Author: bugman
Date: Wed Jan 7 14:32:39 2009
New Revision: 8283
URL: http://svn.gna.org/viewcvs/relax?rev=8283&view=rev
Log:
Merged revisions 8198-8212,8224,8226-8227,8230,8234,8237-8240,8245,8249-8282
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r8198 | bugman | 2008-12-12 00:06:08 +0100 (Fri, 12 Dec 2008) | 3 lines
Fixed a typo bug in the centre() function.
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r8199 | bugman | 2008-12-12 00:12:20 +0100 (Fri, 12 Dec 2008) | 3 lines
Reverted r8198 and added the real fix for the centre() function.
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r8200 | bugman | 2008-12-12 10:28:59 +0100 (Fri, 12 Dec 2008) | 3 lines
Created a directory for putting a number of lactose structures into.
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r8201 | bugman | 2008-12-12 10:29:31 +0100 (Fri, 12 Dec 2008) | 3 lines
Shifted the lactose structure into the lactose directory.
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r8202 | bugman | 2008-12-12 10:31:12 +0100 (Fri, 12 Dec 2008) | 3 lines
Added 3 more lactose structures.
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r8203 | bugman | 2008-12-12 10:44:12 +0100 (Fri, 12 Dec 2008) | 3 lines
Created a directory for storing alignment data such as RDCs and PCSs.
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r8204 | bugman | 2008-12-12 10:47:28 +0100 (Fri, 12 Dec 2008) | 3 lines
Added some lactose RDC and PCS data. Note this is randomised and truncated
for protection!!!
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r8205 | bugman | 2008-12-12 10:56:09 +0100 (Fri, 12 Dec 2008) | 3 lines
Added 10 tag PDB files for the lactose system test.
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r8206 | bugman | 2008-12-12 10:57:13 +0100 (Fri, 12 Dec 2008) | 3 lines
Added a system test script for the lactose N-state analysis using RDCs and
PCSs.
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r8207 | bugman | 2008-12-12 11:02:35 +0100 (Fri, 12 Dec 2008) | 3 lines
Activated the lactose N-state model system test.
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r8208 | bugman | 2008-12-12 11:05:28 +0100 (Fri, 12 Dec 2008) | 3 lines
Fixes for the lactose PDB file reading system tests. The path to the files
has changed!
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r8209 | bugman | 2008-12-12 11:24:10 +0100 (Fri, 12 Dec 2008) | 6 lines
Partial bug fix for the lactose N-state model system test.
The bond vector returning function for the internal PDB reader was
converting the atom_id to
uppercase. This meant that molecule name corresponding to the file name
was not matching!
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r8210 | bugman | 2008-12-12 11:31:06 +0100 (Fri, 12 Dec 2008) | 7 lines
Another bug fix for the load_pdb() internal structure object method.
This was found by the lactose N-state model system test. The
__fill_object_from_pdb() method was
not being called properly and when loading multiple PDB files containing
model information, the
first would contain the atomic information of all files!
........
r8211 | bugman | 2008-12-12 16:07:07 +0100 (Fri, 12 Dec 2008) | 6 lines
Created a new arg 'combine_models' to the structure.load_spins() user
function.
This will allow spins to be extracted separately for each model in an
ensemble or for only one set
of spins for all structures.
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r8212 | bugman | 2008-12-12 16:31:37 +0100 (Fri, 12 Dec 2008) | 3 lines
The combine_models flag is now effective in the load_spins() function.
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r8224 | semor | 2008-12-23 17:04:48 +0100 (Tue, 23 Dec 2008) | 6 lines
Many corrections of formatting.
These were found using the relax 'code_validator' script (E. d'Auvergne)
and mainly include trailing
whitespaces and missing empty lines before functions.
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r8226 | semor | 2009-01-06 19:30:55 +0100 (Tue, 06 Jan 2009) | 3 lines
Corrected a small typo in the development chapter of the manual.
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r8227 | semor | 2009-01-06 19:50:20 +0100 (Tue, 06 Jan 2009) | 3 lines
Removed an unused import.
