Author: bugman
Date: Mon Mar 18 15:35:04 2013
New Revision: 18860
URL: http://svn.gna.org/viewcvs/relax?rev=18860&view=rev
Log:
Merged revisions 18847-18859 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r18847 | bugman | 2013-03-18 13:19:29 +0100 (Mon, 18 Mar 2013) | 11 lines
Added a comment to the output from value.display and value.write to
describe the parameter.
This idea is discussed at
http://thread.gmane.org/gmane.science.nmr.relax.user/1428.
The idea is to take the parameter description from the specific analysis
API and add it to the top
of the file or output. This is to help understand what the Rex value are.
For example for the Rex
parameter the first line would be:
# Parameter description: Chemical exchange relaxation (sigma_ex = Rex /
omega**2).
........
r18848 | bugman | 2013-03-18 13:34:02 +0100 (Mon, 18 Mar 2013) | 8 lines
Created the Structure.test_read_merge system test to test a new concept -
merging of structures.
The idea is to add the merge argument to the structure.read_pdb user
function to allow two different
structures in two PDB files to be merged. This is useful if structures of
individual domains have
have been solved separately and are located in two PDB files. Then with
the merge flag, you will
not need to use and external program or hand edit PDB files to join them.
........
r18849 | bugman | 2013-03-18 13:41:23 +0100 (Mon, 18 Mar 2013) | 5 lines
Added the merge flag to the structure.read_pdb user function.
This currently does nothing.
........
r18850 | bugman | 2013-03-18 13:42:16 +0100 (Mon, 18 Mar 2013) | 3 lines
Docstring fix for the structure.read_pdb user function backend.
........
r18851 | bugman | 2013-03-18 13:51:56 +0100 (Mon, 18 Mar 2013) | 5 lines
The merge flag for the structure.read_pdb user function is now propaged to
the pack_structs() method.
This structure API method calls the ModelList.merge_item() method which is
yet to be implemented.
........
r18852 | bugman | 2013-03-18 13:56:17 +0100 (Mon, 18 Mar 2013) | 6 lines
The MolList.add_item() structural API method now returns the added molecule
container.
This is used by the pack_structs() method to alias the molecule, and will
be required when structure
merging is implemented.
........
r18853 | bugman | 2013-03-18 14:10:36 +0100 (Mon, 18 Mar 2013) | 3 lines
Replaced many instances of the tab character '\t' with 4 spaces.
........
r18854 | bugman | 2013-03-18 14:25:05 +0100 (Mon, 18 Mar 2013) | 3 lines
Fix for a copy and paste error in the Structure.test_read_merge system test.
........
r18855 | bugman | 2013-03-18 14:48:13 +0100 (Mon, 18 Mar 2013) | 5 lines
Fixes for all the Ap4Aase truncated PDB files.
The atom numbers are now sequential, as defined by the PDB standard.
........
r18856 | bugman | 2013-03-18 14:48:59 +0100 (Mon, 18 Mar 2013) | 5 lines
Implemented the merging of structural objects.
This allows the merge flag of the structure.read_pdb user function to work.
........
r18857 | bugman | 2013-03-18 15:18:36 +0100 (Mon, 18 Mar 2013) | 3 lines
Fixes for the test suite for the changes to the Ap4Aase PDB file atom
numbering at r18855.
........
r18858 | bugman | 2013-03-18 15:27:56 +0100 (Mon, 18 Mar 2013) | 5 lines
Bug fix for the structural data consistency test in the pack_structs()
structural API method.
The index was not correct causing failures in certain rare cases.
........
r18859 | bugman | 2013-03-18 15:31:04 +0100 (Mon, 18 Mar 2013) | 5 lines
The printouts from the structure.read_pdb user function are now different
with the merge flag set.
The text now says that the molecules are being merged rather than added.
........
