Author: bugman
Date: Mon Dec 1 18:51:05 2008
New Revision: 8087
URL: http://svn.gna.org/viewcvs/relax?rev=8087&view=rev
Log:
Merged revisions
7866-7873,7876-7878,7937-7940,7942-7948,7952,7961-7963,7965-7968,7971-7973,7975-7983,7991-7992,7996,8014,8016,8026-8028,8061,8064
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r7866 | bugman | 2008-10-20 22:11:40 +0200 (Mon, 20 Oct 2008) | 7 lines
Bug fix for the LaTeX table generating script.
This was identified by Tyler Reddy "TREDDY at dal dot ca" in the message at
https://mail.gna.org/public/relax-users/2008-10/msg00062.html (Message-id:
<20081020162741.yimh96r4oq2ow4w0@xxxxxxxxxx>).
........
r7867 | bugman | 2008-10-20 22:28:02 +0200 (Mon, 20 Oct 2008) | 3 lines
Duplicated the latex_mf_table.py sample script for the creation of a system
test.
........
r7868 | bugman | 2008-10-20 22:45:41 +0200 (Mon, 20 Oct 2008) | 3 lines
Comment fix in the latex_mf_table.py sample script.
........
r7869 | bugman | 2008-10-20 22:46:37 +0200 (Mon, 20 Oct 2008) | 3 lines
Modified the latex_mf_table.py script for the test suite.
........
r7870 | bugman | 2008-10-20 22:51:27 +0200 (Mon, 20 Oct 2008) | 3 lines
Activated the model-free results to LaTeX table sample script.
........
r7871 | bugman | 2008-10-20 22:51:57 +0200 (Mon, 20 Oct 2008) | 3 lines
Missing import.
........
r7872 | bugman | 2008-10-20 22:59:45 +0200 (Mon, 20 Oct 2008) | 3 lines
Fix for the test_latex_table() system test.
........
r7873 | bugman | 2008-10-20 23:00:14 +0200 (Mon, 20 Oct 2008) | 3 lines
Fix for the latex_mf_table.py sample script. This matches the system test
fix in r7872.
........
r7876 | bugman | 2008-10-21 11:50:12 +0200 (Tue, 21 Oct 2008) | 11 lines
Fixes for the model-free LaTeX table generation sample script.
These fixes do not affect the system test result yet - as LaTeX compilation
will not be part of the
test suite - but fix the LaTeX compilation. These will be ported back to
the sample script.
The docstring has been modified as the booktabs package is needed for this
table. The '&'
characters in the spin_id string have been escaped to avoid this being
interpreted as a column
separator. The 'Residue' column has been renamed to 'Spin'. And finally
missing model-free
parameter errors can be handled.
........
r7877 | bugman | 2008-10-21 11:53:58 +0200 (Tue, 21 Oct 2008) | 24 lines
Ported the changes of r7876 from the test suite to the sample script.
The command used was:
svn merge -r7875:7876 test_suite/system_tests/scripts/latex_mf_table.py
sample_scripts/latex_mf_table.py
The LaTeX document starting and ending commands have been removed from this
revision!
.....
r7876 | bugman | 2008-10-21 11:50:12 +0200 (Tue, 21 Oct 2008) | 11 lines
Changed paths:
M /1.3/test_suite/system_tests/scripts/latex_mf_table.py
Fixes for the model-free LaTeX table generation sample script.
These fixes do not affect the system test result yet - as LaTeX
compilation will not be part of the
test suite - but fix the LaTeX compilation. These will be ported back to
the sample script.
The docstring has been modified as the booktabs package is needed for
this table. The '&'
characters in the spin_id string have been escaped to avoid this being
interpreted as a column
separator. The 'Residue' column has been renamed to 'Spin'. And finally
missing model-free
parameter errors can be handled.
.....
........
r7878 | bugman | 2008-10-21 15:17:17 +0200 (Tue, 21 Oct 2008) | 3 lines
Fixes for all the standard deviation and variance variable names.
