Author: bugman
Date: Mon Dec 1 16:00:40 2008
New Revision: 8082
URL: http://svn.gna.org/viewcvs/relax?rev=8082&view=rev
Log:
Merged revisions 8026-8028,8061,8064 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r8026 | bugman | 2008-11-26 18:02:05 +0100 (Wed, 26 Nov 2008) | 3 lines
Wrote 8 system tests for reading various PDB files using the internal and
Scientific python objects.
........
r8027 | bugman | 2008-11-27 09:57:19 +0100 (Thu, 27 Nov 2008) | 3 lines
Added a lactose PDB file and 2 system tests reading this file.
........
r8028 | bugman | 2008-11-27 10:12:55 +0100 (Thu, 27 Nov 2008) | 5 lines
Fix for the __atom_index() method. This is a partial fix for bug #12637
(https://gna.org/bugs/?12637).
The struct_index of None is now handled.
........
r8061 | bugman | 2008-11-29 17:53:30 +0100 (Sat, 29 Nov 2008) | 14 lines
Manually ported the CHANGES file changes to the 1.3 line.
The command used was:
svn merge -r8059:8060 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.3.3 .
.....
r8060 | bugman | 2008-11-29 17:51:50 +0100 (Sat, 29 Nov 2008) | 3 lines
Changed paths:
M /tags/1.3.3/docs/CHANGES
Updated the CHANGES file for relax 1.3.3.
.....
........
r8064 | bugman | 2008-11-29 18:32:37 +0100 (Sat, 29 Nov 2008) | 14 lines
Manually ported the user manual fixes of r8063 from the 1.3.3 tag.
The command used was:
svn merge -r8062:8063 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.3.3 .
.....
r8063 | bugman | 2008-11-29 18:31:20 +0100 (Sat, 29 Nov 2008) | 3 lines
Changed paths:
M /tags/1.3.3/docs/latex/relax.tex
Fixed the spacing in the table of contents of the user manual.
.....
........
Added:
branches/spectral_errors/test_suite/shared_data/structures/lactose_MCMM4_S1_1.pdb
- copied unchanged from r8064,
1.3/test_suite/shared_data/structures/lactose_MCMM4_S1_1.pdb
Modified:
branches/spectral_errors/ (props changed)
branches/spectral_errors/docs/CHANGES
branches/spectral_errors/docs/latex/relax.tex
branches/spectral_errors/generic_fns/structure/internal.py
branches/spectral_errors/test_suite/system_tests/structure.py
Propchange: branches/spectral_errors/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Mon Dec 1 16:00:40 2008
@@ -1,1 +1,1 @@
-/1.3:1-8021
+/1.3:1-8081
Modified: branches/spectral_errors/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/docs/CHANGES?rev=8082&r1=8081&r2=8082&view=diff
==============================================================================
--- branches/spectral_errors/docs/CHANGES (original)
+++ branches/spectral_errors/docs/CHANGES Mon Dec 1 16:00:40 2008
@@ -1,3 +1,46 @@
+Version 1.3.3
+(29 November 2008, from /1.3)
+http://svn.gna.org/svn/relax/tags/1.3.3
+
+ Features:
+ * Dasha can be run from within relax again.
+ * Art Palmer's Modelfree can be run from within relax again.
+ * OpenDX execution and control is once again supported.
+ * NMRView peak lists are now supported.
+ * XEasy peak lists are again supported.
+
+ Changes:
+ * Internal relax cleanups by the addition of the specific
model_loop() method - this should eliminate a series of potential hidden bugs.
+ * The results.write() and results.display() now only support XML
output.
+ * More information is now extracted from the Modelfree mfout files.
+ * The version of the Modelfree program is checked and if it is an
old, buggy version, relax will refuse to execute it.
+ * The system tests can now handle the sometimes large differences in
Modelfree results between the GNU gcc and Portland C compiler versions.
+ * Fixes and improvements to much of the API documentation.
+
+ Bugfixes:
+ * A failure of the minimisation set() function has been fixed.
+ * The reset() user function now works again.
+ * Fixes to the relax data store methods add(), to_xml() and
from_xml().
+ * Many fixes for the support of Art Palmer's Modelfree program.
+ * The mapping of the global parameter space (diffusion tensor, etc.)
for visualisation in OpenDX has been fixed.
+ * state.save() no longer fails after running state.load() (bug
#12437).
+ * Sparky peak lists with the assignment '?-?' are now handled
properly (bug #11913).
