svn+ssh://bugman@.../svn/relax/trunk
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r18573 | bugman | 2013-02-27 19:40:48 +0100 (Wed, 27 Feb 2013) | 7 lines
Created the structure.web_of_motion user function.
This is used to create a special PDB file which represents the atomic motions between different
structural models. Identical atoms of the selected models are concatenated into one model, within
a temporary internal structural object, and linked together using PDB CONECT records.
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r18574 | bugman | 2013-02-27 19:58:36 +0100 (Wed, 27 Feb 2013) | 3 lines
A new PDB file with 3 models and a few atoms for testing of the structure.web_of_motion user function.
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r18575 | bugman | 2013-02-27 20:10:47 +0100 (Wed, 27 Feb 2013) | 5 lines
Created the Structure.test_web_of_motion_all system test.
This is to check the new structure.web_of_motion user function.
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r18576 | bugman | 2013-02-27 20:18:51 +0100 (Wed, 27 Feb 2013) | 3 lines
The structure.web_of_motion user function can now handle file objects as well as file names as input.
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r18577 | bugman | 2013-02-27 20:20:50 +0100 (Wed, 27 Feb 2013) | 3 lines
Small fixes for the Structure.test_web_of_motion_all system test.
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r18578 | bugman | 2013-02-27 20:23:31 +0100 (Wed, 27 Feb 2013) | 3 lines
Created the Structure.test_web_of_motion_12 system test to show how model sets are currently ignored.
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r18579 | bugman | 2013-02-27 20:37:06 +0100 (Wed, 27 Feb 2013) | 6 lines
Implemented the models argument for the structure.web_of_motion user function.
This was previously not being used and was caught by the Structure.test_web_of_motion_12 system
test.
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r18580 | bugman | 2013-02-27 20:37:51 +0100 (Wed, 27 Feb 2013) | 5 lines
Fixes for the Structure.test_web_of_motion_12 system test.
The PDB output was not compared to the correct results.
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r18581 | bugman | 2013-02-27 20:40:05 +0100 (Wed, 27 Feb 2013) | 6 lines
Created the Structure.test_web_of_motion_13 system test.
This was just to be sure that the models argument was correctly handled by the structure.web_of_motion
user function.
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r18582 | bugman | 2013-03-01 14:05:26 +0100 (Fri, 01 Mar 2013) | 5 lines
The structure.find_pivot user function now accepts the func_tol argument.
This is used to terminate the simplex optimisation when this function tolerance value is reached.
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r18583 | bugman | 2013-03-01 15:19:35 +0100 (Fri, 01 Mar 2013) | 3 lines
Shifted the ensemble pivot finding target function into the maths_fns package.
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r18584 | bugman | 2013-03-01 16:02:03 +0100 (Fri, 01 Mar 2013) | 3 lines
Added a sentence to the README file about the sample_scripts directory.
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r18585 | bugman | 2013-03-01 16:07:15 +0100 (Fri, 01 Mar 2013) | 3 lines
Added a document detailing the possible future layout of relax's packages.
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r18586 | bugman | 2013-03-01 16:11:09 +0100 (Fri, 01 Mar 2013) | 3 lines
Import fix for the shift of the pivot finder target function.
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r18587 | bugman | 2013-03-01 17:41:31 +0100 (Fri, 01 Mar 2013) | 9 lines
The structure.find_pivot user function now uses the logarithmic barrier function.
This is for constrained optimisation and requires the newest minfx code. The pivot position is
constrained within a box of +/- 1000 Angstroms from zero. This is needed for when the solution is
an infinite line - i.e. a rotation axis and not a pivot point. Previously the simplex optimisation
would head toward + or - infinity. But now with a logarithmic barrier, the simplex algorithm can
stabilise and find a point on the axis very quickly, long before reaching the edges of the box.
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r18588 | bugman | 2013-03-01 18:18:44 +0100 (Fri, 01 Mar 2013) | 6 lines
The structure.find_pivot user function now accepts the func_tol and box_limit arguments.
This allows the function tolerance for the simplex optimisation to be specified, as well as the
size of the box to constrain the pivot to be within.
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