........
r7937 | bugman | 2008-10-22 22:25:33 +0200 (Wed, 22 Oct 2008) | 3 lines
Epydoc doctring indentation fixes.
........
r7938 | bugman | 2008-10-22 22:47:56 +0200 (Wed, 22 Oct 2008) | 5 lines
Added module docstrings and __docformat__ variables to all of the prompt
modules.
The __docformat__ string is set to 'plaintext' to make epydoc happy.
........
r7939 | bugman | 2008-10-22 22:55:51 +0200 (Wed, 22 Oct 2008) | 5 lines
Lots of epydoc fixes.
This is mainly title underline fixes.
........
r7940 | bugman | 2008-10-22 23:20:40 +0200 (Wed, 22 Oct 2008) | 3 lines
Massive epydoc fixes too all of the maths_fns modules!!!
........
r7942 | bugman | 2008-10-23 16:44:53 +0200 (Thu, 23 Oct 2008) | 6 lines
Fix for the relax IO logging with the -l command line argument.
This is a partial fix for bug #12489 (https://gna.org/bugs/?12489). The
teeing problem still has
to be fixed.
........
r7943 | bugman | 2008-10-23 16:54:43 +0200 (Thu, 23 Oct 2008) | 3 lines
Converted the tee class method into a module function.
........
r7944 | bugman | 2008-10-23 16:56:12 +0200 (Thu, 23 Oct 2008) | 3 lines
Epydoc'd the tee function docstring.
........
r7945 | bugman | 2008-10-23 16:57:45 +0200 (Thu, 23 Oct 2008) | 3 lines
Docstring improvements for the log() function.
........
r7946 | bugman | 2008-10-23 16:58:04 +0200 (Thu, 23 Oct 2008) | 3 lines
Removed a line of redundant code.
........
r7947 | bugman | 2008-10-23 16:58:56 +0200 (Thu, 23 Oct 2008) | 3 lines
Added the missing import of relax_io.tee.
........
r7948 | bugman | 2008-10-23 17:01:18 +0200 (Thu, 23 Oct 2008) | 5 lines
Final fixes for bug #12489 (https://gna.org/bugs/?12489).
The log() and tee() functions are now operational.
........
r7952 | bugman | 2008-10-23 17:39:25 +0200 (Thu, 23 Oct 2008) | 9 lines
Fix for bug #12487 (https://gna.org/bugs/index.php?12487).
This bug was reported by Tyler Reddy (TREDDY at dal dot ca).
The problem was that missing XH bond vector data was being manifested as
the spin.xh_vect object
being set to None. The overfit_deselect() function which is responsible
for deselecting unsuitable
spins prior to optimisation was only checking if the object existed, not if
it was None!
........
r7961 | bugman | 2008-10-24 13:44:28 +0200 (Fri, 24 Oct 2008) | 3 lines
Added a check to the atom_loop() to make sure structural data is loaded.
........
r7962 | bugman | 2008-10-24 13:56:38 +0200 (Fri, 24 Oct 2008) | 3 lines
Added a check for empty PDB files in the internal structural object.
........
r7963 | bugman | 2008-10-24 14:22:44 +0200 (Fri, 24 Oct 2008) | 3 lines
Added another spin to try to catch a program bug (unsuccessfully).
........
r7965 | semor | 2008-10-24 15:41:46 +0200 (Fri, 24 Oct 2008) | 5 lines
Introduced verifications for the '-t' and '-l' options not to erase the
python script used.
This should fix bug 12498 (http://gna.org/bugs/?12498).
........
r7966 | bugman | 2008-10-24 16:14:19 +0200 (Fri, 24 Oct 2008) | 3 lines
Created a system test using Tyler Reddy's bug report - bug #12487
(https://gna.org/bugs/?12487).
........
r7967 | semor | 2008-10-24 16:19:17 +0200 (Fri, 24 Oct 2008) | 7 lines
Modified the '-l' and '-t' options so they check for an existing file and
don't overwrite it.
