relax SVN archive

Created the structural API base are_bonded() method - this is for determining if 2 atoms are bonded.

This is a method stub which raises a RelaxImplementError.

Started to add the backend of the relax_data.dipole_pair user function.

A few changes to the relax_data.dipole_pair user function definition.

Shifted the dipole-dipole graphics to the Wizard directory, as this is a wizard graphic.

Created graphics for the magnetic dipole-dipole interaction.

Removed the bond length from the model-free parameter list.

The bond length setting via value.set has no been merged into relax_data.dipole_pair.

This averaged length is dipole-dipole distance and does not need to be a model-free parameter.

Added the definition for the new relax_data.dipole_pair user function.

Redesigned the model-free dauvergne_protocol.py system test script for the interatomic concept.

The new script will be used to redesign how to set up a model-free analysis using the interatomic
data concept. It adds the new relax_data.dipole_pair user function which will be used to define the
dipolar relaxation interaction (this will inadvertently allow multi-dipole relation). The
heteronuc_type and proton_type parameters have been replaced with the spin_type parameter, as now
both the heternuclear and homonuclear spins need to be loaded into relax.

Merged revisions 16887,16889,16891,16900-16916 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r16887 | bugman | 2012-06-12 21:12:00 +0200 (Tue, 12 Jun 2012) | 3 lines

Created a script for converting svn logs into the format for release messages.
........
r16889 | bugman | 2012-06-12 23:39:44 +0200 (Tue, 12 Jun 2012) | 6 lines

Merged the changes to the CHANGES file from the 2.0.0 tag back into the trunk.

The command used was:
svn merge -r16887:r16888 svn+ssh://bugman@.../svn/relax/tags/2.0.0
........
r16891 | bugman | 2012-06-12 23:52:04 +0200 (Tue, 12 Jun 2012) | 6 lines

Merged the remainder of the 2.0.0 tag CHANGES file changes back to trunk.

The command used was:
svn merge -r16889:r16890 svn+ssh://bugman@.../svn/relax/tags/2.0.0
........
r16900 | bugman | 2012-06-13 17:06:56 +0200 (Wed, 13 Jun 2012) | 3 lines

Hack for the relax_fit C module compilation to detect supported CPUs for Mac OS X cross compilation.
........
r16901 | bugman | 2012-06-13 20:36:49 +0200 (Wed, 13 Jun 2012) | 3 lines

Improved the debugging drawing for the about GUI elements.
........
r16902 | bugman | 2012-06-13 21:10:14 +0200 (Wed, 13 Jun 2012) | 7 lines

Bug fix for sizing of the GUI about dialogs - the virtual sizes are now accurately calculated.

To do this, the window contents (a wx.BufferedDC instance) is created twice, with the virtual window
size exactly calculated in the first pass, and then used to set up the device context in the second.
A space is also now added to the end to ensure the border is there.
........
r16903 | bugman | 2012-06-13 21:11:44 +0200 (Wed, 13 Jun 2012) | 5 lines

Bug fix for the model-free analysis tab about window - sometimes a grey region would appear at the bottom.

This is a problem in at least GTK+ as scrolling is in increments of 20!
........
r16904 | bugman | 2012-06-13 21:45:56 +0200 (Wed, 13 Jun 2012) | 5 lines

Bug fix for the grey about windows on MS Windows!

All the about windows were grey. The temporary wxPython 2.9.3.1 fix was breaking the Windows GUI!
........
r16905 | bugman | 2012-06-13 21:51:27 +0200 (Wed, 13 Jun 2012) | 6 lines

The about model-free dialog no longer has grey at the bottom in MS Windows.

The wx.ScrolledWindow.GetScrollPixelsPerUnit() function is now used to determine how many pixels the
y scrolling is, and rounds up the virtual size based on that.
........
r16906 | bugman | 2012-06-13 22:47:51 +0200 (Wed, 13 Jun 2012) | 3 lines

Added the status/weather-snow-scattered-night Oxygen icon as a wizard graphic for the temperature uf.
........
r16907 | bugman | 2012-06-14 00:05:46 +0200 (Thu, 14 Jun 2012) | 7 lines

Created the gui.misc.bitmap_setup() function for handling bitmap alpha correctly on operating systems.

This function is required to handle alpha in bitmap on MS Windows so that regions with partial
transparency are not blended into the default dark grey colour of Windows' windows.
........
r16908 | bugman | 2012-06-14 14:38:37 +0200 (Thu, 14 Jun 2012) | 6 lines

Initialised a look up table in the cdp.mol structure for faster spin access.

This look up table will be slowly transitioned to, and should significantly speed up certain
operations.
........
r16909 | bugman | 2012-06-14 14:54:56 +0200 (Thu, 14 Jun 2012) | 8 lines

Started to fill up the spin ID look up table.

The index_molecule() and index_residue() functions have been added to determine the MoleculeList and
ResidueList indices of given molecules and residues. These are used by the create_spin for
efficiency and to allow the indices (together with the spin index and spin ID string) to be
assembled into the look up table. This table is not used anywhere yet.
........
r16910 | bugman | 2012-06-14 15:40:44 +0200 (Thu, 14 Jun 2012) | 6 lines

generic_fns.mol_res_spin.create_pseudo_spin() is now adding data to the spin ID look up table.

To support this, the return_residue() method now takes the 'indices' argument and returns the
molecule and residue indices.
........
r16911 | bugman | 2012-06-14 16:07:52 +0200 (Thu, 14 Jun 2012) | 3 lines

Created generic_fns.mol_res_spin.return_spin_from_id() for returning spin containers from spin IDs.
........
r16912 | bugman | 2012-06-14 16:14:08 +0200 (Thu, 14 Jun 2012) | 3 lines

Fix for return_residue() for a bug introduced at r16910.
........
r16913 | bugman | 2012-06-14 16:24:16 +0200 (Thu, 14 Jun 2012) | 3 lines

Fix for the gui.misc.bitmap_setup() function for Mac OS X - all bitmaps with alpha had black backgrounds!
........
r16914 | bugman | 2012-06-14 16:27:58 +0200 (Thu, 14 Jun 2012) | 5 lines

Added the 'pipe' argument to generic_fns.mol_res_spin.return_spin_from_id().

This is to mimic the return_spin() function.
........
r16915 | bugman | 2012-06-14 16:34:52 +0200 (Thu, 14 Jun 2012) | 5 lines

return_spin_from_id() now defaults to return_spin() when the spin ID is not in the lookup table.

The slower return_spin() method will allow return_spin_from_id() to always be functional.
........
r16916 | bugman | 2012-06-14 17:38:57 +0200 (Thu, 14 Jun 2012) | 6 lines

Renamed return_spin_from_id() to return_spin(), and return_spin() to return_spin_from_selection().

This shaves off a number of seconds from the system test - the look up table speed ups will come
with support in the other mol_res_spin module functions.
........