relax SVN archive

Python 3 fix for an import into the generic_fns.structure.internal module.

Removed some debugging printouts.

Merged revisions 18896-18897 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r18896 | bugman | 2013-03-19 18:14:13 +0100 (Tue, 19 Mar 2013) | 6 lines

Created the Structure.test_metadata_xml system test.

This is used to check that the structural metadata (currently helices and sheets) are stored in the
relax XML save files and then can be read back into relax again.
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r18897 | bugman | 2013-03-19 18:31:39 +0100 (Tue, 19 Mar 2013) | 3 lines

The helix and sheet metadata is now stored in and read from relax XML state files.
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The helix and sheet metadata is now stored in and read from relax XML state files.

Created the Structure.test_metadata_xml system test.

This is used to check that the structural metadata (currently helices and sheets) are stored in the
relax XML save files and then can be read back into relax again.

Merged revisions 18866-18892,18894 via svnmerge from
svn+ssh://bugman@.../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.
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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.
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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.

Fixes for the average structure creation component of the frame_order.pdb_model user function.

The correct pivot point for the average domain position rotation is now taken into account for when
the position is set to the CoM.

Fix for the Structure.test_load_scientific_results system test for the atom_loop() structural object changes.

The index_flag argument to the ScientificPython structural object atom_loop() method is now used.