This was proposed by Edward in a post at:
https://mail.gna.org/public/relax-devel/2008-10/msg00087.html
(Message ID: 7f080ed10810240648p19b83da1x4c8990acf1834c5b@xxxxxxxxxxxxxx)
........
r7968 | semor | 2008-10-24 17:55:21 +0200 (Fri, 24 Oct 2008) | 7 lines
Still improved the detection of existing files not to be overwritten when
logging or teeing.
This follows a post by Edward at:
https://mail.gna.org/public/relax-devel/2008-10/msg00091.html
(Message ID: 7f080ed10810240816o30acc1ddlbaa131bc5a9ea1ff@xxxxxxxxxxxxxx)
........
r7971 | bugman | 2008-11-10 23:17:17 +0100 (Mon, 10 Nov 2008) | 6 lines
Added a missing RelaxError import.
This was discovered when trying to replicate bug #12582
(https://gna.org/bugs/index.php?12582)
reported by Chris Brosey (chris dot a dot brosey att vanderbilt dot edu).
........
r7972 | bugman | 2008-11-10 23:31:18 +0100 (Mon, 10 Nov 2008) | 3 lines
Added a system test for replicating bug #12582.
........
r7973 | bugman | 2008-11-10 23:36:36 +0100 (Mon, 10 Nov 2008) | 9 lines
Fix for bug #12582 (https://gna.org/bugs/index.php?12582).
This was reported by Chris Brosey (chris dot a dot brosey att vanderbilt
dot edu).
The problem was that the frq_labels data structure in the SpinContainer was
sometimes set to []
rather than the data structure being missing. Now the structure is being
tested if it is either
None or [] before being accessed in the model-free return_units() method.
........
r7975 | bugman | 2008-11-12 15:57:25 +0100 (Wed, 12 Nov 2008) | 3 lines
Converted some ints to bools.
........
r7976 | bugman | 2008-11-12 20:57:14 +0100 (Wed, 12 Nov 2008) | 3 lines
Modified the system test to additionally catch bug #12591
(https://gna.org/bugs/index.php?12591).
........
r7977 | bugman | 2008-11-12 20:59:05 +0100 (Wed, 12 Nov 2008) | 3 lines
Renamed the system test script.
........
r7978 | bugman | 2008-11-12 20:59:27 +0100 (Wed, 12 Nov 2008) | 3 lines
Deleted the old system test script.
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r7979 | bugman | 2008-11-12 21:00:37 +0100 (Wed, 12 Nov 2008) | 3 lines
Fixes for the system test script rename of the previous commits.
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r7980 | bugman | 2008-11-12 21:18:03 +0100 (Wed, 12 Nov 2008) | 9 lines
Partial fix for bug #12591 (https://gna.org/bugs/index.php?12591).
This was reported by Chris Brosey (chris dot a dot brosey att vanderbilt
dot edu).
If no model is ever selected in the model_selection.select() function, then
relax no longer fails.
The failure is however caused by another problem elsewhere within relax, so
this fix is not
complete.
........
r7981 | bugman | 2008-11-12 21:21:39 +0100 (Wed, 12 Nov 2008) | 9 lines
Final fix for bug #12591 (https://gna.org/bugs/index.php?12591).
This bug was reported by Chris Brosey (chris dot a dot brosey att
vanderbilt dot edu).
The problem was that the global_index counter in the model-free
model_loop() method was supposed to
be incremented at the start of the loop. The deselected spin skipping code
was located before this
though, causing the counter to not be incremented!
........
r7982 | bugman | 2008-11-12 21:35:26 +0100 (Wed, 12 Nov 2008) | 5 lines
Created a very simple system test to catch bug #12588
(https://gna.org/bugs/index.php?12588).
This bug was reported by Tyler Reddy (treddy at dal dot ca).
........
r7983 | bugman | 2008-11-12 21:49:03 +0100 (Wed, 12 Nov 2008) | 8 lines
Fix for bug #12588 (https://gna.org/bugs/index.php?12588).
This bug was reported by Tyler Reddy (treddy at dal dot ca).
The problem was that the results.read() user function was not handling the
directory name being part
of the file name argument. This can now be handled.
