Merged revisions 18474-18509 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk
........
r18474 | bugman | 2013-02-18 11:23:39 +0100 (Mon, 18 Feb 2013) | 5 lines
Created the Structure.test_delete_multi_pipe system test.
This is to check that the structure.delete user function is operating on a single data pipe.
........
r18475 | bugman | 2013-02-18 11:24:08 +0100 (Mon, 18 Feb 2013) | 3 lines
Updated the Freecode instructions in the release checklist document.
........
r18476 | bugman | 2013-02-18 11:58:57 +0100 (Mon, 18 Feb 2013) | 6 lines
Created the simple Structure.test_delete_empty system test.
This is to demonstrate a failure of the structure.delete user function when no structural data is
present.
........
r18477 | bugman | 2013-02-18 12:05:01 +0100 (Mon, 18 Feb 2013) | 7 lines
Fixes for the structure.delete user function.
This can now handle no data being present, the spin and interatomic data containers are now have
their structural data properly deleted, and printouts have been added so the user knows what has
happened.
........
r18478 | bugman | 2013-02-18 12:14:13 +0100 (Mon, 18 Feb 2013) | 3 lines
Added a printout to structure.delete for when no structures are present.
........
r18479 | bugman | 2013-02-18 17:31:35 +0100 (Mon, 18 Feb 2013) | 5 lines
Created the Structure.test_rmsd system test.
This test checks the currently unimplemented structure.add_model and structure.rmsd user functions.
........
r18480 | bugman | 2013-02-18 17:51:51 +0100 (Mon, 18 Feb 2013) | 3 lines
The structural API num_molecules() method can now handle no data being present.
........
r18481 | bugman | 2013-02-18 17:56:39 +0100 (Mon, 18 Feb 2013) | 3 lines
Implemented the structure.add_model user function.
........
r18482 | bugman | 2013-02-18 17:59:31 +0100 (Mon, 18 Feb 2013) | 3 lines
Added some more checks to the Structure.test_rmsd system test.
........
r18483 | bugman | 2013-02-18 18:07:01 +0100 (Mon, 18 Feb 2013) | 3 lines
Modified the structure.add_model calls in the Structure.test_rmsd system test to include model nums.
........
r18484 | bugman | 2013-02-18 18:08:05 +0100 (Mon, 18 Feb 2013) | 3 lines
Added the 'model_num' argument to the structure.add_model user function.
........
r18485 | bugman | 2013-02-18 18:16:32 +0100 (Mon, 18 Feb 2013) | 3 lines
Bug fix for the arg_check.is_float_matrix() function for when the dimensions are not given.
........
r18486 | bugman | 2013-02-18 18:32:51 +0100 (Mon, 18 Feb 2013) | 5 lines
Modified the structure.add_atom user function to allow the position argument to be a rank-2 array.
This allows a different coordinate for each model to be specified.
........
r18487 | bugman | 2013-02-18 18:41:19 +0100 (Mon, 18 Feb 2013) | 6 lines
Spun out the atomic_rmsd() and calc_mean_structure() functions into their own module.
They were previously in the generic_fns.structure.superimpose module but are now in the new
generic_fns.structure.statistics module.
........
r18488 | bugman | 2013-02-18 18:52:39 +0100 (Mon, 18 Feb 2013) | 6 lines
Added checks for the atomic information to the Structure.test_rmsd system test.
This demonstrates a failure of structure.add_atom user function when specifying different positions
for the different models.
........
r18489 | bugman | 2013-02-18 18:54:17 +0100 (Mon, 18 Feb 2013) | 5 lines
Fix for the structure.add_atom user function for the internal structural object.
The atomic positions for each model are now correctly set.
........
r18490 | bugman | 2013-02-18 18:56:49 +0100 (Mon, 18 Feb 2013) | 3 lines
Docstring addition for the generic_fns.structure.statistics.atomic_rmsd() function.
........
r18491 | bugman | 2013-02-18 18:57:13 +0100 (Mon, 18 Feb 2013) | 3 lines
Implemented the structure.rmsd user function.
........
r18492 | bugman | 2013-02-18 19:11:52 +0100 (Mon, 18 Feb 2013) | 3 lines
Fixes for the Structure.test_rmsd system test - it now passes.
........
r18493 | bugman | 2013-02-18 20:56:50 +0100 (Mon, 18 Feb 2013) | 6 lines
Created a new float_object argument type which is used by the 'pos' argument of structure.add_atom.
A new arg_check.float_object() function has been created to handle any float object greater than
rank-0.
