Author: bugman
Date: Sat Dec 2 05:32:43 2006
New Revision: 2901
URL: http://svn.gna.org/viewcvs/relax?rev=2901&view=rev
Log:
Ported r2719 to r2743 from the 1.3 line.
The command used was:
svn merge -r2718:2743 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
Added:
branches/test_suite/docs/data_model_redesign
- copied unchanged from r2743, 1.3/docs/data_model_redesign
Modified:
branches/test_suite/docs/CHANGES
branches/test_suite/docs/Release_Checklist
branches/test_suite/dx/isosurface_3D.py
branches/test_suite/errors.py
branches/test_suite/generic_fns/model_selection.py
branches/test_suite/io.py
branches/test_suite/specific_fns/hybrid.py
branches/test_suite/specific_fns/model_free.py
Modified: branches/test_suite/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/test_suite/docs/CHANGES?rev=2901&r1=2900&r2=2901&view=diff
==============================================================================
--- branches/test_suite/docs/CHANGES (original)
+++ branches/test_suite/docs/CHANGES Sat Dec 2 05:32:43 2006
@@ -1,3 +1,36 @@
+Version 1.2.8
+(4 November 2006, from /1.2)
+http://svn.gna.org/svn/relax/tags/1.2.8
+
+ Features:
+ * Preliminary support for RNA/DNA. (bug #7241)
+ * Significant improvements to the SCons build system (see 'scons
--help').
+ * Expansion and improvement of the relax development chapter.
+ * The grace.write() user function works with reduced spectral
density mapping. (task #4002)
+
+ Changes:
+ * MS Windows installation instructions have been added to the manual.
+ * The RelaxWarning system has been added to standardise warning
messages.
+ * The relax manual now describes the test suite. (task #3781)
+ * The 15N CSA values in the sample scripts are now all -172 ppm.
+ * The ambiguity cased by supplying the option 'None' together with
Newton optimisation has been resolved in the documentation. (task #3630)
+ * Optimisation tests have been added to the test suite.
+
+ Bugfixes:
+ * Model selection between the global diffusion models no longer
fails if all residues of the local tm models have been deselected by model
elimination. (bug #7192)
+ * The 'angles.py' sample script no longer fails when residue
specific relaxation data is missing (corrupt input data). (bug #7224)
+ * Prior to executing Modelfree4, Dasha, Molmol, Grace, or OpenDX,
tests are run to determine if the binary exists, is executable, and is in the
system path. (bug #7225)
+ * Model elimination when using the model-free model 'm0' no longer
fails. (bug #7226)
+ * The strict checking of the Da and Dr diffusion tensor parameters
has been relaxed to allow for optimisation imprecision. (bug #7297)
+ * The reading of Modelfree4 mfout results files no longer fails when
residue specific relaxation data is missing (corrupt input data). (bug #7277)
+ * If optimisation returns an infinit value or a NaN value, these are
now caught and a RelaxError thrown. (bug #6503, task #3621)
+ * The sigma(NOE) equations of Chapter 8 of the manual have been
fixed. (bug #7402)
+ * Files containing relaxation data not consisting of exactly 4
columns will now be read. (bug #7583)
+ * Model-free results files from relax versions prior to 1.2.5 are
now properly read. (bug #7587)
+ * Model selection between the global diffusion models does not fail
when the local tm models are included. (bug #7616)
+
+
+
Version 1.2.7
(18 September 2006, from /1.2)
http://svn.gna.org/svn/relax/tags/1.2.7
Modified: branches/test_suite/docs/Release_Checklist
URL:
http://svn.gna.org/viewcvs/relax/branches/test_suite/docs/Release_Checklist?rev=2901&r1=2900&r2=2901&view=diff
==============================================================================
--- branches/test_suite/docs/Release_Checklist (original)
+++ branches/test_suite/docs/Release_Checklist Sat Dec 2 05:32:43 2006
@@ -1,7 +1,3 @@
-* Review the SVN log and add an entry into the CHANGES file (in the 'docs/'
directory) for the current release. Create three sections titled 'Features',
'Changes', and 'Bugfixes'.
