Author: bugman
Date: Wed Sep 24 14:31:35 2008
New Revision: 7235
URL: http://svn.gna.org/viewcvs/relax?rev=7235&view=rev
Log:
Merged revisions 7041-7233 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r7047 | semor | 2008-07-31 15:43:31 +0200 (Thu, 31 Jul 2008) | 3 lines
Added a missing import.
........
r7048 | semor | 2008-07-31 15:46:13 +0200 (Thu, 31 Jul 2008) | 3 lines
Converted 'self.relax.IO' instances to 'relax_io' and added corresponding
imports.
........
r7049 | semor | 2008-07-31 16:05:37 +0200 (Thu, 31 Jul 2008) | 5 lines
More conversions of 'relax.IO' to 'relax_io'.
Old instances are now completely converted.
........
r7050 | semor | 2008-07-31 16:23:49 +0200 (Thu, 31 Jul 2008) | 3 lines
Removed many unused imports.
........
r7051 | semor | 2008-07-31 16:51:45 +0200 (Thu, 31 Jul 2008) | 5 lines
Started to implement system tests for the use of the external program Dasha.
This code is mimicked on the palmer code for testing interaction with
ModelFree4.
........
r7052 | semor | 2008-07-31 21:07:51 +0200 (Thu, 31 Jul 2008) | 7 lines
Completed the coding for the system tests temporary directory used by
external programs.
This follows the thread started by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2008-07/msg00056.html (message ID:
7f080ed10807310053w4cf118bajab47aad7536db4dc@xxxxxxxxxxxxxx).
........
r7053 | semor | 2008-07-31 21:25:31 +0200 (Thu, 31 Jul 2008) | 3 lines
Added the temporary directory path to the state.save() function.
........
r7054 | semor | 2008-07-31 22:08:08 +0200 (Thu, 31 Jul 2008) | 5 lines
More removal of run arguments.
These changes are part of the new design.
........
r7055 | semor | 2008-07-31 22:11:44 +0200 (Thu, 31 Jul 2008) | 3 lines
Still more removal of run arguments.
........
r7056 | bugman | 2008-08-01 11:08:51 +0200 (Fri, 01 Aug 2008) | 3 lines
Converted the VMD class methods into module functions.
........
r7057 | bugman | 2008-08-01 11:11:39 +0200 (Fri, 01 Aug 2008) | 3 lines
Converted the VMD code to the new relax design.
........
r7058 | bugman | 2008-08-01 11:14:01 +0200 (Fri, 01 Aug 2008) | 3 lines
Shifted the VMD module import check into dep_check.py.
........
r7059 | bugman | 2008-08-01 11:37:54 +0200 (Fri, 01 Aug 2008) | 3 lines
Converted the copy() method to the new design (and converted into a
function).
........
r7060 | bugman | 2008-08-01 11:39:55 +0200 (Fri, 01 Aug 2008) | 3 lines
Converted the diplay() method to the new design and into a module function.
........
r7061 | bugman | 2008-08-01 11:54:11 +0200 (Fri, 01 Aug 2008) | 3 lines
Converted the write() and write_data() methods to the new design and into
module functions.
........
r7062 | semor | 2008-08-01 13:54:49 +0200 (Fri, 01 Aug 2008) | 7 lines
Changed a variable name to avoid confusion.
This is in response to a post by Edward d'Auvergne at:
https://mail.gna.org/public/relax-devel/2008-08/msg00011.html (message ID:
7f080ed10808010103o2bc3db69r385daf7fc8c168d2@xxxxxxxxxxxxxx).
........
r7063 | bugman | 2008-08-01 14:04:34 +0200 (Fri, 01 Aug 2008) | 3 lines
Added the ability to have extra columns written by write_line().
........
r7064 | bugman | 2008-08-01 14:07:34 +0200 (Fri, 01 Aug 2008) | 3 lines
Modified write_header() to write extra columns as well.
........
r7065 | bugman | 2008-08-01 14:17:49 +0200 (Fri, 01 Aug 2008) | 3 lines
Modified the write_data() function to use write_header() and write_line()
from generic_fns.sequence.
........
r7066 | bugman | 2008-08-01 14:19:47 +0200 (Fri, 01 Aug 2008) | 5 lines
Converted the read() class method into a module function.
This completes the conversion of all class methods to functions.
........
r7067 | bugman | 2008-08-01 14:53:53 +0200 (Fri, 01 Aug 2008) | 3 lines
Converted the generic_fns.value.read() function to the new design.
........
r7068 | bugman | 2008-08-01 14:54:39 +0200 (Fri, 01 Aug 2008) | 3 lines
Bug fix, removed a now non-existent reference to 'self'.
........
r7069 | bugman | 2008-08-01 14:55:21 +0200 (Fri, 01 Aug 2008) | 3 lines
Fixed a call to minimise.reset_min_stats().
........
r7070 | bugman | 2008-08-05 22:04:16 +0200 (Tue, 05 Aug 2008) | 3 lines
Fix for the set_selected_sim() method, the args were back to front.