........
r18494 | bugman | 2013-02-18 20:58:10 +0100 (Mon, 18 Feb 2013) | 3 lines
Updated the generic_fns.structure package __all__ variable to include the statistics module.
........
r18495 | bugman | 2013-02-18 21:20:06 +0100 (Mon, 18 Feb 2013) | 3 lines
Printout improvements for the structure.rmsd user function.
........
r18496 | bugman | 2013-02-18 21:26:12 +0100 (Mon, 18 Feb 2013) | 6 lines
Created the Structure.test_rmsd_ubi system test to better check the structure.rmsd user function.
This uses the truncated ubiquitin ensemble in the test suite shared data directories. The RMSD
matches the VMD 1.9.1 output.
........
r18497 | bugman | 2013-02-19 16:46:47 +0100 (Tue, 19 Feb 2013) | 7 lines
Added a new module generic_fns.structure.pdb_write for generating the PDB records.
This decouples the formatting code from the internal structural obect. The PDB format has been
updated to version 3.30. There is one function for each PDB record, allowing this to be easily
extended and kept up to date.
........
r18498 | bugman | 2013-02-19 17:14:24 +0100 (Tue, 19 Feb 2013) | 3 lines
Formatting fixes for the generic_fns.structure.pdb_write module.
........
r18499 | bugman | 2013-02-19 17:37:08 +0100 (Tue, 19 Feb 2013) | 7 lines
Created the generic_fns.structure.pdb_read module.
This replaces the internal structural object _parse_pdb_record() method which was handling both
ATOM+HETATM and CONECT records. It should allow greater flexibility in reading data out of other
PDB records in the future. There is one function per PDB record type in this module.
........
r18500 | bugman | 2013-02-19 17:51:06 +0100 (Tue, 19 Feb 2013) | 6 lines
Fix for the unit tests of the generic_fns.structure package.
The _parse_pdb_record() is now covered by the new pdb_read module, so its unit tests have also been
shifted into a new module.
........
r18501 | bugman | 2013-02-19 17:58:22 +0100 (Tue, 19 Feb 2013) | 6 lines
Added the full 1UBQ PDB structure to the relax test-suite shared data directories.
This is a small, very quick to read structure which will be used for validating the reading and
writing of different PDB record types.
........
r18502 | bugman | 2013-02-19 18:12:54 +0100 (Tue, 19 Feb 2013) | 8 lines
Changes to the internal structural object.
The _parse_models_pdb() method has been renamed to _parse_pdb_coord() and the opening of the PDB
file shifted into the base load_pdb() method. This is in preparation for better parsing of PDB
files to match the main sections of the PDB format, see
http://www.wwpdb.org/documentation/format33/v3.3.html.
........
r18503 | bugman | 2013-02-19 21:33:59 +0100 (Tue, 19 Feb 2013) | 5 lines
Created the Structure.test_read_pdb_1UBQ to check the complete parsing of the complex PDB file.
The test is currently quite basic and needs to check more of the internal structural object.
........
r18504 | bugman | 2013-02-19 21:45:50 +0100 (Tue, 19 Feb 2013) | 3 lines
Better checks for the atomic data in the Structure.test_read_pdb_1UBQ system test.
........
r18505 | bugman | 2013-02-19 21:54:11 +0100 (Tue, 19 Feb 2013) | 8 lines
Added a series of _parse_pdb_*() methods to the internal structural object.
These correspond to each section of the PDB format version 3.30
http://www.wwpdb.org/documentation/format33/v3.3.html. The currently loop over the records of their
section, returning the remaining PDB records. The aim is for fast parsing and breaking into
sections.
........
r18506 | bugman | 2013-02-19 22:03:41 +0100 (Tue, 19 Feb 2013) | 5 lines
Faster PDB parsing by the removal of the use of the re.search() function.
Now line slices are directly compared instead.
........
r18507 | bugman | 2013-02-19 22:13:53 +0100 (Tue, 19 Feb 2013) | 5 lines
Added some more unit tests for the generic_fns.structure.pdb_read module.
These tests are not yet complete, as it is unknown what these unimplemented functions will return.
........
r18508 | bugman | 2013-02-19 22:40:14 +0100 (Tue, 19 Feb 2013) | 3 lines
Completed the unit test of the generic_fns.structure.pdb_read.helix() function.
........
r18509 | bugman | 2013-02-19 22:41:03 +0100 (Tue, 19 Feb 2013) | 3 lines
Implemented the generic_fns.structure.pdb_read.helix() function.
........