........
r7991 | bugman | 2008-11-20 22:53:30 +0100 (Thu, 20 Nov 2008) | 5 lines
Added a catch for bug #12607 (https://gna.org/bugs/?12607) to the
bugs_12582_12591.py script.
This bug was reported by Chris Brosey (chris dot a dot brosey att
vanderbilt dot edu).
........
r7992 | bugman | 2008-11-20 23:23:56 +0100 (Thu, 20 Nov 2008) | 8 lines
Fix for bug #12607 (https://gna.org/bugs/?12607).
This bug was reported by Chris Brosey (chris dot a dot brosey att
vanderbilt dot edu).
The problem was that the fixed flag was being checked for all spins.
However deselected spins
should be ignored.
........
r7996 | bugman | 2008-11-21 09:45:57 +0100 (Fri, 21 Nov 2008) | 3 lines
Renamed the bugs_12582_12591.py system test script to include bug #12607.
........
r8014 | bugman | 2008-11-21 18:35:42 +0100 (Fri, 21 Nov 2008) | 3 lines
The structure.load_spins() user function now tests if a structure has been
loaded.
........
r8016 | bugman | 2008-11-21 18:38:37 +0100 (Fri, 21 Nov 2008) | 3 lines
Added a missing RelaxError import.
........
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/bmrb/test_suite/shared_data/results_files/tylers_peptide_trunc.bz2
- copied unchanged from r8064,
1.3/test_suite/shared_data/results_files/tylers_peptide_trunc.bz2
branches/bmrb/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
branches/bmrb/test_suite/shared_data/structures/tylers_peptide_trunc.pdb
- copied unchanged from r8064,
1.3/test_suite/shared_data/structures/tylers_peptide_trunc.pdb
branches/bmrb/test_suite/system_tests/scripts/bugs_12582_12591_12607.py
- copied unchanged from r8064,
1.3/test_suite/system_tests/scripts/bugs_12582_12591_12607.py
branches/bmrb/test_suite/system_tests/scripts/latex_mf_table.py
- copied unchanged from r8064,
1.3/test_suite/system_tests/scripts/latex_mf_table.py
branches/bmrb/test_suite/system_tests/scripts/tylers_peptide.py
- copied unchanged from r8064,
1.3/test_suite/system_tests/scripts/tylers_peptide.py
Modified:
branches/bmrb/ (props changed)
branches/bmrb/docs/CHANGES
branches/bmrb/docs/latex/relax.tex
branches/bmrb/generic_fns/model_selection.py
branches/bmrb/generic_fns/pipes.py
branches/bmrb/generic_fns/results.py
branches/bmrb/generic_fns/sequence.py
branches/bmrb/generic_fns/structure/internal.py
branches/bmrb/generic_fns/structure/main.py
branches/bmrb/maths_fns/correlation_time.py
branches/bmrb/maths_fns/direction_cosine.py
branches/bmrb/maths_fns/jw_mf.py
branches/bmrb/maths_fns/jw_mf_comps.py
branches/bmrb/maths_fns/mf.py
branches/bmrb/maths_fns/n_state_model.py
branches/bmrb/maths_fns/ri.py
branches/bmrb/maths_fns/ri_comps.py
branches/bmrb/maths_fns/ri_prime.py
branches/bmrb/maths_fns/rotation_matrix.py
branches/bmrb/maths_fns/weights.py
branches/bmrb/prompt/align_tensor.py
branches/bmrb/prompt/angles.py
branches/bmrb/prompt/consistency_tests.py
branches/bmrb/prompt/dasha.py
branches/bmrb/prompt/deselect.py
branches/bmrb/prompt/diffusion_tensor.py
branches/bmrb/prompt/dx.py
branches/bmrb/prompt/eliminate.py
branches/bmrb/prompt/fix.py
branches/bmrb/prompt/frq.py
branches/bmrb/prompt/gpl.py
branches/bmrb/prompt/grace.py
branches/bmrb/prompt/jw_mapping.py
branches/bmrb/prompt/minimisation.py
branches/bmrb/prompt/model_free.py
branches/bmrb/prompt/model_selection.py
branches/bmrb/prompt/molecule.py
branches/bmrb/prompt/molmol.py
branches/bmrb/prompt/monte_carlo.py
branches/bmrb/prompt/n_state_model.py
branches/bmrb/prompt/noe.py
branches/bmrb/prompt/palmer.py
branches/bmrb/prompt/pcs.py