........
r7071 | bugman | 2008-08-05 22:20:04 +0200 (Tue, 05 Aug 2008) | 3 lines
Changed the instance arg to model_index in the model-free
set_selected_sim() method.
........
r7072 | bugman | 2008-08-05 22:22:15 +0200 (Tue, 05 Aug 2008) | 5 lines
Fixes for the J(w) mapping set_selected_sim() method.
The spin index and not spin container is passed into the method.
........
r7073 | bugman | 2008-08-05 22:28:10 +0200 (Tue, 05 Aug 2008) | 3 lines
Added a missing import.
........
r7074 | bugman | 2008-08-05 23:29:30 +0200 (Tue, 05 Aug 2008) | 3 lines
Converted the spin loop in create_data() to a loop over the models.
........
r7075 | semor | 2008-08-06 15:13:23 +0200 (Wed, 06 Aug 2008) | 7 lines
Ported r7070, r7072 and r7073 to the consistency tests code.
r7070: http://svn.gna.org/viewcvs/relax?rev=7070&view=rev
r7072: http://svn.gna.org/viewcvs/relax?rev=7072&view=rev
r7073: http://svn.gna.org/viewcvs/relax?rev=7073&view=rev
........
r7094 | bugman | 2008-08-07 21:53:33 +0200 (Thu, 07 Aug 2008) | 3 lines
Modified the create_data() method to use the unimplemented base_data_loop()
generator method.
........
r7095 | bugman | 2008-08-07 22:11:42 +0200 (Thu, 07 Aug 2008) | 3 lines
Created the base_data_loop() generator method for the base class for
looping over spins.
........
r7096 | bugman | 2008-08-07 22:23:30 +0200 (Thu, 07 Aug 2008) | 3 lines
Made the base_data_loop() generator method accessible to the specific
analyses.
........
r7097 | bugman | 2008-08-07 22:47:31 +0200 (Thu, 07 Aug 2008) | 3 lines
Updated create_mc_data() and sim_pack_data() to accept the spin_id yielded
by base_data_loop().
........
r7098 | bugman | 2008-08-07 22:54:36 +0200 (Thu, 07 Aug 2008) | 5 lines
Updated the return_error() method to accept the spin_id arg.
This change doesn't actually do anything.
........
r7099 | bugman | 2008-08-07 23:11:24 +0200 (Thu, 07 Aug 2008) | 5 lines
Implemented the create_mc_data() method.
In the 1.2 line, this was simply aliased to the return_data() method.
........
r7100 | bugman | 2008-08-07 23:17:34 +0200 (Thu, 07 Aug 2008) | 3 lines
Added the missing self arg to create_mc_data().
........
r7101 | bugman | 2008-08-07 23:28:31 +0200 (Thu, 07 Aug 2008) | 3 lines
Added a missing import.
........
r7102 | bugman | 2008-08-07 23:34:36 +0200 (Thu, 07 Aug 2008) | 3 lines
Updated the return_error() to accept the spin_id arg.
........
r7103 | bugman | 2008-08-07 23:53:41 +0200 (Thu, 07 Aug 2008) | 3 lines
Updated the sim_pack_data() method to the new design.
........
r7104 | bugman | 2008-08-07 23:58:28 +0200 (Thu, 07 Aug 2008) | 3 lines
Fixed a call to the data_init() method.
........
r7128 | bugman | 2008-08-10 00:02:18 +0200 (Sun, 10 Aug 2008) | 3 lines
Renamed the 'clean_temp' and 'clean' scons targets to 'clean' and
'clean_all' respectively.
........
r7129 | bugman | 2008-08-10 13:50:55 +0200 (Sun, 10 Aug 2008) | 3 lines
The Monte Carlo error_analysis() function now uses the unimplemented
specific model_loop() method.
........
r7190 | semor | 2008-08-12 23:06:07 +0200 (Tue, 12 Aug 2008) | 3 lines
Ported r7099, r7100, r7101, r7103 and r7104 to the consistency tests code.
........
r7209 | bugman | 2008-08-19 16:54:28 +0200 (Tue, 19 Aug 2008) | 3 lines
Added a RelaxError for when the PDB MODEL record is corrupted.
........
r7210 | bugman | 2008-08-20 20:22:16 +0200 (Wed, 20 Aug 2008) | 3 lines
Fixed a call to atom_add().
........
r7211 | bugman | 2008-08-20 20:23:32 +0200 (Wed, 20 Aug 2008) | 3 lines
Typo bug fix for another call to the structural method atom_add().
........
r7212 | bugman | 2008-08-20 20:27:46 +0200 (Wed, 20 Aug 2008) | 3 lines
Fixed some more calls to the structural method atom_add().
........
r7213 | bugman | 2008-08-20 20:29:22 +0200 (Wed, 20 Aug 2008) | 3 lines
Fixed a call to the structural PDB writer.
........
r7214 | bugman | 2008-08-20 20:42:37 +0200 (Wed, 20 Aug 2008) | 3 lines
The structural data structure for the cone is now properly initialised.