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r8230 | semor | 2009-01-06 21:13:44 +0100 (Tue, 06 Jan 2009) | 3 lines
Removed some unused imports.
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r8234 | semor | 2009-01-06 21:38:49 +0100 (Tue, 06 Jan 2009) | 3 lines
Removed an unused import.
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r8237 | semor | 2009-01-06 21:54:22 +0100 (Tue, 06 Jan 2009) | 3 lines
Removed an unused import.
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r8238 | semor | 2009-01-06 21:58:29 +0100 (Tue, 06 Jan 2009) | 3 lines
Removed unused imports.
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r8239 | semor | 2009-01-06 22:02:54 +0100 (Tue, 06 Jan 2009) | 3 lines
Removed an unused import.
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r8240 | semor | 2009-01-06 22:07:04 +0100 (Tue, 06 Jan 2009) | 3 lines
Removed another unused import...
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r8245 | semor | 2009-01-06 22:27:39 +0100 (Tue, 06 Jan 2009) | 3 lines
Removed an unused import.
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r8249 | semor | 2009-01-06 23:32:30 +0100 (Tue, 06 Jan 2009) | 3 lines
Removed unused imports.
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r8250 | semor | 2009-01-06 23:36:25 +0100 (Tue, 06 Jan 2009) | 3 lines
Removed an unused import.
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r8251 | semor | 2009-01-06 23:39:45 +0100 (Tue, 06 Jan 2009) | 3 lines
Removed more unused imports.
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r8252 | semor | 2009-01-06 23:43:31 +0100 (Tue, 06 Jan 2009) | 3 lines
Removed other unused imports.
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r8253 | semor | 2009-01-06 23:55:48 +0100 (Tue, 06 Jan 2009) | 3 lines
Removed unused imports.
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r8254 | semor | 2009-01-06 23:59:48 +0100 (Tue, 06 Jan 2009) | 3 lines
Removed more unused imports.
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r8255 | semor | 2009-01-07 00:03:21 +0100 (Wed, 07 Jan 2009) | 3 lines
Removed an unused import.
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r8256 | semor | 2009-01-07 00:07:24 +0100 (Wed, 07 Jan 2009) | 3 lines
Removed another unused import.
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r8257 | semor | 2009-01-07 00:11:03 +0100 (Wed, 07 Jan 2009) | 3 lines
Removed more unused imports.
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r8258 | semor | 2009-01-07 00:18:05 +0100 (Wed, 07 Jan 2009) | 3 lines
Removed another unused import.
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r8259 | semor | 2009-01-07 00:21:37 +0100 (Wed, 07 Jan 2009) | 3 lines
More unused imports removed.
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r8260 | semor | 2009-01-07 00:24:55 +0100 (Wed, 07 Jan 2009) | 3 lines
One more unused import removed.
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r8261 | semor | 2009-01-07 00:31:07 +0100 (Wed, 07 Jan 2009) | 3 lines
A few more unused imports removed.
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r8262 | semor | 2009-01-07 00:34:29 +0100 (Wed, 07 Jan 2009) | 3 lines
A few more unused imports removed.
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r8263 | semor | 2009-01-07 00:37:39 +0100 (Wed, 07 Jan 2009) | 3 lines
Removed one more unused import.
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r8264 | semor | 2009-01-07 00:41:35 +0100 (Wed, 07 Jan 2009) | 3 lines
Removed other unused imports.
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r8265 | semor | 2009-01-07 00:47:44 +0100 (Wed, 07 Jan 2009) | 3 lines
Again an unused import.
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r8266 | semor | 2009-01-07 00:53:32 +0100 (Wed, 07 Jan 2009) | 3 lines
Again, an unused import.
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r8267 | semor | 2009-01-07 01:08:55 +0100 (Wed, 07 Jan 2009) | 3 lines
A few more unused imports removed.
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r8268 | semor | 2009-01-07 01:14:09 +0100 (Wed, 07 Jan 2009) | 3 lines
Added a missing import and removed a few unused ones.
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r8269 | semor | 2009-01-07 02:32:01 +0100 (Wed, 07 Jan 2009) | 3 lines
Added a missing import.
