relax SVN archive

Massive speed up of the internal structural object add_model() method.

This speeds up the structure.add_model user function, as well as many internal relax operations on
the structural object. Instead of using the copy.deepcopy() function to duplicate an already
existing structural model, now new molecule container objects are created and then the individual
elements of the original molecule container data lists are copied one by one. This avoids copying a
lot of internal Python junk and hence the copying operation is now orders of magnitude faster.

Merged revisions 25982 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25982 | tlinnet | 2014-09-23 20:06:27 +0200 (Tue, 23 Sep 2014) | 3 lines

Implemented the sampling sparseness instead of NI on the graph axis.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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Updated the lib.frame_order.simulation.brownian() function.

This now uses the internal structural object selection object logic - the selection() method is
called to obtain the Internal_selection object, and this is then passed into the rotation() method.

Implemented the sampling sparseness instead of NI on the graph axis.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.

Fixes for the specific_analyses.frame_order.geometric.average_position() function.

The recent trunk changes with the structural object Internal_selection class required a change in
this function.

Merged revisions 25971-25979 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r25971 | bugman | 2014-09-23 18:02:05 +0200 (Tue, 23 Sep 2014) | 8 lines

Created a special internal structural object selection object.

This will be used for massively speeding up the internal structural object. The use of the
lib.selection module by the internal structural object is currently very slow as a huge number of
calls to re.search() are required. The idea is to avoid this by using lib.selection once to
populate this new selection object, and then reusing this object to loop over molecules and atoms.
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r25972 | bugman | 2014-09-23 18:05:23 +0200 (Tue, 23 Sep 2014) | 8 lines

Added the selection() method to the internal structural object.

This parses the atom ID string using the lib.selection module, loops over the molecules and atoms,
performs matches using re.search() via lib.selection, and populates and returns the new
Internal_selection object. This can be used to pre-process the atom ID string to save huge amounts
of time.
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r25973 | bugman | 2014-09-23 18:12:45 +0200 (Tue, 23 Sep 2014) | 5 lines

The internal structural object validate_models() method now accepts the verbosity argument.

This is used to silence printouts.
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r25974 | bugman | 2014-09-23 18:13:12 +0200 (Tue, 23 Sep 2014) | 3 lines

Missing import of the Internal_selection class.
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r25975 | bugman | 2014-09-23 18:14:12 +0200 (Tue, 23 Sep 2014) | 3 lines

Indentation fix for the internal structural object validate_model() method.
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r25976 | bugman | 2014-09-23 18:21:42 +0200 (Tue, 23 Sep 2014) | 5 lines

Fixes for the new structural object Internal_selection object.

The atom indices are not stored via the molecule index.
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r25977 | bugman | 2014-09-23 18:43:56 +0200 (Tue, 23 Sep 2014) | 6 lines

Converted the rotate() and translate() structural object methods to use the new selection object.

The atom_id arguments have been replaced with selection arguments. Therefore all parts of relax
which call these methods must first call selection() to obtain the Internal_selection instance.
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r25978 | bugman | 2014-09-23 18:55:47 +0200 (Tue, 23 Sep 2014) | 5 lines

Created the structural object Internal_selection.mol_loop() method.

This is to simply quickly loop over all molecule indices of the selection object.
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r25979 | bugman | 2014-09-23 19:50:46 +0200 (Tue, 23 Sep 2014) | 8 lines

Converted all structural object methods to use the selection object rather that atom ID strings.

This should have a significant impact on the speed of certain operations within relax. The most
obvious effect will be a huge speed up of the interatom.define user function. There should be speed
ups with a number of other user functions relating to structural information. All parts of relax
have been updated for the change.
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Converted all structural object methods to use the selection object rather that atom ID strings.

This should have a significant impact on the speed of certain operations within relax. The most
obvious effect will be a huge speed up of the interatom.define user function. There should be speed
ups with a number of other user functions relating to structural information. All parts of relax
have been updated for the change.

Created the structural object Internal_selection.mol_loop() method.

This is to simply quickly loop over all molecule indices of the selection object.

Converted the rotate() and translate() structural object methods to use the new selection object.

The atom_id arguments have been replaced with selection arguments. Therefore all parts of relax
which call these methods must first call selection() to obtain the Internal_selection instance.

Fixes for the new structural object Internal_selection object.

The atom indices are not stored via the molecule index.