Author: bugman
Date: Thu Feb 7 13:58:01 2008
New Revision: 4937
URL: http://svn.gna.org/viewcvs/relax?rev=4937&view=rev
Log:
Merged revisions 4898-4936 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r4898 | bugman | 2008-02-04 14:32:53 +0100 (Mon, 04 Feb 2008) | 3 lines
Removed a junk comment.
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r4899 | bugman | 2008-02-04 14:38:37 +0100 (Mon, 04 Feb 2008) | 3 lines
Converted all methods in the Structure class into functions of the
generic_fns.structure module.
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r4900 | bugman | 2008-02-04 14:40:22 +0100 (Mon, 04 Feb 2008) | 3 lines
The args of the read_pdb() fn are no longer placed into self.
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r4901 | bugman | 2008-02-04 14:42:37 +0100 (Mon, 04 Feb 2008) | 3 lines
Removed all references to 'self' from the generic_fns.structure module.
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r4902 | bugman | 2008-02-04 14:54:07 +0100 (Mon, 04 Feb 2008) | 3 lines
Updated all the tests of the read_pdb() function to the new relax design.
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r4903 | bugman | 2008-02-04 15:03:34 +0100 (Mon, 04 Feb 2008) | 3 lines
Removed an unused import of SpecificData.
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r4904 | bugman | 2008-02-04 15:04:19 +0100 (Mon, 04 Feb 2008) | 3 lines
Changed the 3D structure data structure from a SpecificData class to the
Element class.
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r4905 | bugman | 2008-02-04 15:05:10 +0100 (Mon, 04 Feb 2008) | 3 lines
Deleted the SpecificData container as nothing now uses it.
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r4906 | bugman | 2008-02-04 16:07:25 +0100 (Mon, 04 Feb 2008) | 3 lines
Removed the adding of the 'run' to the 3D structure data structure.
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r4907 | bugman | 2008-02-04 16:08:29 +0100 (Mon, 04 Feb 2008) | 3 lines
Replaced all 'relax_data_store.pdb[run]' with 'cdp.structure'.
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r4908 | bugman | 2008-02-04 16:19:41 +0100 (Mon, 04 Feb 2008) | 3 lines
Converted the load_structures() function to the new relax design.
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r4909 | bugman | 2008-02-04 16:22:14 +0100 (Mon, 04 Feb 2008) | 3 lines
Finished converting the read_pdb() function to the new relax design.
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r4910 | bugman | 2008-02-04 18:06:15 +0100 (Mon, 04 Feb 2008) | 6 lines
Huge redesign of the load_PDB_sequence() function (and converted it to the
new relax design).
This new function should give much more flexibility and abstraction in the
mapping from the
molecular structure to the relax mol-res-spin data structure.
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r4911 | bugman | 2008-02-07 10:33:14 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the Molmol 'command_history' structure into a module variable.
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r4912 | bugman | 2008-02-07 10:35:21 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted all the Molmol class methods into module functions.
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r4913 | bugman | 2008-02-07 10:36:42 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the Molmol command() function to the new relax design.
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r4914 | bugman | 2008-02-07 11:04:05 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the Molmol create_macro() function to the new relax design.
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r4915 | bugman | 2008-02-07 11:06:52 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the Molmol macro_exec() function to the new relax design.
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r4916 | bugman | 2008-02-07 11:08:02 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the Molmol open_pdb() function to the new relax design.
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r4917 | bugman | 2008-02-07 11:09:56 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the test_binary() method into a module function.
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r4918 | bugman | 2008-02-07 11:11:17 +0100 (Thu, 07 Feb 2008) | 3 lines
Updated the generic_fns.molmol module to import the relevent functions from
the relax_io module.
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r4919 | bugman | 2008-02-07 11:13:02 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the Molmol pipe_open() function to the new relax design.
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r4920 | bugman | 2008-02-07 11:15:04 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the Molmol pipe_open_test() function to the new relax design.
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r4921 | bugman | 2008-02-07 11:27:46 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the Molmol pipe_write() function to the new relax design.
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r4922 | bugman | 2008-02-07 11:28:36 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the Molmol ribbon() function to the new relax design.
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r4923 | bugman | 2008-02-07 11:30:01 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the Molmol tensor_pdb() function to the new relax design.
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r4924 | bugman | 2008-02-07 11:30:29 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the Molmol view() function to the new relax design.