-
-
-
* Make a copy of the current head to the tags directory using a command such
as:
$ svn cp svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.2.4
@@ -13,6 +9,10 @@
* Checkout the tagged version with:
$ svn co svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.2.4 relax-1.2.4
+
+
+
+* Review the SVN logs and add an entry into the CHANGES file (in the 'docs/'
directory) for the current release. Create three sections titled 'Features',
'Changes', and 'Bugfixes'. Commit the changes and then port the revision
back into the main line.
@@ -49,4 +49,4 @@
-* Post the release message to the relax-announce mailing list and as a news
item on the relax Gna! website.
+* Post the release message to the relax-announce mailing list, as a news
item on the relax Gna! website, and on the freshmeat website.
Modified: branches/test_suite/dx/isosurface_3D.py
URL:
http://svn.gna.org/viewcvs/relax/branches/test_suite/dx/isosurface_3D.py?rev=2901&r1=2900&r2=2901&view=diff
==============================================================================
--- branches/test_suite/dx/isosurface_3D.py (original)
+++ branches/test_suite/dx/isosurface_3D.py Sat Dec 2 05:32:43 2006
@@ -104,7 +104,7 @@
self.calculate(run=self.run, res_num=self.res_num,
print_flag=0)
# Get the minimisation statistics for the model.
- k, n, chi2 = self.model_stats(run=self.run,
instance=self.index, min_instances=1)
+ k, n, chi2 = self.model_stats(run=self.run,
instance=self.index)
# Set maximum value to 1e20 to stop the OpenDX server
connection from breaking.
if chi2 > 1e20:
Modified: branches/test_suite/errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/test_suite/errors.py?rev=2901&r1=2900&r2=2901&view=diff
==============================================================================
--- branches/test_suite/errors.py (original)
+++ branches/test_suite/errors.py Sat Dec 2 05:32:43 2006
@@ -167,7 +167,7 @@
if Debug:
self.save_state()
- # PDB data corresponding to the run already exists.
+ # No chains within the PDB file.
class RelaxNoPdbChainError(BaseError):
def __init__(self):
self.text = "No peptide or nucleotide chains can be found within
the PDB file."
Modified: branches/test_suite/generic_fns/model_selection.py
URL:
http://svn.gna.org/viewcvs/relax/branches/test_suite/generic_fns/model_selection.py?rev=2901&r1=2900&r2=2901&view=diff
==============================================================================
--- branches/test_suite/generic_fns/model_selection.py (original)
+++ branches/test_suite/generic_fns/model_selection.py Sat Dec 2 05:32:43
2006
@@ -207,8 +207,14 @@
if self.skip_function[run](run=run, instance=i,
min_instances=self.min_instances, num_instances=self.num_instances[j]):
continue
+ # Global stats.
+ if self.num_instances[j] > self.min_instances or
self.num_instances[j] == 1:
+ global_stats = 1
+ else:
+ global_stats = 0
+
# Get the model statistics.
- k, n, chi2 = self.model_statistics[run](run=run,
instance=i, min_instances=self.min_instances)
+ k, n, chi2 = self.model_statistics[run](run=run,
instance=i, global_stats=global_stats)
# Missing data sets.
if k == None or n == None or chi2 == None:
Modified: branches/test_suite/io.py
URL:
http://svn.gna.org/viewcvs/relax/branches/test_suite/io.py?rev=2901&r1=2900&r2=2901&view=diff
==============================================================================
--- branches/test_suite/io.py (original)
