Author: bugman
Date: Mon Apr 7 23:08:50 2008
New Revision: 5397
URL: http://svn.gna.org/viewcvs/relax?rev=5397&view=rev
Log:
Blocked revisions 5258-5272,5274,5276-5394 via svnmerge
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r5258 | semor | 2008-04-03 17:15:07 +0200 (Thu, 03 Apr 2008) | 3 lines
Removed the run argument as part of the moving to the new design.
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r5259 | semor | 2008-04-03 17:18:46 +0200 (Thu, 03 Apr 2008) | 3 lines
More removal of the run argument as part of the moving to the new design.
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r5260 | semor | 2008-04-03 17:21:17 +0200 (Thu, 03 Apr 2008) | 3 lines
More removal of the run argument as part of the moving to the new design.
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r5261 | semor | 2008-04-03 17:25:11 +0200 (Thu, 03 Apr 2008) | 3 lines
More removal of the run argument as part of the moving to the new design.
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r5262 | semor | 2008-04-03 17:26:29 +0200 (Thu, 03 Apr 2008) | 3 lines
More removal of the run argument as part of the moving to the new design.
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r5263 | semor | 2008-04-03 17:32:39 +0200 (Thu, 03 Apr 2008) | 8 lines
Reverted revision 5262.
The command used was:
svn merge -r5262:5261 .
There is still a function called run() in prompt.interpreter which should
not be removed...
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r5264 | semor | 2008-04-03 17:47:42 +0200 (Thu, 03 Apr 2008) | 3 lines
More removal of the run argument as part of the moving to the new design.
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r5265 | semor | 2008-04-03 18:02:29 +0200 (Thu, 03 Apr 2008) | 3 lines
More removal of the run argument as part of the moving to the new design.
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r5266 | semor | 2008-04-03 18:56:44 +0200 (Thu, 03 Apr 2008) | 7 lines
Fixed a few bugs introduced while modifying the code to the new design.
These bugs were noticed by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2008-04/msg00011.html (Message-id:
<7f080ed10804030921h2703a004o65501fbd89cb08ed@xxxxxxxxxxxxxx>)
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r5267 | semor | 2008-04-03 18:57:52 +0200 (Thu, 03 Apr 2008) | 3 lines
Added missing imports.
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r5268 | semor | 2008-04-03 19:04:26 +0200 (Thu, 03 Apr 2008) | 7 lines
Changed "for i in xrange(len(cdp.res)):" to the spin_loop.
This was proposed by Edward d'Auvergne in a post at :
https://mail.gna.org/public/relax-devel/2008-04/msg00012.html (Message-id:
<7f080ed10804030926p4be2e72apa2ccef85a9062e57@xxxxxxxxxxxxxx>)
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r5269 | semor | 2008-04-03 19:05:03 +0200 (Thu, 03 Apr 2008) | 3 lines
Added missing imports.
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r5270 | semor | 2008-04-03 19:06:25 +0200 (Thu, 03 Apr 2008) | 3 lines
Updated the listing of the files in the prompt/ directory.
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r5271 | semor | 2008-04-03 19:27:23 +0200 (Thu, 03 Apr 2008) | 3 lines
More removal of the run argument as part of the moving to the new design.
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r5272 | semor | 2008-04-03 19:30:39 +0200 (Thu, 03 Apr 2008) | 3 lines
Corrected a typo.
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r5274 | semor | 2008-04-03 20:11:24 +0200 (Thu, 03 Apr 2008) | 8 lines
Merged the consistency tests branch back into the 1.3 line.
The command used was:
svn merge -r3321:HEAD
svn+ssh://semor@xxxxxxxxxxx/svn/relax/branches/consistency_tests_1.3/ .
The code is almost ready and further changes will not affect the rest of
the code.
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r5276 | semor | 2008-04-03 20:39:49 +0200 (Thu, 03 Apr 2008) | 3 lines
More removal of the run argument as part of the moving to the new design.
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r5277 | semor | 2008-04-03 20:41:48 +0200 (Thu, 03 Apr 2008) | 3 lines
More removal of the run argument as part of the moving to the new design.
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r5278 | semor | 2008-04-03 20:48:09 +0200 (Thu, 03 Apr 2008) | 3 lines
More removal of the run argument as part of the moving to the new design.
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r5279 | semor | 2008-04-03 22:24:13 +0200 (Thu, 03 Apr 2008) | 10 lines
Reverted revision 5268.
