relax SVN archive

Merged revisions 9068-9069,9081,9194-9196,9198-9200,9202-9230 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

................
r9068 | bugman | 2009-06-08 16:21:38 +0200 (Mon, 08 Jun 2009) | 3 lines

Added a function for calculating the Kronecker product.
................
r9069 | bugman | 2009-06-08 17:13:54 +0200 (Mon, 08 Jun 2009) | 3 lines

Added a copyright notice and spun out the T14 transpose into its own function.
................
r9081 | bugman | 2009-06-18 15:01:00 +0200 (Thu, 18 Jun 2009) | 3 lines

Added numpy int and float data types to the list of tested user function args.
................
r9194 | bugman | 2009-07-12 23:55:17 +0200 (Sun, 12 Jul 2009) | 3 lines

Commented out a data type temporarily until someone complains about int32 types.
................
r9195 | bugman | 2009-07-13 00:03:51 +0200 (Mon, 13 Jul 2009) | 5 lines

Created lists of number types (python and numpy).

These are in the prompt.num_types module and are now used by value.set() for argument checking.
................
r9196 | bugman | 2009-07-13 00:05:31 +0200 (Mon, 13 Jul 2009) | 6 lines

Reverted r9194, the temporary commenting out of a data type.

The command used was:
svn merge -r9194:9193 .
................
r9198 | bugman | 2009-07-13 00:07:41 +0200 (Mon, 13 Jul 2009) | 3 lines

Initialized merge tracking via "svnmerge" with revisions "1-9069" from
svn+ssh://bugman@.../svn/relax/branches/frame_order
................
r9199 | bugman | 2009-07-13 00:11:11 +0200 (Mon, 13 Jul 2009) | 566 lines

Merged revisions 9070-9187,9190-9196,9198 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order

........
r9070 | bugman | 2009-06-17 19:27:42 +0200 (Wed, 17 Jun 2009) | 3 lines

Created a branch for the new Frame Order theories.
........
r9071 | bugman | 2009-06-17 19:34:39 +0200 (Wed, 17 Jun 2009) | 3 lines

Added Frame Order to the list of allowable data pipes.
........
r9072 | bugman | 2009-06-17 19:36:36 +0200 (Wed, 17 Jun 2009) | 3 lines

Added a stub package for Frame Order related calculation code.
........
r9073 | bugman | 2009-06-17 20:03:58 +0200 (Wed, 17 Jun 2009) | 3 lines

Added a function for printing out the 2nd degree Frame Order matrix.
........
r9074 | bugman | 2009-06-17 20:05:50 +0200 (Wed, 17 Jun 2009) | 3 lines

Shifted the print_frame_order_2nd_degree() function to generic_fns.
........
r9075 | bugman | 2009-06-17 20:10:17 +0200 (Wed, 17 Jun 2009) | 3 lines

Added a missing import.
........
r9076 | bugman | 2009-06-17 20:30:26 +0200 (Wed, 17 Jun 2009) | 3 lines

Added functions for populating the Frame Order matrices for isotropic cones.
........
r9077 | bugman | 2009-06-18 10:41:27 +0200 (Thu, 18 Jun 2009) | 5 lines

Renamed the frame_order package to frame_order_matrix_ops.

This is to make way for the target function code.
........
r9078 | bugman | 2009-06-18 10:42:31 +0200 (Thu, 18 Jun 2009) | 6 lines

Added the Frame Order target function class.

It currently contains only one target function for an isotropic cone model directly optimised to the
Frame Order matrix elements.
........
r9079 | bugman | 2009-06-18 10:47:30 +0200 (Thu, 18 Jun 2009) | 3 lines

A few fixes for the Frame_order class.
........
r9080 | bugman | 2009-06-18 11:29:22 +0200 (Thu, 18 Jun 2009) | 3 lines

Aliased self.func_iso_cone_elements to self.func.
........
r9082 | bugman | 2009-06-18 22:04:39 +0200 (Thu, 18 Jun 2009) | 3 lines

Renamed the user function n_state_model.set_type() to align_tensor.reduction().
........
r9083 | bugman | 2009-06-18 22:15:18 +0200 (Thu, 18 Jun 2009) | 3 lines

Shifted the N-state model set_type() method to the align_tensor function reduction().
........
r9084 | bugman | 2009-06-19 10:18:35 +0200 (Fri, 19 Jun 2009) | 3 lines

Added the Frame Order theories to the setup of the specific code.
........
r9085 | bugman | 2009-06-19 10:30:00 +0200 (Fri, 19 Jun 2009) | 3 lines

Added the skeleton of the Frame Order specific code.
........
r9086 | bugman | 2009-06-19 10:31:03 +0200 (Fri, 19 Jun 2009) | 3 lines

Added the Frame Order type to get_string().
........
r9087 | bugman | 2009-06-19 10:43:37 +0200 (Fri, 19 Jun 2009) | 3 lines

Implemented most of the grid_search() method.
........
r9088 | bugman | 2009-06-19 10:50:19 +0200 (Fri, 19 Jun 2009) | 5 lines

Created the Frame Order user function class.