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r8270 | semor | 2009-01-07 02:56:38 +0100 (Wed, 07 Jan 2009) | 3 lines
Added two missing imports.
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r8271 | semor | 2009-01-07 03:01:43 +0100 (Wed, 07 Jan 2009) | 3 lines
Removed an unused import.
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r8272 | semor | 2009-01-07 03:04:29 +0100 (Wed, 07 Jan 2009) | 3 lines
Removed more unused imports.
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r8273 | semor | 2009-01-07 03:09:15 +0100 (Wed, 07 Jan 2009) | 3 lines
Removed more unused imports.
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r8274 | semor | 2009-01-07 03:12:22 +0100 (Wed, 07 Jan 2009) | 3 lines
Removed another unused import.
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r8275 | semor | 2009-01-07 03:25:00 +0100 (Wed, 07 Jan 2009) | 3 lines
Added a missing import and removed an unused one.
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r8276 | semor | 2009-01-07 03:34:14 +0100 (Wed, 07 Jan 2009) | 3 lines
Removed an unused import.
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r8277 | semor | 2009-01-07 03:37:13 +0100 (Wed, 07 Jan 2009) | 3 lines
Removed an unused import.
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r8278 | semor | 2009-01-07 03:40:15 +0100 (Wed, 07 Jan 2009) | 3 lines
Removed another unused import.
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r8279 | semor | 2009-01-07 03:43:14 +0100 (Wed, 07 Jan 2009) | 3 lines
Removed an unused import.
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r8280 | semor | 2009-01-07 03:53:52 +0100 (Wed, 07 Jan 2009) | 3 lines
Removed more unused imports.
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r8281 | semor | 2009-01-07 04:01:31 +0100 (Wed, 07 Jan 2009) | 3 lines
Removed an unused import.
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r8282 | semor | 2009-01-07 04:07:25 +0100 (Wed, 07 Jan 2009) | 3 lines
Removed an unused import.
........
Added:
branches/ave_noe/test_suite/shared_data/align_data/
- copied from r8282, 1.3/test_suite/shared_data/align_data/
branches/ave_noe/test_suite/shared_data/structures/lactose/
- copied from r8282, 1.3/test_suite/shared_data/structures/lactose/
branches/ave_noe/test_suite/system_tests/scripts/lactose_n_state.py
- copied unchanged from r8282,
1.3/test_suite/system_tests/scripts/lactose_n_state.py
Removed:
branches/ave_noe/test_suite/shared_data/structures/lactose_MCMM4_S1_1.pdb
Modified:
branches/ave_noe/ (props changed)
branches/ave_noe/data/diff_tensor.py
branches/ave_noe/data/mol_res_spin.py
branches/ave_noe/data/pipe_container.py
branches/ave_noe/docs/latex/develop.tex
branches/ave_noe/generic_fns/align_tensor.py
branches/ave_noe/generic_fns/dasha.py
branches/ave_noe/generic_fns/eliminate.py
branches/ave_noe/generic_fns/fix.py
branches/ave_noe/generic_fns/grace.py
branches/ave_noe/generic_fns/model_selection.py
branches/ave_noe/generic_fns/mol_res_spin.py
branches/ave_noe/generic_fns/monte_carlo.py
branches/ave_noe/generic_fns/palmer.py
branches/ave_noe/generic_fns/pcs.py
branches/ave_noe/generic_fns/pymol.py
branches/ave_noe/generic_fns/rdc.py
branches/ave_noe/generic_fns/results.py
branches/ave_noe/generic_fns/sequence.py
branches/ave_noe/generic_fns/spectrum.py
branches/ave_noe/generic_fns/structure/internal.py
branches/ave_noe/generic_fns/structure/main.py
branches/ave_noe/generic_fns/value.py
branches/ave_noe/generic_fns/vmd.py
branches/ave_noe/maths_fns/jw_mf_comps.py
branches/ave_noe/maths_fns/mf.py
branches/ave_noe/maths_fns/n_state_model.py
branches/ave_noe/maths_fns/ri_comps.py
branches/ave_noe/opendx/main.py
branches/ave_noe/physical_constants.py
branches/ave_noe/prompt/align_tensor.py
branches/ave_noe/prompt/angles.py
branches/ave_noe/prompt/dasha.py
branches/ave_noe/prompt/help.py
branches/ave_noe/prompt/interpreter.py
branches/ave_noe/prompt/relax_data.py
branches/ave_noe/prompt/sequence.py
branches/ave_noe/prompt/spectrum.py
branches/ave_noe/prompt/state.py
branches/ave_noe/prompt/structure.py
branches/ave_noe/prompt/value.py
branches/ave_noe/prompt/vmd.py
branches/ave_noe/relax_io.py
branches/ave_noe/sample_scripts/latex_mf_table.py
branches/ave_noe/specific_fns/base_class.py
branches/ave_noe/specific_fns/consistency_tests.py
branches/ave_noe/specific_fns/jw_mapping.py
branches/ave_noe/specific_fns/model_free/main.py
branches/ave_noe/specific_fns/n_state_model.py
branches/ave_noe/specific_fns/noe.py
branches/ave_noe/specific_fns/relax_fit.py
branches/ave_noe/test_suite/shared_data/structures/generate_str_internal_results.py
branches/ave_noe/test_suite/shared_data/structures/generate_str_scientific_results.py
branches/ave_noe/test_suite/system_tests/angles.py
branches/ave_noe/test_suite/system_tests/diffusion_tensor.py
branches/ave_noe/test_suite/system_tests/n_state_model.py
branches/ave_noe/test_suite/system_tests/peak_lists.py
branches/ave_noe/test_suite/system_tests/relax_fit.py
branches/ave_noe/test_suite/system_tests/scripts/5_state_xz.py
branches/ave_noe/test_suite/system_tests/structure.py
