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Commit Date  
[r18499] by bugman

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.

2013-02-19 16:37:08 Tree
[r18498] by bugman

Formatting fixes for the generic_fns.structure.pdb_write module.

2013-02-19 16:14:24 Tree
[r18497] by bugman

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.

2013-02-19 15:46:47 Tree
[r18496] by bugman

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.

2013-02-18 20:26:12 Tree
[r18495] by bugman

Printout improvements for the structure.rmsd user function.

2013-02-18 20:20:06 Tree
[r18494] by bugman

Updated the generic_fns.structure package __all__ variable to include the statistics module.

2013-02-18 19:58:10 Tree
[r18493] by bugman

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.

2013-02-18 19:56:50 Tree
[r18492] by bugman

Fixes for the Structure.test_rmsd system test - it now passes.

2013-02-18 18:11:52 Tree
[r18491] by bugman

Implemented the structure.rmsd user function.

2013-02-18 17:57:13 Tree
[r18490] by bugman

Docstring addition for the generic_fns.structure.statistics.atomic_rmsd() function.

2013-02-18 17:56:49 Tree
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