The only user function yet available is frame_order.select_model().
........
r9089 | bugman | 2009-06-19 10:51:59 +0200 (Fri, 19 Jun 2009) | 3 lines

Registered the Frame Order user function class into the interpreter.
........
r9090 | bugman | 2009-06-19 10:55:28 +0200 (Fri, 19 Jun 2009) | 3 lines

Wrote the select_model() method.
........
r9091 | bugman | 2009-06-19 10:58:47 +0200 (Fri, 19 Jun 2009) | 3 lines

Added the __update_model() method.
........
r9092 | bugman | 2009-06-19 11:01:22 +0200 (Fri, 19 Jun 2009) | 3 lines

Some fixed for the grid_search() method.
........
r9093 | bugman | 2009-06-19 11:29:00 +0200 (Fri, 19 Jun 2009) | 3 lines

Modifications to the __update_model() method.
........
r9094 | bugman | 2009-06-19 11:44:57 +0200 (Fri, 19 Jun 2009) | 5 lines

Wrote the minimise() and __unpack_opt_results() methods.

The minimise() method is rudimentary and will not work.
........
r9095 | bugman | 2009-06-19 11:50:26 +0200 (Fri, 19 Jun 2009) | 3 lines

Modified the __init__() method and spun of some code into __init_iso_cone_elements().
........
r9096 | bugman | 2009-06-19 11:51:24 +0200 (Fri, 19 Jun 2009) | 3 lines

Docstring update.
........
r9097 | bugman | 2009-06-19 11:52:00 +0200 (Fri, 19 Jun 2009) | 3 lines

Missing RelaxError import.
........
r9098 | bugman | 2009-06-19 15:27:08 +0200 (Fri, 19 Jun 2009) | 3 lines

Fixes for the minimise() method.
........
r9099 | bugman | 2009-06-19 15:57:11 +0200 (Fri, 19 Jun 2009) | 3 lines

Created the compile_2nd_matrix_iso_cone() function for building the 2nd degree Frame Order matrix.
........
r9100 | bugman | 2009-06-19 16:03:20 +0200 (Fri, 19 Jun 2009) | 3 lines

Shifted more code into the compile_2nd_matrix_iso_cone() function.
........
r9101 | bugman | 2009-06-19 16:05:14 +0200 (Fri, 19 Jun 2009) | 3 lines

Fixed the arguments of compile_2nd_matrix_iso_cone().
........
r9102 | bugman | 2009-06-19 16:06:39 +0200 (Fri, 19 Jun 2009) | 3 lines

Missing numpy imports.
........
r9103 | bugman | 2009-06-19 16:07:41 +0200 (Fri, 19 Jun 2009) | 5 lines

Preliminary support for optimisation against alignment tensors.

Added the func_iso_cone() and __init_iso_cone() methods.
........
r9104 | bugman | 2009-06-19 16:09:33 +0200 (Fri, 19 Jun 2009) | 3 lines

Added a check for incorrectly supplied arguments.
........
r9105 | bugman | 2009-06-19 16:35:47 +0200 (Fri, 19 Jun 2009) | 3 lines

Created the __minimise_setup_tensors() method to compile the data needed for optimisation.
........
r9106 | bugman | 2009-06-19 16:39:03 +0200 (Fri, 19 Jun 2009) | 3 lines

Modified the reduction() function to store alignment tensor indices rather than names.
........
r9107 | bugman | 2009-06-19 16:41:15 +0200 (Fri, 19 Jun 2009) | 3 lines

Fixed for the __minimise_setup_tensors() method.
........
r9108 | bugman | 2009-06-19 16:42:19 +0200 (Fri, 19 Jun 2009) | 3 lines

Fix for the frame_order_models.Frame_order setup within minimise().
........
r9109 | bugman | 2009-06-19 16:43:16 +0200 (Fri, 19 Jun 2009) | 3 lines

Removed an unused print statement.
........
r9110 | bugman | 2009-06-19 16:50:03 +0200 (Fri, 19 Jun 2009) | 3 lines

