Merged revisions 4898-4936,4939,4970-4971,5003,5005-5006,5008-5010,5013,5015-5023,5033-5037,5040-5045,5047 via svnmerge from
svn+ssh://semor@.../svn/relax/1.3
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r4898 | bugman | 2008-02-04 08:32:53 -0500 (Mon, 04 Feb 2008) | 3 lines
Removed a junk comment.
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r4899 | bugman | 2008-02-04 08:38:37 -0500 (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 08:40:22 -0500 (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 08:42:37 -0500 (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 08:54:07 -0500 (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 09:03:34 -0500 (Mon, 04 Feb 2008) | 3 lines
Removed an unused import of SpecificData.
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r4904 | bugman | 2008-02-04 09:04:19 -0500 (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 09:05:10 -0500 (Mon, 04 Feb 2008) | 3 lines
Deleted the SpecificData container as nothing now uses it.
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r4906 | bugman | 2008-02-04 10:07:25 -0500 (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 10:08:29 -0500 (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 10:19:41 -0500 (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 10:22:14 -0500 (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 12:06:15 -0500 (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 04:33:14 -0500 (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 04:35:21 -0500 (Thu, 07 Feb 2008) | 3 lines
Converted all the Molmol class methods into module functions.
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r4913 | bugman | 2008-02-07 04:36:42 -0500 (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 05:04:05 -0500 (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 05:06:52 -0500 (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 05:08:02 -0500 (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 05:09:56 -0500 (Thu, 07 Feb 2008) | 3 lines
Converted the test_binary() method into a module function.
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r4918 | bugman | 2008-02-07 05:11:17 -0500 (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 05:13:02 -0500 (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 05:15:04 -0500 (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 05:27:46 -0500 (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 05:28:36 -0500 (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 05:30:01 -0500 (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 05:30:29 -0500 (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 05:34:37 -0500 (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 05:36:08 -0500 (Thu, 07 Feb 2008) | 3 lines
Updated the calls to the create_macro() function.
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r4927 | bugman | 2008-02-07 05:43:09 -0500 (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 07:34:48 -0500 (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 07:38:09 -0500 (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 07:40:04 -0500 (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 07:41:23 -0500 (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 07:42:25 -0500 (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 07:48:15 -0500 (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 07:49:35 -0500 (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 07:50:37 -0500 (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 07:53:32 -0500 (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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r4939 | semor | 2008-02-08 13:24:56 -0500 (Fri, 08 Feb 2008) | 9 lines
Corrected a few errors in the manual concerning the diffusion_tensor.init() function.
Some wrong 'param_types' were given in the examples.
This was pointed in a post by Sebastien morin at:
https://mail.gna.org/public/relax-devel/2008-02/msg00004.html (Message-id:
<47AC8138.9050703@...>)
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r4970 | bugman | 2008-02-13 08:27:32 -0500 (Wed, 13 Feb 2008) | 5 lines
Separated the set up of the specific code into the setup.py module.
The design was crap! It causes massive circular import headaches!
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r4971 | bugman | 2008-02-13 08:30:07 -0500 (Wed, 13 Feb 2008) | 3 lines
Fixes for the imports of the get_specific_fn function.
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r5003 | bugman | 2008-02-15 04:28:40 -0500 (Fri, 15 Feb 2008) | 6 lines
Merged in r4999 to r5002 from the N_state_model branch as they should have gone into the 1.3 line!
The command used was:
svn merge -r4998:5002 svn+ssh://bugman@.../svn/relax/branches/N_state_model
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r5005 | bugman | 2008-02-15 05:06:25 -0500 (Fri, 15 Feb 2008) | 3 lines
Modified the centre_of_mass() function to use obey the selections in the mol-res-spin structure.
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r5006 | bugman | 2008-02-15 05:10:27 -0500 (Fri, 15 Feb 2008) | 3 lines
Converted the generic_fns.structure.centre_of_mass() docstring to epydoc format.
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r5008 | bugman | 2008-02-15 05:36:16 -0500 (Fri, 15 Feb 2008) | 3 lines
Added select flags to the molecule and residue container and list data structures.
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r5009 | bugman | 2008-02-15 05:37:58 -0500 (Fri, 15 Feb 2008) | 3 lines
Converted all the select variables of the mol-res-spin structures to booleans.
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r5010 | bugman | 2008-02-15 05:42:55 -0500 (Fri, 15 Feb 2008) | 3 lines
Added some missing imports.
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r5013 | bugman | 2008-02-15 06:21:59 -0500 (Fri, 15 Feb 2008) | 5 lines
Bug fix for the generic_fns.structure.centre_of_mass() function.
