Author: bugman
Date: Thu Jul 28 16:53:50 2011
New Revision: 13962
URL: http://svn.gna.org/viewcvs/relax?rev=13962&view=rev
Log:
Merged revisions
13835-13836,13845-13857,13904-13906,13909,13919,13926-13927,13929,13932,13951,13956,13958
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r13835 | bugman | 2011-07-22 16:30:29 +0200 (Fri, 22 Jul 2011) | 6 lines
Fix for the model-free _determine_model_type() method when the spin
container has no 'local_tm'.
This code was failing in certain rare circumstances (when the setting up of
the diffusion tensor was
forgotten).
........
r13836 | bugman | 2011-07-22 16:57:05 +0200 (Fri, 22 Jul 2011) | 3 lines
Created a script for byte compiling the Python source files.
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r13845 | bugman | 2011-07-25 10:07:31 +0200 (Mon, 25 Jul 2011) | 5 lines
Added some old 2004 scripts for creating a uniform vector distribution and
calculating relaxation data.
This will be used in the end to build a quick test for the
dauvergne_protocol auto-analysis.
........
r13846 | bugman | 2011-07-25 10:13:27 +0200 (Mon, 25 Jul 2011) | 3 lines
Modified the spherical vector distribution script in preparation for Python
3.
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r13847 | bugman | 2011-07-25 10:15:19 +0200 (Mon, 25 Jul 2011) | 3 lines
Modified the script to only have 3 incs.
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r13848 | bugman | 2011-07-25 10:15:51 +0200 (Mon, 25 Jul 2011) | 3 lines
Created the PDB representation of the spherical vector distribution for 9
vectors.
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r13849 | bugman | 2011-07-25 10:37:49 +0200 (Mon, 25 Jul 2011) | 3 lines
Converted the relaxation data generation script from relax 1.0 format to
relax 1.3.
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r13850 | bugman | 2011-07-25 12:02:17 +0200 (Mon, 25 Jul 2011) | 9 lines
Added initial support for determining protein connectivities in the
internal structural reader.
This is currently only for intra-residue connectivities in the protein
backbone. A number of new
methods have been added:
_mol_type()
_protein_connect()
_protein_intra_connect()
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r13851 | bugman | 2011-07-25 12:20:43 +0200 (Mon, 25 Jul 2011) | 5 lines
Fixes for the test suite relaxation data creation script.
The code was not fully compatible with the relax 1.3 design.
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r13852 | bugman | 2011-07-25 12:21:13 +0200 (Mon, 25 Jul 2011) | 3 lines
Fixes to the relaxation data generation sample script based on the changes
of r13851.
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r13853 | bugman | 2011-07-25 12:22:22 +0200 (Mon, 25 Jul 2011) | 5 lines
The relaxation data is now for 500 and 900 MHz.
This larger difference should hopefully speed up optimisation in the test
suite.
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r13854 | bugman | 2011-07-25 12:23:36 +0200 (Mon, 25 Jul 2011) | 3 lines
Added the relaxation data.
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r13855 | bugman | 2011-07-25 13:45:04 +0200 (Mon, 25 Jul 2011) | 5 lines
Added the argument 'bc' to the relax_data.write() user function front end.
This currently doesn't do anything.
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r13856 | bugman | 2011-07-25 14:33:28 +0200 (Mon, 25 Jul 2011) | 5 lines
The 'bc' arg is now part of the value.write() user function, and all of the
return_value functions.
The arg is also propagated to the back-end of the relax_data.write() user
function.
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r13857 | bugman | 2011-07-25 14:34:12 +0200 (Mon, 25 Jul 2011) | 3 lines
The back calculated data is now written out to file in the synthetic
relaxation data script.
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r13904 | bugman | 2011-07-26 21:40:15 +0200 (Tue, 26 Jul 2011) | 5 lines
Added the data_type() method to the specific functions API.
This will be used to determine the type that a given parameter from
data_names() should be.
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r13905 | bugman | 2011-07-26 21:52:58 +0200 (Tue, 26 Jul 2011) | 3 lines
Modified the specific functions API method data_type() so that Python type
objects should be returned.
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r13906 | bugman | 2011-07-26 21:55:53 +0200 (Tue, 26 Jul 2011) | 3 lines
Implemented the model-free version of the data_type() API method.
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r13909 | bugman | 2011-07-26 22:18:51 +0200 (Tue, 26 Jul 2011) | 3 lines
The data_type() API method is now exposed.
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r13919 | bugman | 2011-07-27 09:37:48 +0200 (Wed, 27 Jul 2011) | 3 lines
The heteronucleus and proton type parameters can now be specified by their
parameter names aas well.
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r13926 | bugman | 2011-07-27 16:01:22 +0200 (Wed, 27 Jul 2011) | 5 lines
The create_molecule, create_residue, and create_spin functions now returned
the created container.
This should not affect any of the current code using these, as normally
None would be returned.
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r13927 | bugman | 2011-07-27 16:05:49 +0200 (Wed, 27 Jul 2011) | 6 lines
Invisible fix for the test_opendx_theta_phi_da() system test.
The spins are extracted from the structure, so they don't need to be read
from the relaxation data
file as well. This is causing problems in the xyz branch, but is not an
issue in the main line.
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r13929 | bugman | 2011-07-27 16:15:41 +0200 (Wed, 27 Jul 2011) | 3 lines
Modified the create_spin() function to overwrite the first spin if empty.
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r13932 | bugman | 2011-07-27 17:54:24 +0200 (Wed, 27 Jul 2011) | 13 lines
Redesign of the structure.load_spins user function back end.
This redesign is required due to problems encountered by Han in the xyz
branch. See the thread
starting at https://mail.gna.org/public/relax-devel/2011-07/msg00021.html.