+ * Error analysis in relaxation curve-fitting was incorrectly
implemented with standard deviation rather than variance averaging (bug
#12456).
+ * A number of fixes for the LaTeX table generating sample script.
+ * Fixes for the teeing and logging via the -l and -t command line
arguments (bug #12489).
+ * Fix for when XH bond vector data from a PDB file is missing for a
spin system (bug #12487).
+ * Many fixes for when structural data is missing.
+ * The relax script is no longer overwritten if the log or tee file
is not specified on the command line (bug #12498).
+ * Missing RelaxError failure in the sequence handling code (found
when trying to solve bug #12582).
+ * A failure in the results.write() user function has been fixed (bug
#12582).
+ * Model selection no longer fails if no model is ever selected.
+ * Model selection was failing if spins were deselected (bug #12591).
+ * The directory name can now be part of the file name argument to
results.read() (bug #12588).
+ * Optimisation of only the diffusion tensor after calling fix() was
failing if some spins were deselected (bug #12607).
+ * The internal PDB reader was failing when the PDB file contained
CONECT records (bug #12637).
+
+
+
Version 1.3.2
(8 October 2008, from /1.3)
http://svn.gna.org/svn/relax/tags/1.3.2
Modified: branches/spectral_errors/docs/latex/relax.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/docs/latex/relax.tex?rev=8082&r1=8081&r2=8082&view=diff
==============================================================================
--- branches/spectral_errors/docs/latex/relax.tex (original)
+++ branches/spectral_errors/docs/latex/relax.tex Mon Dec 1 16:00:40 2008
@@ -14,6 +14,9 @@
% Obliterate those painful LaTeX margins!
\usepackage{vmargin}
+
+% Better Table of contents (Toc), List of figures (Lof), and List of tables
(Lot).
+\usepackage{tocloft}
% Better maths.
\usepackage{amsmath}
@@ -35,6 +38,11 @@
% New environment.
\newenvironment{exampleenv}{\footnotesize \begin{ttfamily} \sloppy}{\fussy
\end{ttfamily}}
\newenvironment{spacedpara}{\setlength{\parindent}{0pt}
\setlength{\parskip}{2ex plus 0.5ex minus 0.2ex}}{}
+
+% Modify the Toc, Lof, and Lot layout.
+\setlength{\cftsecnumwidth}{10mm}
+\setlength{\cftsubsecnumwidth}{16mm}
+\setlength{\cftfignumwidth}{12mm}
% Maths commands.
\newcommand{\Par}{{\scriptscriptstyle \parallel}}
Modified: branches/spectral_errors/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/generic_fns/structure/internal.py?rev=8082&r1=8081&r2=8082&view=diff
==============================================================================
--- branches/spectral_errors/generic_fns/structure/internal.py (original)
+++ branches/spectral_errors/generic_fns/structure/internal.py Mon Dec 1
16:00:40 2008
@@ -123,11 +123,17 @@
@rtype: int
"""
- # Loop over the atoms.
- for i in xrange(len(self.structural_data[struct_index].atom_num)):
- # Return the index.
- if self.structural_data[struct_index].atom_num[i] == atom_num:
- return i
+ # Loop over the structures.
+ for i in xrange(self.num):
+ # Skip non-matching structures.
+ if struct_index != None and struct_index != i:
+ continue
+
+ # Loop over the atoms.
+ for j in xrange(len(self.structural_data[i].atom_num)):
+ # Return the index.
+ if self.structural_data[i].atom_num[j] == atom_num:
+ return j
# Should not be here, the PDB connect records are incorrect.
warn(RelaxWarning("The atom number " + `atom_num` + " from the
CONECT record cannot be found within the ATOM and HETATM records."))
Modified: branches/spectral_errors/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spectral_errors/test_suite/system_tests/structure.py?rev=8082&r1=8081&r2=8082&view=diff
==============================================================================
--- branches/spectral_errors/test_suite/system_tests/structure.py (original)
+++ branches/spectral_errors/test_suite/system_tests/structure.py Mon Dec 1
16:00:40 2008
@@ -128,3 +128,106 @@
# Check the atomic data.
self.assertEqual(cdp.structure.structural_data[0].peptide_chains[0].sequence(),
res_name)
+
+
+ def test_read_pdb_internal1(self):
+ """Load the '1F35_N_H_molmol.pdb' PDB file (using the internal
structural object PDB reader)."""
+
+ # Path of the files.