+++ branches/test_suite/io.py Sat Dec 2 05:32:43 2006
@@ -42,7 +42,7 @@
__builtin__.devnull_import_message = message.args[0]
from os import F_OK, X_OK, access, altsep, getenv, makedirs, pathsep,
remove, sep, stat
-from os.path import expanduser
+from os.path import expanduser, basename, splitext
from re import match, search
from string import split
import sys
@@ -154,6 +154,13 @@
# Return the file path.
return file_path
+
+
+ def file_root(self, file_path):
+ """Return the root file name, striped of path and extension
details"""
+
+ root,ext = splitext(file_path)
+ return basename(root)
def log(self, file_name=None, dir=None, compress_type=0, print_flag=1):
Modified: branches/test_suite/specific_fns/hybrid.py
URL:
http://svn.gna.org/viewcvs/relax/branches/test_suite/specific_fns/hybrid.py?rev=2901&r1=2900&r2=2901&view=diff
==============================================================================
--- branches/test_suite/specific_fns/hybrid.py (original)
+++ branches/test_suite/specific_fns/hybrid.py Sat Dec 2 05:32:43 2006
@@ -89,7 +89,7 @@
self.relax.data.hybrid_runs[hybrid] = runs
- def model_statistics(self, run=None, instance=None, min_instances=None):
+ def model_statistics(self, run=None, instance=None, global_stats=None):
"""Function for returning the values k, n, and chi2 of the hybrid.
k - number of parameters.
@@ -116,7 +116,7 @@
# Loop over the instances.
for i in xrange(num):
# Get the statistics.
- k, n, chi2 = model_statistics(run, instance=i)
+ k, n, chi2 = model_statistics(run, instance=i,
global_stats=global_stats)
# Bad stats.
if k == None or n == None or chi2 == None:
Modified: branches/test_suite/specific_fns/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/test_suite/specific_fns/model_free.py?rev=2901&r1=2900&r2=2901&view=diff
==============================================================================
--- branches/test_suite/specific_fns/model_free.py (original)
+++ branches/test_suite/specific_fns/model_free.py Sat Dec 2 05:32:43 2006
@@ -2505,7 +2505,7 @@
self.relax.data.res[run][i].params = params
- def model_statistics(self, run=None, instance=None, min_instances=None):
+ def model_statistics(self, run=None, instance=None, global_stats=None):
"""Function for returning k, n, and chi2.
k - number of parameters.
@@ -2517,11 +2517,12 @@
self.run = run
# Determine if local or global statistics will be returned.
- global_stats = 1
- for i in xrange(len(self.relax.data.res[self.run])):
- if hasattr(self.relax.data.res[self.run][i], 'chi2') and
self.relax.data.res[self.run][i].chi2 != None:
- global_stats = 0
- break
+ if global_stats == None:
+ global_stats = 1
+ for i in xrange(len(self.relax.data.res[self.run])):
+ if hasattr(self.relax.data.res[self.run][i], 'chi2') and
self.relax.data.res[self.run][i].chi2 != None:
+ global_stats = 0
+ break
# Determine the parameter set type.
self.param_set = self.determine_param_set_type()
@@ -2554,6 +2555,7 @@
# Count the number of data points.
n = 0
+ chi2 = 0
for i in xrange(len(self.relax.data.res[self.run])):
# Skip unselected residues.
if not self.relax.data.res[self.run][i].select:
@@ -2565,8 +2567,13 @@
n = n + len(self.relax.data.res[self.run][i].relax_data)
+ # Local tm models.
+ if self.param_set == 'local_tm':
+ chi2 = chi2 + self.relax.data.res[self.run][i].chi2
+
# The chi2 value.
- chi2 = self.relax.data.chi2[self.run]
+ if self.param_set != 'local_tm':
+ chi2 = self.relax.data.chi2[self.run]
# Return the data.
return k, n, chi2
@@ -2927,9 +2934,21 @@
# Set up the model-free models.
if self.data_set == 'value':
+ # Get the model-free model.
model = self.file_line[self.col['model']]
+
+ # Get the model-free equation.
equation = self.file_line[self.col['eqi']]
+
+ # Get the model-free parameters.
params = eval(self.file_line[self.col['params']])
+
+ # Fix for the 1.2 relax versions whereby the parameter 'tm' was
renamed to 'local_tm' (which occurred in version 1.2.5).
+ for i in xrange(len(params)):
+ if params[i] == 'tm':
+ params[i] = 'local_tm'
+
+ # Set up the model-free model.
if model and equation:
self.model_setup(self.run, model=model, equation=equation,
params=params, res_num=self.res_num)
r2901 - in /branches/test_suite: ./ docs/ dx/ generic_fns/ specific_fns/