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r4925 | bugman | 2008-02-07 11:34:37 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the Molmol write() function to the new relax design.
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r4926 | bugman | 2008-02-07 11:36:08 +0100 (Thu, 07 Feb 2008) | 3 lines
Updated the calls to the create_macro() function.
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r4927 | bugman | 2008-02-07 11:43:09 +0100 (Thu, 07 Feb 2008) | 3 lines
Shifted the core of the angles system test into a relax script.
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r4928 | bugman | 2008-02-07 13:34:48 +0100 (Thu, 07 Feb 2008) | 3 lines
Converted the generic_fns.structure.vectors() function to the new relax
design.
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r4929 | bugman | 2008-02-07 13:38:09 +0100 (Thu, 07 Feb 2008) | 3 lines
Replaced all calls to count_spins() with exists_mol_res_spin_data().
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r4930 | bugman | 2008-02-07 13:40:04 +0100 (Thu, 07 Feb 2008) | 3 lines
Updated the RelaxPdbError class to not require the pipe argument.
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r4931 | bugman | 2008-02-07 13:41:23 +0100 (Thu, 07 Feb 2008) | 5 lines
Bug fix for the generic_fns.structure.vectors() function.
The test for the structure was back to front.
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r4932 | bugman | 2008-02-07 13:42:25 +0100 (Thu, 07 Feb 2008) | 3 lines
Removed the tests for the res_num and res_name args as they no longer exist.
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r4933 | bugman | 2008-02-07 13:48:15 +0100 (Thu, 07 Feb 2008) | 3 lines
Added the verbosity argument to the structure.vectors() user function.
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r4934 | bugman | 2008-02-07 13:49:35 +0100 (Thu, 07 Feb 2008) | 3 lines
Added the verbosity argument to the generic_fns.structure.vectors()
function.
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r4935 | bugman | 2008-02-07 13:50:37 +0100 (Thu, 07 Feb 2008) | 5 lines
Bug fix for the generic_fns.structure.xh_vector() function.
The 'cdp' was not being aliased.
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r4936 | bugman | 2008-02-07 13:53:32 +0100 (Thu, 07 Feb 2008) | 5 lines
Bug fix for the generic_fns.structure.vectors() function.
There was a problem with the new numpy arrays (which has no problems as
Numeric arrays).
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Added:
branches/N_state_model/test_suite/system_tests/scripts/angles.py
- copied unchanged from r4936,
1.3/test_suite/system_tests/scripts/angles.py
Modified:
branches/N_state_model/ (props changed)
branches/N_state_model/data/data_classes.py
branches/N_state_model/data/diff_tensor.py
branches/N_state_model/data/pipe_container.py
branches/N_state_model/generic_fns/molmol.py
branches/N_state_model/generic_fns/sequence.py
branches/N_state_model/generic_fns/structure.py
branches/N_state_model/prompt/structure.py
branches/N_state_model/relax_errors.py
branches/N_state_model/relax_io.py
branches/N_state_model/test_suite/system_tests/angles.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/N_state_model/data/data_classes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/data/data_classes.py?rev=4937&r1=4936&r2=4937&view=diff
Modified: branches/N_state_model/data/diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/data/diff_tensor.py?rev=4937&r1=4936&r2=4937&view=diff
Modified: branches/N_state_model/data/pipe_container.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/data/pipe_container.py?rev=4937&r1=4936&r2=4937&view=diff
Modified: branches/N_state_model/generic_fns/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/molmol.py?rev=4937&r1=4936&r2=4937&view=diff
Modified: branches/N_state_model/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/sequence.py?rev=4937&r1=4936&r2=4937&view=diff
Modified: branches/N_state_model/generic_fns/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/structure.py?rev=4937&r1=4936&r2=4937&view=diff
Modified: branches/N_state_model/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/structure.py?rev=4937&r1=4936&r2=4937&view=diff
Modified: branches/N_state_model/relax_errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/relax_errors.py?rev=4937&r1=4936&r2=4937&view=diff
Modified: branches/N_state_model/relax_io.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/relax_io.py?rev=4937&r1=4936&r2=4937&view=diff
Modified: branches/N_state_model/test_suite/system_tests/angles.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/system_tests/angles.py?rev=4937&r1=4936&r2=4937&view=diff
r4937 - in /branches/N_state_model: ./ data/ generic_fns/ prompt/ test_suite/system_tests/ test_suite/system_tests/scripts/