The command used was:
svn merge -r5268:5267 .
Too many errors were present as noted by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2008-04/msg00022.html (Message-id:
<7f080ed10804031148r75a295a2u99569bb13b99ffc5@xxxxxxxxxxxxxx>)
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r5280 | semor | 2008-04-03 22:37:16 +0200 (Thu, 03 Apr 2008) | 3 lines
More modifications for the new design and the removal of a 'tab' character.
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r5281 | semor | 2008-04-03 23:00:27 +0200 (Thu, 03 Apr 2008) | 3 lines
More removal of the run argument as part of the moving to the new design.
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r5282 | semor | 2008-04-03 23:07:22 +0200 (Thu, 03 Apr 2008) | 3 lines
More removal of the run argument as part of the moving to the new design.
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r5283 | semor | 2008-04-03 23:10:44 +0200 (Thu, 03 Apr 2008) | 3 lines
More removal of the run argument as part of the moving to the new design.
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r5284 | bugman | 2008-04-04 10:59:15 +0200 (Fri, 04 Apr 2008) | 3 lines
Updated the generic_fns.structure.set_vector() function to the new design.
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r5285 | bugman | 2008-04-04 11:09:57 +0200 (Fri, 04 Apr 2008) | 15 lines
Created a new directory for the new 'structure' package.
This will eventually contain numerous structure related operations
including:
A number of PDB parsers,
A PDB writer,
CIF parsers,
Other structural data file parsers,
Functions for creating geometric objects in structural format,
Mass and inertia related functions.
This package will eventually have a well defined API for accessing
structural data independent of
the structure parser used.
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r5286 | bugman | 2008-04-04 11:12:13 +0200 (Fri, 04 Apr 2008) | 3 lines
Updated physical_constants.return_atomic_mass() to better match
generic_fns.structure.atomic_mass().
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r5287 | bugman | 2008-04-04 11:13:40 +0200 (Fri, 04 Apr 2008) | 3 lines
The fn physical_constants.return_atomic_mass() is now used instead of the
old atomic_mass() fn.
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r5288 | bugman | 2008-04-04 11:14:11 +0200 (Fri, 04 Apr 2008) | 3 lines
Deletion of the generic_fns.structure.atomic_mass() function.
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r5289 | bugman | 2008-04-04 11:25:38 +0200 (Fri, 04 Apr 2008) | 6 lines
Started to create the structure package.
The package is now initialised and has a docstring describing it. The
structure module has also
been shifted from generic_fns to structure.
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r5290 | bugman | 2008-04-04 12:01:52 +0200 (Fri, 04 Apr 2008) | 3 lines
Started to create the structural object and the API for accessing,
creating, modifying info.
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r5291 | bugman | 2008-04-04 14:13:28 +0200 (Fri, 04 Apr 2008) | 8 lines
Modifications to the structure.read_pdb() user function.
The 'parser' argument has been added to allow different PDB parsers to be
selected in the future.
To allow for the new relax design, the docstring has been updated with
respect to the loading of the
sequence and the 'spin_id' argument has been added to allow the selection
of specific atoms of the
PDB file to be placed as SpinContainers in the relax data store.
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r5292 | semor | 2008-04-04 14:23:52 +0200 (Fri, 04 Apr 2008) | 7 lines
Corrected a few errors created while changing the code to the new design.
These were noticed by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2008-04/msg00028.html (# Message-id:
<7f080ed10804040040v3fdeb265p959479026923d71a@xxxxxxxxxxxxxx>)
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r5293 | bugman | 2008-04-04 14:29:12 +0200 (Fri, 04 Apr 2008) | 3 lines
Shifted all the functions relating to geometric objects into
structure.generic.
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r5294 | bugman | 2008-04-04 14:30:41 +0200 (Fri, 04 Apr 2008) | 3 lines
Fixed the import of the structure package.
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r5295 | bugman | 2008-04-04 14:43:38 +0200 (Fri, 04 Apr 2008) | 3 lines
Added the 'geometric' module to the __all__ list.
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r5296 | bugman | 2008-04-04 14:45:52 +0200 (Fri, 04 Apr 2008) | 5 lines
Converted the 'structure' package into a subpackage of 'generic_fns'.
This solves a module import issue, and is a logical place for the code.
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r5297 | bugman | 2008-04-04 14:48:57 +0200 (Fri, 04 Apr 2008) | 3 lines
Fixed all the 'structure' user functions to use the new package.