........
r7215 | bugman | 2008-08-20 21:10:20 +0200 (Wed, 20 Aug 2008) | 3 lines
Fixed the creation of the PIV and AVE residues for the cone models.
........
r7216 | bugman | 2008-08-21 14:55:19 +0200 (Thu, 21 Aug 2008) | 3 lines
Fixes for the cone_edge() function for the structural API changes.
........
r7217 | bugman | 2008-08-21 15:50:13 +0200 (Thu, 21 Aug 2008) | 3 lines
Removed some debugging code.
........
r7218 | bugman | 2008-08-21 16:18:14 +0200 (Thu, 21 Aug 2008) | 3 lines
Removed some useless code in generate_vector_residues().
........
r7219 | bugman | 2008-08-21 17:57:51 +0200 (Thu, 21 Aug 2008) | 3 lines
First try at fixing the generate_vector_dist() function.
........
r7220 | bugman | 2008-08-21 18:00:28 +0200 (Thu, 21 Aug 2008) | 3 lines
Atom number fixes for the cone_edge() function.
........
r7221 | bugman | 2008-08-21 18:01:36 +0200 (Thu, 21 Aug 2008) | 3 lines
Fixed calls to the atom_connect() structural API method.
........
r7222 | bugman | 2008-08-21 18:11:32 +0200 (Thu, 21 Aug 2008) | 3 lines
Fixed the call to and the execution of the stitch_cap_to_cone() function.
........
r7223 | bugman | 2008-08-21 18:23:33 +0200 (Thu, 21 Aug 2008) | 3 lines
Fixed the cone_edge() function.
........
r7224 | bugman | 2008-08-21 19:01:29 +0200 (Thu, 21 Aug 2008) | 3 lines
Fixed the generation of the diffusion in a cone geometric object.
........
r7225 | bugman | 2008-08-21 22:07:54 +0200 (Thu, 21 Aug 2008) | 3 lines
Removed some debugging print statements.
........
Added:
branches/bmrb/test_suite/system_tests/dasha.py
- copied unchanged from r7225, 1.3/test_suite/system_tests/dasha.py
branches/bmrb/test_suite/system_tests/scripts/dasha.py
- copied unchanged from r7225,
1.3/test_suite/system_tests/scripts/dasha.py
Modified:
branches/bmrb/ (props changed)
branches/bmrb/dep_check.py
branches/bmrb/generic_fns/align_tensor.py
branches/bmrb/generic_fns/dasha.py
branches/bmrb/generic_fns/diffusion_tensor.py
branches/bmrb/generic_fns/grace.py
branches/bmrb/generic_fns/mol_res_spin.py
branches/bmrb/generic_fns/molmol.py
branches/bmrb/generic_fns/monte_carlo.py
branches/bmrb/generic_fns/pymol.py
branches/bmrb/generic_fns/relax_data.py
branches/bmrb/generic_fns/sequence.py
branches/bmrb/generic_fns/structure/geometric.py
branches/bmrb/generic_fns/structure/internal.py
branches/bmrb/generic_fns/structure/scientific.py
branches/bmrb/generic_fns/value.py
branches/bmrb/generic_fns/vmd.py
branches/bmrb/physical_constants.py
branches/bmrb/prompt/dasha.py
branches/bmrb/relax_errors.py
branches/bmrb/sconstruct
branches/bmrb/specific_fns/base_class.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/n_state_model.py
branches/bmrb/specific_fns/noe.py
branches/bmrb/specific_fns/relax_fit.py
branches/bmrb/specific_fns/setup.py
branches/bmrb/test_suite/system_tests/__init__.py
branches/bmrb/test_suite/system_tests/palmer.py
branches/bmrb/test_suite/system_tests/scripts/palmer.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/bmrb/dep_check.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/dep_check.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/generic_fns/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/align_tensor.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/generic_fns/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/dasha.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/generic_fns/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/diffusion_tensor.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/generic_fns/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/grace.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/mol_res_spin.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/generic_fns/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/molmol.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/generic_fns/monte_carlo.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/monte_carlo.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/generic_fns/pymol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/pymol.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/relax_data.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/sequence.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/structure/geometric.py?rev=7235&r1=7234&r2=7235&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=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/structure/scientific.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/generic_fns/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/value.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/generic_fns/vmd.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/vmd.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/physical_constants.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/physical_constants.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/prompt/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/dasha.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/relax_errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/relax_errors.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/sconstruct
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/sconstruct?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/specific_fns/base_class.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/base_class.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/consistency_tests.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/jw_mapping.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/model_free/main.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/n_state_model.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/specific_fns/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/noe.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/relax_fit.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/specific_fns/setup.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/setup.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/test_suite/system_tests/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/system_tests/__init__.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/test_suite/system_tests/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/system_tests/palmer.py?rev=7235&r1=7234&r2=7235&view=diff
Modified: branches/bmrb/test_suite/system_tests/scripts/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/system_tests/scripts/palmer.py?rev=7235&r1=7234&r2=7235&view=diff
r7235 - in /branches/bmrb: ./ generic_fns/ generic_fns/structure/ prompt/ specific_fns/ specific_fns/model_free/ test_suite/...