svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup
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r24352 | bugman | 2014-06-27 17:47:15 +0200 (Fri, 27 Jun 2014) | 7 lines
Shifted the rotor generation for the frame order geometric representation into its own function.
This is the specific_analyses.frame_order.geometric.add_rotors() function which adds the rotors are
new structures to a given internal structural object. The code has been extended to add support for
the double rotor model.
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r24358 | bugman | 2014-06-27 18:36:44 +0200 (Fri, 27 Jun 2014) | 6 lines
Removed unused imports.
This is from the splitting of the specific_analyses.frame_order.uf module into the new geometric
module.
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r24366 | bugman | 2014-07-01 09:13:39 +0200 (Tue, 01 Jul 2014) | 6 lines
Fix for the pivots created by the specific_analyses.frame_order.data.generate_pivot() function.
This is for the double rotor model where the 1st mode of motion is about the 2nd pivot, and the 2nd
mode of motion about the 1st pivot.
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r24367 | bugman | 2014-07-01 11:11:25 +0200 (Tue, 01 Jul 2014) | 5 lines
Fixes for the cone geometric representation in the internal structural object.
The representation can now be created if the given MoleculeContainer object is empty.
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r24368 | bugman | 2014-07-01 11:40:21 +0200 (Tue, 01 Jul 2014) | 10 lines
Refactored the frame order geometric motional representation code.
The code of the specific_analyses.frame_order.geometric.create_geometric_rep() function has been
spun out into 3 new functions: add_rotors(), add_axes(), and add_cones(). This is to better isolate
the various elements to allow for better control. Each function now adds the atoms for its
geometric representation to a separate molecule called 'axes' or 'cones'. The add_rotors() does not
create a molecule as the lib.structure.represent.rotor.rotor_pdb() function creates its own. As
part of the rafactorisation, the neg_cone flag has been eliminated.
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r24369 | bugman | 2014-07-01 11:46:58 +0200 (Tue, 01 Jul 2014) | 7 lines
Renamed the residues of the rotor geometric object representation.
The rotor axis atoms now belong to the RTX residue and the propeller blades to the RTB residue. The
'RT' at the start represents the rotor and this will allow all the geometric objects to be better
isolated.
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r24370 | bugman | 2014-07-01 11:59:05 +0200 (Tue, 01 Jul 2014) | 7 lines
Improvements to the internal structural object _get_chemical_name() method.
This now uses a translation table to convert the hetID or residue name into a description, for
example as used in the PDB HETNAM records to give a human readable description of the residue inside
the PDB file itself. The new rotor RTX and RTB residue names have been added to the table as well.
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r24371 | bugman | 2014-07-01 12:04:41 +0200 (Tue, 01 Jul 2014) | 3 lines
Typo fix for r24368, the 'cones' molecule was mistyped.
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r24372 | bugman | 2014-07-01 12:18:03 +0200 (Tue, 01 Jul 2014) | 10 lines
Renaming of the residues of the cone geometric representation.
The cone apex or centre is now the CNC residue, the cone axis is now CNX and the cone edge is now
CNE. These used to be APX, AXE, and EDG respectively. The aim is to make these names 100% specific
to the cone object so that they can be more easily selected for manipulating the representation and
so that they are more easily identifiable. The internal structural object _get_chemical_name()
function now returns a description for each of these. Note that the main cone object is still named
CON.
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r24373 | bugman | 2014-07-01 12:42:41 +0200 (Tue, 01 Jul 2014) | 8 lines
The motional pivots for the frame order models are now labelled in the geometric representation.
The pivot points are now added as a new molecule called 'pivots' in the frame_order.pdb_model user
function. The atoms all belong to the PIV residue. The pymol.frame_order user function now selects
this residue, hides its atoms, and then shows the atom name 'Piv' as the label. For the double
rotor model, the atom names 'Piv1' and 'Piv2' are used to differentiate the pivots.
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r24374 | bugman | 2014-07-01 12:51:23 +0200 (Tue, 01 Jul 2014) | 6 lines
Renamed the lib.structure.represent.rotor.rotor_pdb() function to rotor().
This function is not PDB specific and it just creates a 3D structural representation of a rotor
object.
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r24375 | bugman | 2014-07-01 13:49:54 +0200 (Tue, 01 Jul 2014) | 15 lines
Added support for labels in the rotor geometric object for the internal structural object.
The labels are created by the frame_order.pdb_model user function backend. For the double rotor
model, these are 'x-ax' and 'y-ax'. For all other models, the label is 'z-ax'.
The labels are then sent into the lib.structure.represent.rotor.rotor() function via the new label
argument. This function adds two new atoms to the rotor molecule which are 2 Angstrom outside of
the rotor span and lying on the rotor axis. These then have their atom name set to the label. The
residue name is set to the new RTL name which has been added to the internal structural object
_get_chemical_name() method to describe the residue in the PDB file for the user.
Finally the pymol.frame_order user function selects these atoms, hides them and then labels them
using the atom name (x-ax, y-ax, or z-ax).
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r24376 | bugman | 2014-07-01 14:20:02 +0200 (Tue, 01 Jul 2014) | 5 lines
Modified the rotor representation generated by the pymol.frame_order user function.