branches/bmrb/prompt/pipe.py
branches/bmrb/prompt/pymol.py
branches/bmrb/prompt/rdc.py
branches/bmrb/prompt/relax_data.py
branches/bmrb/prompt/relax_fit.py
branches/bmrb/prompt/residue.py
branches/bmrb/prompt/results.py
branches/bmrb/prompt/select.py
branches/bmrb/prompt/sequence.py
branches/bmrb/prompt/spin.py
branches/bmrb/prompt/state.py
branches/bmrb/prompt/structure.py
branches/bmrb/prompt/temperature.py
branches/bmrb/prompt/value.py
branches/bmrb/prompt/view.py
branches/bmrb/prompt/vmd.py
branches/bmrb/relax
branches/bmrb/relax_io.py
branches/bmrb/sample_scripts/latex_mf_table.py
branches/bmrb/specific_fns/consistency_tests.py
branches/bmrb/specific_fns/jw_mapping.py
branches/bmrb/specific_fns/model_free/main.py
branches/bmrb/specific_fns/relax_fit.py
branches/bmrb/test_suite/system_tests/model_free.py
branches/bmrb/test_suite/system_tests/structure.py
branches/bmrb/test_suite/test_suite_runner.py
branches/bmrb/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/bmrb/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/docs/CHANGES?rev=8087&r1=8086&r2=8087&view=diff
Modified: branches/bmrb/docs/latex/relax.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/docs/latex/relax.tex?rev=8087&r1=8086&r2=8087&view=diff
Modified: branches/bmrb/generic_fns/model_selection.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/model_selection.py?rev=8087&r1=8086&r2=8087&view=diff
Modified: branches/bmrb/generic_fns/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/pipes.py?rev=8087&r1=8086&r2=8087&view=diff
Modified: branches/bmrb/generic_fns/results.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/results.py?rev=8087&r1=8086&r2=8087&view=diff
Modified: branches/bmrb/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/sequence.py?rev=8087&r1=8086&r2=8087&view=diff
Modified: branches/bmrb/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/structure/internal.py?rev=8087&r1=8086&r2=8087&view=diff
Modified: branches/bmrb/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/structure/main.py?rev=8087&r1=8086&r2=8087&view=diff
Modified: branches/bmrb/maths_fns/correlation_time.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/maths_fns/correlation_time.py?rev=8087&r1=8086&r2=8087&view=diff
Modified: branches/bmrb/maths_fns/direction_cosine.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/maths_fns/direction_cosine.py?rev=8087&r1=8086&r2=8087&view=diff
Modified: branches/bmrb/maths_fns/jw_mf.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/maths_fns/jw_mf.py?rev=8087&r1=8086&r2=8087&view=diff
Modified: branches/bmrb/maths_fns/jw_mf_comps.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/maths_fns/jw_mf_comps.py?rev=8087&r1=8086&r2=8087&view=diff
Modified: branches/bmrb/maths_fns/mf.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/maths_fns/mf.py?rev=8087&r1=8086&r2=8087&view=diff
Modified: branches/bmrb/maths_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/maths_fns/n_state_model.py?rev=8087&r1=8086&r2=8087&view=diff
Modified: branches/bmrb/maths_fns/ri.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/maths_fns/ri.py?rev=8087&r1=8086&r2=8087&view=diff
Modified: branches/bmrb/maths_fns/ri_comps.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/maths_fns/ri_comps.py?rev=8087&r1=8086&r2=8087&view=diff
Modified: branches/bmrb/maths_fns/ri_prime.py
[... 158 lines stripped ...]
r8087 - in /branches/bmrb: ./ docs/ docs/latex/ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ sample_scripts/ speci...