branches/ave_noe/test_suite/system_tests/unit_vectors.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/ave_noe/data/diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/data/diff_tensor.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/data/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/data/mol_res_spin.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/data/pipe_container.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/data/pipe_container.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/docs/latex/develop.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/docs/latex/develop.tex?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/align_tensor.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/dasha.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/eliminate.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/eliminate.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/fix.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/fix.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/grace.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/model_selection.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/model_selection.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/mol_res_spin.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/monte_carlo.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/monte_carlo.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/palmer.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/pcs.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/pymol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/pymol.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/rdc.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/results.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/results.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/sequence.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/spectrum.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/structure/internal.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/structure/main.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/value.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/generic_fns/vmd.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/generic_fns/vmd.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/maths_fns/jw_mf_comps.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/maths_fns/jw_mf_comps.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/maths_fns/mf.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/maths_fns/mf.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/maths_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/maths_fns/n_state_model.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/maths_fns/ri_comps.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/maths_fns/ri_comps.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/opendx/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/opendx/main.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/physical_constants.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/physical_constants.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/prompt/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/prompt/align_tensor.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/prompt/angles.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/prompt/angles.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/prompt/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/prompt/dasha.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/prompt/help.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/prompt/help.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/prompt/interpreter.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/prompt/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/prompt/relax_data.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/prompt/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/prompt/sequence.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/prompt/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/prompt/spectrum.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/prompt/state.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/prompt/state.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/prompt/structure.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/prompt/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/prompt/value.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/prompt/vmd.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/prompt/vmd.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/relax_io.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/relax_io.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/sample_scripts/latex_mf_table.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/sample_scripts/latex_mf_table.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/specific_fns/base_class.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/specific_fns/base_class.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/specific_fns/consistency_tests.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/specific_fns/jw_mapping.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/specific_fns/model_free/main.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/specific_fns/n_state_model.py?rev=8283&r1=8282&r2=8283&view=diff
Modified: branches/ave_noe/specific_fns/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/specific_fns/noe.py?rev=8283&r1=8282&r2=8283&view=diff
[... 36 lines stripped ...]
r8283 - in /branches/ave_noe: ./ data/ docs/latex/ generic_fns/ generic_fns/structure/ maths_fns/ opendx/ prompt/ sample_scr...