Author: bugman
Date: Fri Mar 1 19:16:46 2013
New Revision: 18589
URL: http://svn.gna.org/viewcvs/relax?rev=18589&view=rev
Log:
Merged revisions 18573-18588 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
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.
........
Added:
branches/frame_order_testing/docs/package_layout
- copied unchanged from r18588, trunk/docs/package_layout
branches/frame_order_testing/maths_fns/ens_pivot_finder.py
- copied unchanged from r18588, trunk/maths_fns/ens_pivot_finder.py
branches/frame_order_testing/test_suite/shared_data/structures/web_of_motion.pdb
- copied unchanged from r18588,
trunk/test_suite/shared_data/structures/web_of_motion.pdb
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/README
branches/frame_order_testing/generic_fns/structure/main.py
branches/frame_order_testing/generic_fns/structure/superimpose.py
branches/frame_order_testing/test_suite/system_tests/structure.py
branches/frame_order_testing/user_functions/structure.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_testing/README
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/README?rev=18589&r1=18588&r2=18589&view=diff
Modified: branches/frame_order_testing/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/main.py?rev=18589&r1=18588&r2=18589&view=diff
Modified: branches/frame_order_testing/generic_fns/structure/superimpose.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/superimpose.py?rev=18589&r1=18588&r2=18589&view=diff
Modified: branches/frame_order_testing/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/structure.py?rev=18589&r1=18588&r2=18589&view=diff
Modified: branches/frame_order_testing/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/user_functions/structure.py?rev=18589&r1=18588&r2=18589&view=diff
r18589 - in /branches/frame_order_testing: ./ docs/ generic_fns/structure/ maths_fns/ test_suite/shared_data/structures/ tes...