This is to make the object less bulky.
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r24377 | bugman | 2014-07-01 16:17:10 +0200 (Tue, 01 Jul 2014) | 17 lines
Redesign of the axis geometric representation for the frame order motions.
This is now much more model dependent to avoid clashes with the rotor objects and other
representations:
- For the torsionless isotropic cone, a single z-axis is created.
- For the double rotor, a single z-axis is produced connecting the two pivots, from pivot2 to pivot1.
- For the pseudo-ellipse and free rotor pseudo-ellipse, the x and y-axes are created.
- For the torsionless pseudo-ellipse, all three x, y and z-axes are created.
- For all other models, no axis system is produced as this has been made redundant by the rotor
objects.
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r24378 | bugman | 2014-07-01 16:26:41 +0200 (Tue, 01 Jul 2014) | 5 lines
Fixes for the cone geometric object created by the frame_order.pdb_model user function.
This was broken by the code refactoring and now works again for the pseudo-ellipse models.
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r24379 | bugman | 2014-07-01 16:46:08 +0200 (Tue, 01 Jul 2014) | 8 lines
Fix for the pymol.frame_order user function.
The representation function for the rotor objects was hiding all parts of the representation, hence
the pivot labels where being hidden. To fix this, the hiding of the geometric object now occurs in
the base frame_order_geometric() function prior to setting up the representations for the various
objects.
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r24385 | bugman | 2014-07-01 18:08:30 +0200 (Tue, 01 Jul 2014) | 11 lines
Started to redesign the frame_order.pdb_model user function.
Instead of having the positive and negative representations in different PDB models, and the Monte
Carlo simulations in different molecules, these will now all be shifted into separate files.
For this to be possible, the file root rather than file names must now be supplied to the
frame_order.pdb_model user function. To allow for different file compression, the compress_type
argument is now used. The backend code correctly handles the file root change, but the multiple
files are not created yet.
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r24397 | bugman | 2014-07-02 09:54:00 +0200 (Wed, 02 Jul 2014) | 19 lines
Python 3 fixes using the 2to3 script.
Fatal changes to the multi.processor module were reverted.
The command used was:
2to3 -j 4 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
.
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r24402 | bugman | 2014-07-02 11:57:18 +0200 (Wed, 02 Jul 2014) | 5 lines
Improvements to the lib.structure.represent.rotor.rotor() function for handling models.
The 'rotor', 'rotor2', or 'rotor3' molecule name determination is now also model specific.
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r24403 | bugman | 2014-07-02 11:59:23 +0200 (Wed, 02 Jul 2014) | 7 lines
The frame order generate_pivot() function can now return the pivots for Monte Carlo simulations.
This is the specific_analyses.frame_order.data.generate_pivot() function. The sim_index argument
has been added to the function which will allow the pivots from the Monte Carlo simulations to be
returned. If the pivot was fixed, then the original pivot will be returned instead.
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r24404 | bugman | 2014-07-02 13:40:45 +0200 (Wed, 02 Jul 2014) | 3 lines
Test suite fixes for the recent redesign of the frame_order.pdb_model user function.
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r24405 | bugman | 2014-07-02 13:42:36 +0200 (Wed, 02 Jul 2014) | 3 lines
Fixes for the frame_order.pdb_model user function for the rotor and free rotor models.
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r24406 | bugman | 2014-07-02 13:59:36 +0200 (Wed, 02 Jul 2014) | 17 lines
Redesign of the geometric object representation part of the frame_order.pdb_model user function.
The positive and negative representations of the frame order motions have been separated out into
two PDB files rather than being two models of one PDB file. This will help the user understand that
there are two identical representations of the motions, as both will now be displayed rather than
having to understand the model concept of PyMOL. The file root is taken, for example 'frame_order',
and the files 'frame_order_pos.pdb' and 'frame_order_neg.pdb' are created. If no inverse
representation exists for the model, the file 'frame_order.pdb' will be created instead.
The Monte Carlo simulations are now also treated differently. Rather than showing multiple vectors
in the axes representation component within one molecule in the same file as the frame order
representation, these are now in their own file and each simulation is now a different model. If an
inverse representation is present, then the positive representation will go into the file
'frame_order_sim_pos.pdb', for example, and the negative representation into the file
'frame_order_sim_neg.pdb'. Otherwise the file 'frame_order_sim.pdb' will be created.
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r24409 | bugman | 2014-07-02 14:51:29 +0200 (Wed, 02 Jul 2014) | 5 lines
Clean up of the frame_order.pdb_model user function definitions.
Some elements were no longer of use, and some descriptions have been updated.
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r24410 | bugman | 2014-07-02 14:53:21 +0200 (Wed, 02 Jul 2014) | 6 lines
Redesign of the pymol.frame_order user function to match the redesign of frame_order.pdb_model.
The file names are no longer given but rather the file root. Then all PDB files matching that file
root in the given directory will be loaded into PyMOL.
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r24411 | bugman | 2014-07-02 15:19:46 +0200 (Wed, 02 Jul 2014) | 5 lines
Updated all of the frame order scripts for the frame_order.pdb_model and pymol.frame_order changes.
These are the scripts for the CaM frame order test data.
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