This commit consists of a number of changes:
- The combine_models argument has been removed as it is a relic, and
isn't used at all.
- The spins are now created in the standard way via the
generic_fns.mol_res_spin.create_spin()
function, eliminating all of the issues and complications of the old code.
- The atomic positions are now converted to numpy arrays.
- Only the created spins are included in the print out, and not
replicated for each model.
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r13951 | bugman | 2011-07-28 15:14:55 +0200 (Thu, 28 Jul 2011) | 7 lines
Redesign of the main relax module.
The module has been renamed to 'relax.py', and the original file 'relax' is
now a very basic python
script which simply loads the module and runs the new start() function for
launching relax. The MS
Windows BAT file has also been updated to feed the module into python.
........
r13956 | bugman | 2011-07-28 16:26:16 +0200 (Thu, 28 Jul 2011) | 3 lines
The relax mode normally specified by the command line can now be overridden.
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r13958 | bugman | 2011-07-28 16:35:58 +0200 (Thu, 28 Jul 2011) | 3 lines
Removed the executable svn property on the info module.
........
Added:
branches/relax_disp/relax.py
- copied unchanged from r13958, 1.3/relax.py
branches/relax_disp/scripts/byte_compile
- copied unchanged from r13958, 1.3/scripts/byte_compile
branches/relax_disp/test_suite/shared_data/model_free/sphere/
- copied from r13958, 1.3/test_suite/shared_data/model_free/sphere/
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/generic_fns/mol_res_spin.py
branches/relax_disp/generic_fns/relax_data.py
branches/relax_disp/generic_fns/structure/internal.py
branches/relax_disp/generic_fns/structure/main.py
branches/relax_disp/generic_fns/value.py
branches/relax_disp/info.py (props changed)
branches/relax_disp/prompt/relax_data.py
branches/relax_disp/prompt/structure.py
branches/relax_disp/prompt/value.py
branches/relax_disp/relax
branches/relax_disp/relax.bat
branches/relax_disp/sample_scripts/generate_ri.py
branches/relax_disp/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py
branches/relax_disp/specific_fns/api_base.py
branches/relax_disp/specific_fns/api_common.py
branches/relax_disp/specific_fns/model_free/main.py
branches/relax_disp/specific_fns/setup.py
branches/relax_disp/test_suite/shared_data/align_data/population_model/generate.py
branches/relax_disp/test_suite/system_tests/model_free.py
branches/relax_disp/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
branches/relax_disp/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
branches/relax_disp/test_suite/system_tests/scripts/n_state_model/populations.py
branches/relax_disp/test_suite/system_tests/scripts/n_state_model/vector_loading.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/relax_disp/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/mol_res_spin.py?rev=13962&r1=13961&r2=13962&view=diff
Modified: branches/relax_disp/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/relax_data.py?rev=13962&r1=13961&r2=13962&view=diff
Modified: branches/relax_disp/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/structure/internal.py?rev=13962&r1=13961&r2=13962&view=diff
Modified: branches/relax_disp/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/structure/main.py?rev=13962&r1=13961&r2=13962&view=diff
Modified: branches/relax_disp/generic_fns/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/value.py?rev=13962&r1=13961&r2=13962&view=diff
Modified: branches/relax_disp/prompt/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/prompt/relax_data.py?rev=13962&r1=13961&r2=13962&view=diff
Modified: branches/relax_disp/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/prompt/structure.py?rev=13962&r1=13961&r2=13962&view=diff
Modified: branches/relax_disp/prompt/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/prompt/value.py?rev=13962&r1=13961&r2=13962&view=diff
Modified: branches/relax_disp/relax
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/relax?rev=13962&r1=13961&r2=13962&view=diff
Modified: branches/relax_disp/relax.bat
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/relax.bat?rev=13962&r1=13961&r2=13962&view=diff
Modified: branches/relax_disp/sample_scripts/generate_ri.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/sample_scripts/generate_ri.py?rev=13962&r1=13961&r2=13962&view=diff
Modified:
branches/relax_disp/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/sample_scripts/n_state_model/conformation_analysis_rdc%2Bpcs.py?rev=13962&r1=13961&r2=13962&view=diff
Modified: branches/relax_disp/specific_fns/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_fns/api_base.py?rev=13962&r1=13961&r2=13962&view=diff
Modified: branches/relax_disp/specific_fns/api_common.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_fns/api_common.py?rev=13962&r1=13961&r2=13962&view=diff
Modified: branches/relax_disp/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_fns/model_free/main.py?rev=13962&r1=13961&r2=13962&view=diff
Modified: branches/relax_disp/specific_fns/setup.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_fns/setup.py?rev=13962&r1=13961&r2=13962&view=diff
Modified:
branches/relax_disp/test_suite/shared_data/align_data/population_model/generate.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/align_data/population_model/generate.py?rev=13962&r1=13961&r2=13962&view=diff
Modified: branches/relax_disp/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/model_free.py?rev=13962&r1=13961&r2=13962&view=diff
Modified:
branches/relax_disp/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py?rev=13962&r1=13961&r2=13962&view=diff
Modified:
branches/relax_disp/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/n_state_model/missing_data_test.py?rev=13962&r1=13961&r2=13962&view=diff
Modified:
branches/relax_disp/test_suite/system_tests/scripts/n_state_model/populations.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/n_state_model/populations.py?rev=13962&r1=13961&r2=13962&view=diff
Modified:
branches/relax_disp/test_suite/system_tests/scripts/n_state_model/vector_loading.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/n_state_model/vector_loading.py?rev=13962&r1=13961&r2=13962&view=diff
r13962 - in /branches/relax_disp: ./ generic_fns/ generic_fns/structure/ prompt/ sample_scripts/ sample_scripts/n_state_mode...