+ path = sys.path[-1] + '/test_suite/shared_data/structures'
+
+ # Read the PDB.
+
self.relax.interpreter._Structure.read_pdb(file='1F35_N_H_molmol.pdb',
dir=path, parser='internal')
+
+
+ def test_read_pdb_internal2(self):
+ """Load the 'Ap4Aase_res1-12.pdb' PDB file (using the internal
structural object PDB reader)."""
+
+ # Path of the files.
+ path = sys.path[-1] + '/test_suite/shared_data/structures'
+
+ # Read the PDB.
+
self.relax.interpreter._Structure.read_pdb(file='Ap4Aase_res1-12.pdb',
dir=path, parser='internal')
+
+
+ def test_read_pdb_internal3(self):
+ """Load the 'gromacs_phthalic_acid.pdb' PDB file (using the internal
structural object PDB reader)."""
+
+ # Path of the files.
+ path = sys.path[-1] + '/test_suite/shared_data/structures'
+
+ # Read the PDB.
+
self.relax.interpreter._Structure.read_pdb(file='gromacs_phthalic_acid.pdb',
dir=path, parser='internal')
+
+
+ def test_read_pdb_internal4(self):
+ """Load the 'tylers_peptide_trunc.pdb' PDB file (using the internal
structural object PDB reader)."""
+
+ # Path of the files.
+ path = sys.path[-1] + '/test_suite/shared_data/structures'
+
+ # Read the PDB.
+
self.relax.interpreter._Structure.read_pdb(file='tylers_peptide_trunc.pdb',
dir=path, parser='internal')
+
+
+ def test_read_pdb_internal5(self):
+ """Load the 'lactose_MCMM4_S1_1.pdb' PDB file (using the internal
structural object PDB reader)."""
+
+ # Path of the files.
+ path = sys.path[-1] + '/test_suite/shared_data/structures'
+
+ # Read the PDB.
+
self.relax.interpreter._Structure.read_pdb(file='lactose_MCMM4_S1_1.pdb',
dir=path, parser='internal')
+
+
+ def test_read_pdb_scientific1(self):
+ """Load the '1F35_N_H_molmol.pdb' PDB file (using the Scientific
python structural object PDB reader)."""
+
+ # Path of the files.
+ path = sys.path[-1] + '/test_suite/shared_data/structures'
+
+ # Read the PDB.
+
self.relax.interpreter._Structure.read_pdb(file='1F35_N_H_molmol.pdb',
dir=path, parser='scientific')
+
+
+ def test_read_pdb_scientific2(self):
+ """Load the 'Ap4Aase_res1-12.pdb' PDB file (using the Scientific
python structural object PDB reader)."""
+
+ # Path of the files.
+ path = sys.path[-1] + '/test_suite/shared_data/structures'
+
+ # Read the PDB.
+
self.relax.interpreter._Structure.read_pdb(file='Ap4Aase_res1-12.pdb',
dir=path, parser='scientific')
+
+
+ def test_read_pdb_scientific3(self):
+ """Load the 'gromacs_phthalic_acid.pdb' PDB file (using the
Scientific python structural object PDB reader)."""
+
+ # Path of the files.
+ path = sys.path[-1] + '/test_suite/shared_data/structures'
+
+ # Read the PDB.
+
self.relax.interpreter._Structure.read_pdb(file='gromacs_phthalic_acid.pdb',
dir=path, parser='scientific')
+
+
+ def test_read_pdb_scientific4(self):
+ """Load the 'tylers_peptide_trunc.pdb' PDB file (using the
Scientific python structural object PDB reader)."""
+
+ # Path of the files.
+ path = sys.path[-1] + '/test_suite/shared_data/structures'
+
+ # Read the PDB.
+
self.relax.interpreter._Structure.read_pdb(file='tylers_peptide_trunc.pdb',
dir=path, parser='scientific')
+
+
+ def test_read_pdb_scientific5(self):
+ """Load the 'lactose_MCMM4_S1_1.pdb' PDB file (using the Scientific
python structural object PDB reader)."""
+
+ # Path of the files.
+ path = sys.path[-1] + '/test_suite/shared_data/structures'
+
+ # Read the PDB.
+
self.relax.interpreter._Structure.read_pdb(file='lactose_MCMM4_S1_1.pdb',
dir=path, parser='scientific')
+
+
+
r8082 - in /branches/spectral_errors: ./ docs/ docs/latex/ generic_fns/structure/ test_suite/shared_data/structures/ test_su...