Author: bugman
Date: Tue Mar 19 17:36:36 2013
New Revision: 18895
URL: http://svn.gna.org/viewcvs/relax?rev=18895&view=rev
Log:
Merged revisions 18866-18892,18894 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
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r18866 | bugman | 2013-03-19 10:05:43 +0100 (Tue, 19 Mar 2013) | 16 lines
Reverted r18858 as this change was incorrect.
The command used was:
svn merge -r18858:r18857 .
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r18858 | bugman | 2013-03-18 15:27:56 +0100 (Mon, 18 Mar 2013) | 5 lines
Changed paths:
M /trunk/generic_fns/structure/api_base.py
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.
.....
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r18867 | bugman | 2013-03-19 10:18:19 +0100 (Tue, 19 Mar 2013) | 5 lines
Proper fix for the pack_structs() structural API method.
This was incorrectly done in r18858, but now the index of the new molecule
is handled correctly.
........
r18868 | bugman | 2013-03-19 11:04:15 +0100 (Tue, 19 Mar 2013) | 6 lines
Sections of molecules can now be deleted using the structure.delete user
function.
The atom ID argument has been added and this is now propagated into the
internal structural object.
This ID string can be used to delete subsets of the 3D structural data in
the relax data store.
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r18869 | bugman | 2013-03-19 11:05:09 +0100 (Tue, 19 Mar 2013) | 5 lines
Created the Structure.test_read_write_pdb_1UBQ system test.
This is for checking the use of the structure.delete user function with the
atom ID argument.
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r18870 | bugman | 2013-03-19 11:09:17 +0100 (Tue, 19 Mar 2013) | 7 lines
The Structure.test_read_write_pdb_1UBQ system test now checks for HELIX and
SHEET records.
This is not implemented yet, but the idea is that the structure.read_pdb
and structure.write_pdb
should preserve the helix and sheet information present in the original PDB
and that the internal
structural object should store this information.
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r18871 | bugman | 2013-03-19 11:18:15 +0100 (Tue, 19 Mar 2013) | 3 lines
Trailing whitespace removal.
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r18872 | bugman | 2013-03-19 11:35:11 +0100 (Tue, 19 Mar 2013) | 6 lines
Created the internal structural object _pdb_chain_id_to_mol_index() method.
This will be used to convert PDB chain IDs, which are used to indicate
different molecules in the
PDB, into molecule indices for the internal structural object.
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r18873 | bugman | 2013-03-19 11:37:50 +0100 (Tue, 19 Mar 2013) | 5 lines
Fix for the internal structural object _pdb_chain_id_to_mol_index() method.
This was accidentally set to be a method of the MolContainer class and not
the internal object.
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r18874 | bugman | 2013-03-19 13:48:34 +0100 (Tue, 19 Mar 2013) | 6 lines
HELIX PDB records are now read, stored, and written out by the internal
structural object.
This affects the structure.read_pdb and structure.write_pdb user functions.
The helix is stored as
a metadata type object - its elements do not correspond to the atoms in the
structural object.
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r18875 | bugman | 2013-03-19 13:55:15 +0100 (Tue, 19 Mar 2013) | 6 lines
SHEET PDB records are now read, stored, and written out by the internal
structural object.
This affects the structure.read_pdb and structure.write_pdb user functions.
The sheet is stored as
a metadata type object - its elements do not correspond to the atoms in the
structural object.
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r18876 | bugman | 2013-03-19 14:50:58 +0100 (Tue, 19 Mar 2013) | 3 lines
Created 13 unit tests of the Internal._trim_helix() internal structural
object method.
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r18877 | bugman | 2013-03-19 15:03:22 +0100 (Tue, 19 Mar 2013) | 3 lines
Added the index_flag argument to all structural API atom_loop() methods.
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r18878 | bugman | 2013-03-19 15:04:36 +0100 (Tue, 19 Mar 2013) | 3 lines
Docstring editing of the ScientificPython structural object atom_loop()
method.
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r18879 | bugman | 2013-03-19 15:08:55 +0100 (Tue, 19 Mar 2013) | 5 lines
Fixes for some unit tests of the internal structural object for the changes
to the atom_loop().
Single elements are now returned as single elements rather than a tuple of
length 1.
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r18880 | bugman | 2013-03-19 15:11:20 +0100 (Tue, 19 Mar 2013) | 5 lines
Fix for the unit test of the generic_fns.structure.pdb_write.helix()
function.
The init_seq_id argument is now called init_seq_num to match the PDB
notation.