The fetching of molecular, residue, and spin containers is now done correctly.
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r5015 | bugman | 2008-02-19 05:44:18 -0500 (Tue, 19 Feb 2008) | 3 lines
Converted the angles.py sample script to the new relax design.
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r5016 | bugman | 2008-02-19 05:44:42 -0500 (Tue, 19 Feb 2008) | 3 lines
Converted the cv.py sample script to the new relax design.
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r5017 | bugman | 2008-02-19 05:45:25 -0500 (Tue, 19 Feb 2008) | 3 lines
A small comment fix for the cv.py sample script.
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r5018 | bugman | 2008-02-19 05:47:57 -0500 (Tue, 19 Feb 2008) | 3 lines
Converted the dasha.py sample script to the new relax design.
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r5019 | bugman | 2008-02-19 05:50:03 -0500 (Tue, 19 Feb 2008) | 3 lines
Converted the diff_min.py sample script to the new relax design.
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r5020 | bugman | 2008-02-19 05:51:00 -0500 (Tue, 19 Feb 2008) | 3 lines
Converted the diff_tensor.py sample script to the new relax design.
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r5021 | bugman | 2008-02-19 07:26:36 -0500 (Tue, 19 Feb 2008) | 3 lines
Created the spin_index_loop() fn for looping over spins and returning the mol-res-spin indecies.
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r5022 | bugman | 2008-02-19 07:30:01 -0500 (Tue, 19 Feb 2008) | 3 lines
Converted the full_analysis.py sample script to the new relax design.
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r5023 | bugman | 2008-02-19 08:18:04 -0500 (Tue, 19 Feb 2008) | 3 lines
Converted the generate_ri.py sample script to the new relax design.
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r5033 | bugman | 2008-02-20 03:23:23 -0500 (Wed, 20 Feb 2008) | 5 lines
Fixes for the generic_fns.structure.atom_add() function.
The atomic_data dictionary is now expected to be passed into the function.
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r5034 | bugman | 2008-02-20 03:24:01 -0500 (Wed, 20 Feb 2008) | 5 lines
Fixes for the generic_fns.structure.atom_connect() function.
The atomic_data dictionary is now expected to be passed into the function.
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r5035 | bugman | 2008-02-20 03:31:00 -0500 (Wed, 20 Feb 2008) | 3 lines
Shifted all the relative atomic mass values into the physical_constants module.
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r5036 | bugman | 2008-02-20 03:32:44 -0500 (Wed, 20 Feb 2008) | 3 lines
Updated the docstring of the generic_fns.structure.atomic_mass() function to epydoc format.
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r5037 | bugman | 2008-02-20 03:36:10 -0500 (Wed, 20 Feb 2008) | 6 lines
Updated the generic_fns.structure.autoscale_tensor() function.
The docstring was changed to epydoc format, the default method changed from None to 'mass', and a
few comments were added.
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r5040 | bugman | 2008-02-20 05:03:41 -0500 (Wed, 20 Feb 2008) | 7 lines
Created the new function generic_fns.structure.generate_vector_residues().
This new function should allow greater flexibility for creating PDB representations of any type of
vector (and its MC sims). It will also replace the generate_spheroid_axes() and
generate_ellipsoid_axes() functions.
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r5041 | bugman | 2008-02-20 05:56:31 -0500 (Wed, 20 Feb 2008) | 3 lines
All calls to generic_fns.structure.atom_add() now have the atomic_data object passed into it.
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r5042 | bugman | 2008-02-20 05:57:33 -0500 (Wed, 20 Feb 2008) | 3 lines
All calls to generic_fns.structure.atom_connect() now have the atomic_data object passed into it.
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r5043 | bugman | 2008-02-20 06:11:34 -0500 (Wed, 20 Feb 2008) | 3 lines
Converted the generic_fns.structure.create_diff_tensor_pdb() to the new relax design.
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r5044 | bugman | 2008-02-20 08:19:39 -0500 (Wed, 20 Feb 2008) | 5 lines
Removed the calls to generate_spheroid_axes() and generate_ellipsoid_axes() fns.
These have been replaced with calls to generate_vector_residues().
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r5045 | bugman | 2008-02-20 08:20:43 -0500 (Wed, 20 Feb 2008) | 3 lines
Deleted the generate_spheroid_axes() and generate_ellipsoid_axes() fns.
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r5047 | bugman | 2008-02-20 08:39:00 -0500 (Wed, 20 Feb 2008) | 5 lines
Bug fix for the generate_vector_residues() function.
The variable 'pdb_vect' no longer exists.
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