relax SVN archive

Updated the test_suite.unit_tests package __all__ list to be more modern.

Updated the maths_fns package __all__ list.

Added empty packages to the unit tests for the lib and lib.geometry packages.

Initialised the lib.geometry package.

This will be a library of all mathematics functions relating to geometry.

Initialised a new package called 'lib'.

This will in the future be an extensive collection of functions, methods, classes, objects, etc.
useful for the study of all types of molecular dynamics.

Merged revisions 18573-18588 via svnmerge from
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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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.

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.

Import fix for the shift of the pivot finder target function.

Added a document detailing the possible future layout of relax's packages.