Added:
branches/frame_order_testing/test_suite/shared_data/structures/Ap4Aase_res1-6.pdb
- copied unchanged from r18859,
trunk/test_suite/shared_data/structures/Ap4Aase_res1-6.pdb
branches/frame_order_testing/test_suite/shared_data/structures/Ap4Aase_res7-12.pdb
- copied unchanged from r18859,
trunk/test_suite/shared_data/structures/Ap4Aase_res7-12.pdb
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/generic_fns/relax_data.py
branches/frame_order_testing/generic_fns/structure/api_base.py
branches/frame_order_testing/generic_fns/structure/internal.py
branches/frame_order_testing/generic_fns/structure/main.py
branches/frame_order_testing/generic_fns/structure/scientific.py
branches/frame_order_testing/generic_fns/value.py
branches/frame_order_testing/gui/analyses/elements.py
branches/frame_order_testing/maths_fns/c_chi2.c
branches/frame_order_testing/maths_fns/exponential.c
branches/frame_order_testing/multi/uni_processor.py
branches/frame_order_testing/opendx/isosurface_3D.py
branches/frame_order_testing/test_suite/shared_data/structures/Ap4Aase_res1-12.pdb
branches/frame_order_testing/test_suite/system_tests/angles.py
branches/frame_order_testing/test_suite/system_tests/scripts/curve_fitting/bug_18789_no_grace_errors.py
branches/frame_order_testing/test_suite/system_tests/sequence.py
branches/frame_order_testing/test_suite/system_tests/structure.py
branches/frame_order_testing/test_suite/system_tests/unit_vectors.py
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/test_internal.py
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/test_scientific.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/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/relax_data.py?rev=18860&r1=18859&r2=18860&view=diff
Modified: branches/frame_order_testing/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/api_base.py?rev=18860&r1=18859&r2=18860&view=diff
Modified: branches/frame_order_testing/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/internal.py?rev=18860&r1=18859&r2=18860&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=18860&r1=18859&r2=18860&view=diff
Modified: branches/frame_order_testing/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/scientific.py?rev=18860&r1=18859&r2=18860&view=diff
Modified: branches/frame_order_testing/generic_fns/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/value.py?rev=18860&r1=18859&r2=18860&view=diff
Modified: branches/frame_order_testing/gui/analyses/elements.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/gui/analyses/elements.py?rev=18860&r1=18859&r2=18860&view=diff
Modified: branches/frame_order_testing/maths_fns/c_chi2.c
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/maths_fns/c_chi2.c?rev=18860&r1=18859&r2=18860&view=diff
Modified: branches/frame_order_testing/maths_fns/exponential.c
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/maths_fns/exponential.c?rev=18860&r1=18859&r2=18860&view=diff
Modified: branches/frame_order_testing/multi/uni_processor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/multi/uni_processor.py?rev=18860&r1=18859&r2=18860&view=diff
Modified: branches/frame_order_testing/opendx/isosurface_3D.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/opendx/isosurface_3D.py?rev=18860&r1=18859&r2=18860&view=diff
Modified:
branches/frame_order_testing/test_suite/shared_data/structures/Ap4Aase_res1-12.pdb
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/structures/Ap4Aase_res1-12.pdb?rev=18860&r1=18859&r2=18860&view=diff
Modified: branches/frame_order_testing/test_suite/system_tests/angles.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/angles.py?rev=18860&r1=18859&r2=18860&view=diff
Modified:
branches/frame_order_testing/test_suite/system_tests/scripts/curve_fitting/bug_18789_no_grace_errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/scripts/curve_fitting/bug_18789_no_grace_errors.py?rev=18860&r1=18859&r2=18860&view=diff
Modified: branches/frame_order_testing/test_suite/system_tests/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/sequence.py?rev=18860&r1=18859&r2=18860&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=18860&r1=18859&r2=18860&view=diff
Modified: branches/frame_order_testing/test_suite/system_tests/unit_vectors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/unit_vectors.py?rev=18860&r1=18859&r2=18860&view=diff
Modified:
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/test_internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/test_internal.py?rev=18860&r1=18859&r2=18860&view=diff
Modified:
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py?rev=18860&r1=18859&r2=18860&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=18860&r1=18859&r2=18860&view=diff
r18860 - in /branches/frame_order_testing: ./ generic_fns/ generic_fns/structure/ gui/analyses/ maths_fns/ multi/ opendx/ te...