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r18881 | bugman | 2013-03-19 15:31:17 +0100 (Tue, 19 Mar 2013) | 3 lines
Fixes for some of the new unit tests of the internal structural object
_trim_helix() method.
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r18882 | bugman | 2013-03-19 15:40:02 +0100 (Tue, 19 Mar 2013) | 8 lines
Implemented the internal structural object _trim_helix() method.
This is used when the structure.delete user function is called to trim and
remove the helix
metadata. For this to work, the additional method _residue_data() was
written to create a
dictionary with residue numbers as keys and the residue names as numbers.
This dictionary is used
by _trim_helix() to change the residue names in the helix metadata.
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r18883 | bugman | 2013-03-19 15:53:52 +0100 (Tue, 19 Mar 2013) | 5 lines
Modified all of the unit tests of the internal structural object
_trim_helix() method.
The structure of the helix metadata in the internal structural object was
not correctly mimicked.
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r18884 | bugman | 2013-03-19 15:54:28 +0100 (Tue, 19 Mar 2013) | 3 lines
Fix for the internal structural object _trim_helix() method for the helix
metadata format.
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r18885 | bugman | 2013-03-19 16:24:02 +0100 (Tue, 19 Mar 2013) | 5 lines
Fixes for the helix metadata deletion for the internal structural object.
This affects the structure.delete user function.
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r18886 | bugman | 2013-03-19 16:45:03 +0100 (Tue, 19 Mar 2013) | 5 lines
Created 13 unit tests of the Internal._trim_sheet() internal structural
object method.
These are mirror the 13 unit tests of Internal._trim_helix().
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r18887 | bugman | 2013-03-19 16:50:27 +0100 (Tue, 19 Mar 2013) | 6 lines
Implemented the Internal._trim_sheet() internal structural object method.
This is also now used by the structure.delete user function to remove sheet
metadata for residues
which no longer exist.
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r18888 | bugman | 2013-03-19 17:02:52 +0100 (Tue, 19 Mar 2013) | 6 lines
Modified the ScientificPython structural object atom_loop() method to match
the internal object.
If only one element is returned from the atom_loop(), then this is returned
as a single item rather
than a tuple of length 1.
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r18889 | bugman | 2013-03-19 17:04:24 +0100 (Tue, 19 Mar 2013) | 5 lines
Lots of fixes for the change to the structural API atom_loop() method.
This method when returning a single item now returns a single item rather
than a tuple of length 1.
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r18890 | bugman | 2013-03-19 17:07:16 +0100 (Tue, 19 Mar 2013) | 5 lines
Fix for the structure.write_pdb user function for the internal structural
object.
Helix and sheet PDB record creation is now skipped if no helices or sheets
are defined.
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r18891 | bugman | 2013-03-19 17:09:28 +0100 (Tue, 19 Mar 2013) | 3 lines
The index_flag argument to the ScientificPython structural object
atom_loop() method is now used.
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r18892 | bugman | 2013-03-19 17:11:04 +0100 (Tue, 19 Mar 2013) | 3 lines
Fix for the Structure.test_load_scientific_results system test for the
atom_loop() structural object changes.
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r18894 | bugman | 2013-03-19 17:26:00 +0100 (Tue, 19 Mar 2013) | 5 lines
Fix for some unit tests of the Scientific_data.atom_loop() method.
This is for the recent changes to the structural API atom_loop() method.
........
Modified:
branches/frame_order_testing/ (props changed)
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/pdb_write.py
branches/frame_order_testing/generic_fns/structure/scientific.py
branches/frame_order_testing/test_suite/system_tests/structure.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_pdb_write.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/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/api_base.py?rev=18895&r1=18894&r2=18895&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=18895&r1=18894&r2=18895&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=18895&r1=18894&r2=18895&view=diff
Modified: branches/frame_order_testing/generic_fns/structure/pdb_write.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/pdb_write.py?rev=18895&r1=18894&r2=18895&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=18895&r1=18894&r2=18895&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=18895&r1=18894&r2=18895&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=18895&r1=18894&r2=18895&view=diff
Modified:
branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/test_pdb_write.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/unit_tests/_generic_fns/_structure/test_pdb_write.py?rev=18895&r1=18894&r2=18895&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=18895&r1=18894&r2=18895&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=18895&r1=18894&r2=18895&view=diff
r18895 - in /branches/frame_order_testing: ./ generic_fns/structure/ test_suite/system_tests/ test_suite/unit_tests/_generic...