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r5298 | bugman | 2008-04-04 14:52:25 +0200 (Fri, 04 Apr 2008) | 3 lines
Fixed the test_read_pdb_argfail_load_seq() unit test.
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r5299 | bugman | 2008-04-04 14:53:15 +0200 (Fri, 04 Apr 2008) | 3 lines
Added a missing RelaxError import.
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r5300 | bugman | 2008-04-04 15:10:44 +0200 (Fri, 04 Apr 2008) | 3 lines
Added 2 unit tests for the new args of the structure.read_pdb() user
function.
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r5301 | bugman | 2008-04-04 15:20:14 +0200 (Fri, 04 Apr 2008) | 3 lines
Removed many unused imports.
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r5302 | semor | 2008-04-04 15:32:41 +0200 (Fri, 04 Apr 2008) | 3 lines
Fixed a typo causing several unit tests to fail.
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r5303 | bugman | 2008-04-04 15:33:46 +0200 (Fri, 04 Apr 2008) | 3 lines
Spun out the Scientific Python specific code into its own module.
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r5304 | bugman | 2008-04-04 15:41:42 +0200 (Fri, 04 Apr 2008) | 6 lines
Converted Scientific Python from a dependancy to an optional Python package.
Of course since this is the only PDB parser in relax at the moment, if
Scientific Python is not
installed, then PDB files cannot be read.
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r5305 | bugman | 2008-04-04 16:03:20 +0200 (Fri, 04 Apr 2008) | 6 lines
Created the Scientific Python specific data object.
The functions specific to Scientific Python have been converted into
methods of the object. The new
object inherits from api_base.Str_object.
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r5306 | bugman | 2008-04-04 16:19:51 +0200 (Fri, 04 Apr 2008) | 3 lines
Added a module docstring.
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r5307 | bugman | 2008-04-04 16:20:24 +0200 (Fri, 04 Apr 2008) | 3 lines
Bug fix for the system test for the loading of the sequence from a PDB file.
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r5308 | semor | 2008-04-04 16:21:27 +0200 (Fri, 04 Apr 2008) | 3 lines
Partially fixed the code so the Jw mapping system test can go further
before failure.
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r5309 | bugman | 2008-04-04 16:22:25 +0200 (Fri, 04 Apr 2008) | 3 lines
Changed the parser specific data object name to 'structural_data' and
initialised it to [].
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r5310 | semor | 2008-04-04 16:33:02 +0200 (Fri, 04 Apr 2008) | 3 lines
Re-introduced the test for the existence of the current pipe and correcte a
comment.
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r5311 | semor | 2008-04-04 16:42:09 +0200 (Fri, 04 Apr 2008) | 3 lines
Partially fixed more of the code so the Jw mapping system test can go
further before failure.
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r5312 | bugman | 2008-04-04 16:56:01 +0200 (Fri, 04 Apr 2008) | 5 lines
Updated the methods of the Scientific Python PDB specific structural object
class.
These now use the structure of the new object.
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r5313 | bugman | 2008-04-04 16:57:23 +0200 (Fri, 04 Apr 2008) | 3 lines
Added a string used to identify the structural object.
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r5314 | semor | 2008-04-04 17:03:09 +0200 (Fri, 04 Apr 2008) | 10 lines
Reverted changes of the variable 'nucleus' to 'heteronucleus'.
The command used was:
svn merge -r5308:5302 ./physical_constants.py
This error was noticed by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2008-04/msg00033.html (# Message-id:
<7f080ed10804040741x3e26f862r808982451ab522c8@xxxxxxxxxxxxxx>)
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r5315 | bugman | 2008-04-04 17:04:18 +0200 (Fri, 04 Apr 2008) | 3 lines
Added the load_structures() prototype method stub.
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r5316 | semor | 2008-04-04 17:05:11 +0200 (Fri, 04 Apr 2008) | 7 lines
Corrected the location of the get_string() function.
This was noted by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2008-04/msg00034.html (# Message-id:
<7f080ed10804040747q36313c26mcc60989634028b56@xxxxxxxxxxxxxx>)
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r5317 | semor | 2008-04-04 17:11:20 +0200 (Fri, 04 Apr 2008) | 3 lines
Changed all instances of 'run.create' to 'pipe.create' as in the new design.
