/consistency_tests_1.3/ (props changed)
branches/consistency_tests_1.3/data/data_classes.py
branches/consistency_tests_1.3/data/diff_tensor.py
branches/consistency_tests_1.3/generic_fns/palmer.py
Propchange: branches/consistency_tests_1.3/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Jan 10 16:32:48 2008
@@ -1,1 +1,1 @@
-/1.3:1-3320,3333-4175,4223,4241-4335,4338-4433,4440-4461,4473,4476-4493,4523-4551,4567-4577,4579
+/1.3:1-3320,3333-4175,4223,4241-4335,4338-4433,4440-4461,4473,4476-4493,4523-4551,4567-4577,4579,4585-4586
Modified: branches/consistency_tests_1.3/data/data_classes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/data/data_classes.py?rev=4598&r1=4597&r2=4598&view=diff
==============================================================================
--- branches/consistency_tests_1.3/data/data_classes.py (original)
+++ branches/consistency_tests_1.3/data/data_classes.py Thu Jan 10 16:32:48
2008
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2004, 2006-2007 Edward d'Auvergne
#
+# Copyright (C) 2003-2004, 2006-2008 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -30,9 +30,7 @@
#######################
class Element:
- def __init__(self):
- """Empty data container."""
-
+ """Empty data container."""
def __repr__(self):
# Header.
@@ -52,9 +50,7 @@
######################
class SpecificData(DictType):
- def __init__(self):
- """Dictionary type class for specific data."""
-
+ """Dictionary type class for specific data."""
def __repr__(self):
text = "Data:\n"
@@ -89,8 +85,7 @@
########################
class Residue(DictType):
- def __init__(self):
- """Class containing all the residue specific data."""
+ """Class containing all the residue specific data."""
def __repr__(self):
@@ -117,9 +112,7 @@
class ResidueList(ListType):
- def __init__(self):
- """Empty data container for residue specific data."""
-
+ """Empty data container for residue specific data."""
def __repr__(self):
text = "Sequence data.\n\n"
Modified: branches/consistency_tests_1.3/data/diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/data/diff_tensor.py?rev=4598&r1=4597&r2=4598&view=diff
==============================================================================
--- branches/consistency_tests_1.3/data/diff_tensor.py (original)
+++ branches/consistency_tests_1.3/data/diff_tensor.py Thu Jan 10 16:32:48
2008
@@ -551,11 +551,10 @@
#################################
class DiffTensorData(Element):
- def __init__(self):
- """An empty data container for the diffusion tensor elements."""
-
- # Set the initial diffusion type to None.
- self.type = None
+ """An empty data container for the diffusion tensor elements."""
+
+ # Set the initial diffusion type to None.
+ type = None
def __setattr__(self, name, value):
Modified: branches/consistency_tests_1.3/generic_fns/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/generic_fns/palmer.py?rev=4598&r1=4597&r2=4598&view=diff
==============================================================================
--- branches/consistency_tests_1.3/generic_fns/palmer.py (original)
+++ branches/consistency_tests_1.3/generic_fns/palmer.py Thu Jan 10 16:32:48
2008
@@ -583,8 +583,13 @@
data_rex_err = None
# Get the chi-squared data.
- row = split(self.mfout_lines[self.mfout_chi2_pos + pos])
- data.chi2 = float(row[1])
+ if not sims:
+ row = split(self.mfout_lines[self.mfout_chi2_pos + pos])
+ data.chi2 = float(row[1])
+ else:
+ # The mfout chi2 position (with no sims) plus 2 (for the
extra XML) plus the residue position times 22 (because of the simulated SSE
rows).
+ row = split(self.mfout_lines[self.mfout_chi2_pos + 2 +
22*pos])
+ data.chi2 = float(row[1])
# Increment the residue position.
pos = pos + 1
r4598 - in /branches/consistency_tests_1.3: ./ data/data_classes.py data/diff_tensor.py generic_fns/palmer.py