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r5318 | semor | 2008-04-04 17:18:02 +0200 (Fri, 04 Apr 2008) | 3 lines
Partially fixed the code so the consistency tests system test can go
further before failure.
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r5319 | semor | 2008-04-04 17:19:18 +0200 (Fri, 04 Apr 2008) | 3 lines
Added a missing import.
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r5320 | semor | 2008-04-04 17:21:16 +0200 (Fri, 04 Apr 2008) | 3 lines
Partially fixed more code so the consistency tests system test can go
further before failure.
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r5321 | semor | 2008-04-04 17:23:26 +0200 (Fri, 04 Apr 2008) | 3 lines
Partially fixed more code so the consistency tests system test can go
further before failure...
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r5322 | semor | 2008-04-04 17:25:14 +0200 (Fri, 04 Apr 2008) | 3 lines
Partially fixed more code so the consistency tests system test can go
further before failure...
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r5323 | semor | 2008-04-04 17:25:44 +0200 (Fri, 04 Apr 2008) | 3 lines
Corrected a docstring and a comment.
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r5324 | semor | 2008-04-04 17:26:54 +0200 (Fri, 04 Apr 2008) | 5 lines
Partially fixed more code so the consistency tests system test can go
further before failure...
Added a missing variable.
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r5325 | bugman | 2008-04-04 17:29:43 +0200 (Fri, 04 Apr 2008) | 3 lines
Added the xh_vector() prototype method stub to the structure API.
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r5326 | semor | 2008-04-04 17:29:57 +0200 (Fri, 04 Apr 2008) | 5 lines
Partially fixed more code so the consistency tests system test can go
further before failure...
Set missing parameter values in system test code.
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r5327 | semor | 2008-04-04 17:33:41 +0200 (Fri, 04 Apr 2008) | 5 lines
Corrected errors causing failures of the unit test for consistency testing
variables set up.
The variable 'heteronuc_type' was used instead of 'heteronucleus'.
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r5328 | bugman | 2008-04-04 17:39:21 +0200 (Fri, 04 Apr 2008) | 5 lines
Spun out all of the functions accessing 'atomic_data'.
These will be converted to methods of a new type of internal PDB object.
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r5329 | bugman | 2008-04-04 17:44:18 +0200 (Fri, 04 Apr 2008) | 3 lines
Created the internal relax PDB object class.
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r5330 | bugman | 2008-04-04 17:48:08 +0200 (Fri, 04 Apr 2008) | 3 lines
Removed many unused imports.
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r5331 | bugman | 2008-04-04 18:12:47 +0200 (Fri, 04 Apr 2008) | 3 lines
Updated the __all__ list.
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r5332 | semor | 2008-04-04 20:21:08 +0200 (Fri, 04 Apr 2008) | 3 lines
Corrected calls to the heteronucleus in the model-free system test code.
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r5333 | semor | 2008-04-04 20:22:33 +0200 (Fri, 04 Apr 2008) | 3 lines
Corrected calls to the heteronucleus in the opendx system test script code.
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r5334 | semor | 2008-04-04 20:24:45 +0200 (Fri, 04 Apr 2008) | 3 lines
Corrected some comments.
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r5335 | bugman | 2008-04-07 10:49:17 +0200 (Mon, 07 Apr 2008) | 7 lines
Updated the internal PDB structural object to use the self.structural_data
object.
The atomic_data structure has been replaced by self.structural_data, and is
no longer passed into
each method. The description of this object has also shifted from the
methods into the class
docstring.
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r5336 | bugman | 2008-04-07 10:50:15 +0200 (Mon, 07 Apr 2008) | 3 lines
Removed some useless epydoc text.
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r5337 | bugman | 2008-04-07 10:55:49 +0200 (Mon, 07 Apr 2008) | 3 lines
Added the atom_add prototype method stub to the structral data API.
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r5338 | bugman | 2008-04-07 10:58:25 +0200 (Mon, 07 Apr 2008) | 3 lines
Added the atom_connect prototype method stub to the structral data API.
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r5339 | bugman | 2008-04-07 11:00:45 +0200 (Mon, 07 Apr 2008) | 3 lines
Added the terminate prototype method stub to the structral data API.
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r5340 | bugman | 2008-04-07 11:04:13 +0200 (Mon, 07 Apr 2008) | 3 lines
A number of docstring updates for the structural data API.
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r5341 | bugman | 2008-04-07 11:10:53 +0200 (Mon, 07 Apr 2008) | 5 lines
Added the write_pdb_file prototype method stub to the structral data API.
All the PDB record documentation has been shifted to the API stub method.
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r5342 | bugman | 2008-04-07 11:45:38 +0200 (Mon, 07 Apr 2008) | 3 lines
Improvements to the generic_fns.structure package docstring.
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r5343 | bugman | 2008-04-07 11:47:35 +0200 (Mon, 07 Apr 2008) | 3 lines
Included generic_fns/structure/ in the API docs.
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r5344 | bugman | 2008-04-07 11:57:49 +0200 (Mon, 07 Apr 2008) | 3 lines
Added a module docstring to the relax internal PDB structural object.
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r5345 | bugman | 2008-04-07 13:48:19 +0200 (Mon, 07 Apr 2008) | 3 lines
Changed all the docstrings to say 'method' rather than 'function'.
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r5346 | bugman | 2008-04-07 13:49:36 +0200 (Mon, 07 Apr 2008) | 3 lines
Made one of the methods private by renaming to __get_chemical_name().
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r5347 | bugman | 2008-04-07 13:50:51 +0200 (Mon, 07 Apr 2008) | 3 lines
Fixed the internal call to the atom_add() method.
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r5348 | bugman | 2008-04-07 13:57:27 +0200 (Mon, 07 Apr 2008) | 5 lines
Spun out the centre_of_mass() function to its own module.
This new module will contain all functions related to mass and inertia.
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r5349 | bugman | 2008-04-07 13:59:17 +0200 (Mon, 07 Apr 2008) | 3 lines
Docstring improvements.
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r5350 | bugman | 2008-04-07 14:00:11 +0200 (Mon, 07 Apr 2008) | 3 lines
Renamed the generic_fns.structure.structure module to
generic_fns.structure.main.
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r5351 | bugman | 2008-04-07 14:01:00 +0200 (Mon, 07 Apr 2008) | 3 lines
Updated the __all__ package list.
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r5352 | bugman | 2008-04-07 14:03:21 +0200 (Mon, 07 Apr 2008) | 3 lines
Fixed the structure user functions for the module rename of r5350.
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r5353 | bugman | 2008-04-07 14:20:06 +0200 (Mon, 07 Apr 2008) | 3 lines
Converted the read_pdb() function to the new relax design.
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r5354 | bugman | 2008-04-07 14:26:50 +0200 (Mon, 07 Apr 2008) | 5 lines
The cdp.structure object is now set to the Scientific Python structural
data object.
Some code has also been shifted into the load_structures() method.
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r5355 | bugman | 2008-04-07 14:28:26 +0200 (Mon, 07 Apr 2008) | 3 lines
The load_structures() method is now properly called.
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r5356 | bugman | 2008-04-07 14:29:50 +0200 (Mon, 07 Apr 2008) | 3 lines
Removal of a few comments.
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r5357 | bugman | 2008-04-07 14:33:38 +0200 (Mon, 07 Apr 2008) | 3 lines
An initial print out for the parser type.
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r5358 | bugman | 2008-04-07 14:35:43 +0200 (Mon, 07 Apr 2008) | 3 lines
Removed a broken and now useless test.
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r5359 | bugman | 2008-04-07 14:38:33 +0200 (Mon, 07 Apr 2008) | 3 lines
Fixed the call to the centre_of_mass() function in the N-state model code.
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r5360 | bugman | 2008-04-07 14:40:51 +0200 (Mon, 07 Apr 2008) | 3 lines
Fixed a test for the presence of structural data in the current data pipe.
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r5361 | bugman | 2008-04-07 14:42:18 +0200 (Mon, 07 Apr 2008) | 3 lines
Added a missing import.
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r5362 | bugman | 2008-04-07 15:00:46 +0200 (Mon, 07 Apr 2008) | 3 lines
Modified centre_of_mass() to call a new generator function atom_loop() in
the structural data object.
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r5363 | bugman | 2008-04-07 16:29:16 +0200 (Mon, 07 Apr 2008) | 6 lines
The centre of mass function now works if the sequence does not exist in the
current data pipe.
The spin_num and spin_name have been renamed to atom_num and atom_name
respectively in the function
as well.
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r5364 | bugman | 2008-04-07 16:30:28 +0200 (Mon, 07 Apr 2008) | 3 lines
Wrote the atom_loop() API function for the Scientific Python PDB structure
object.
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[... 141 lines stripped ...]
r5397 - /1.2/