Docstring fixes and variable renaming in __minimise_setup_tensors().
........
r9111 | bugman | 2009-06-19 16:51:53 +0200 (Fri, 19 Jun 2009) | 3 lines

Docstring updates.
........
r9112 | bugman | 2009-06-19 16:52:04 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fix for the tensor optimisation.
........
r9113 | bugman | 2009-06-19 17:12:57 +0200 (Fri, 19 Jun 2009) | 3 lines

Temporary fix for func_iso_cone().
........
r9114 | bugman | 2009-06-19 17:15:33 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fixes for the __unpack_opt_results() method.
........
r9115 | bugman | 2009-06-19 17:21:56 +0200 (Fri, 19 Jun 2009) | 3 lines

Parameter values are initialised to zero so that a grid search is not necessary.
........
r9116 | bugman | 2009-06-19 17:31:41 +0200 (Fri, 19 Jun 2009) | 6 lines

Fix for the compilation of the Frame Order matrix.

The compile_2nd_matrix_iso_cone() function now returns the matrix as it is now in a different
memory location.
........
r9117 | bugman | 2009-06-19 19:22:07 +0200 (Fri, 19 Jun 2009) | 5 lines

Added the function reduce_alignment_tensor().

This calculates how the Frame Order matrix reduces the alignment tensor.
........
r9118 | bugman | 2009-06-19 19:22:29 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fix for reduce_alignment_tensor().
........
r9119 | bugman | 2009-06-19 19:22:59 +0200 (Fri, 19 Jun 2009) | 3 lines

The reduced tensors are now back calculated.
........
r9120 | bugman | 2009-06-19 19:23:23 +0200 (Fri, 19 Jun 2009) | 3 lines

Simplification of func_iso_cone().
........
r9121 | bugman | 2009-06-19 19:23:48 +0200 (Fri, 19 Jun 2009) | 3 lines

Another bug fix for reduce_alignment_tensor().
........
r9122 | bugman | 2009-06-19 19:24:19 +0200 (Fri, 19 Jun 2009) | 3 lines

Imported reduce_alignment_tensor().
........
r9123 | bugman | 2009-06-19 19:25:09 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fix for func_iso_cone().
........
r9124 | bugman | 2009-06-19 19:25:33 +0200 (Fri, 19 Jun 2009) | 3 lines

Another bug fix for reduce_alignment_tensor().
........
r9125 | bugman | 2009-06-19 19:30:06 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fix for the initialisation of self.red_tensors_bc.
........
r9126 | bugman | 2009-06-19 19:42:51 +0200 (Fri, 19 Jun 2009) | 3 lines

Made the default errors more reasonable.
........
r9127 | bugman | 2009-06-22 19:52:00 +0200 (Mon, 22 Jun 2009) | 3 lines

Bug fix for the reduce_alignment_tensor() function.
........
r9128 | bugman | 2009-06-23 11:14:13 +0200 (Tue, 23 Jun 2009) | 5 lines

Elimination of an Euler angle from the isotropic cone model.

Only the cone axis theta and phi angles are now optimised.
........
r9129 | bugman | 2009-06-23 11:20:16 +0200 (Tue, 23 Jun 2009) | 3 lines

Set up the z-axis data structures.
........
r9130 | bugman | 2009-06-23 11:31:59 +0200 (Tue, 23 Jun 2009) | 3 lines

Added the cone axis storage structure.
........
r9131 | bugman | 2009-06-23 11:32:19 +0200 (Tue, 23 Jun 2009) | 3 lines

Updated the compile_2nd_matrix_iso_cone() function to use the cone axis angles rather than Euler.
........
r9132 | bugman | 2009-06-23 11:37:05 +0200 (Tue, 23 Jun 2009) | 5 lines

Bug fix for compile_2nd_matrix_iso_cone().

The rotation matrix uses the polar angle, not the cone angle.
........
r9133 | bugman | 2009-06-23 12:58:40 +0200 (Tue, 23 Jun 2009) | 5 lines

Bug fix for the compile_2nd_matrix_iso_cone() function.

The cross product of 2 normal vectors is not a normal vector!!!
........
r9134 | bugman | 2009-06-23 13:42:26 +0200 (Tue, 23 Jun 2009) | 5 lines

Removed the sequence test in the Monte Carlo create_data() function.

No all data pipes in relax require sequence info.
........
r9135 | bugman | 2009-06-23 14:23:53 +0200 (Tue, 23 Jun 2009) | 3 lines

Added a dummy eliminate() method.
........
r9136 | bugman | 2009-06-23 16:22:12 +0200 (Tue, 23 Jun 2009) | 19 lines

Added the ability to perform Monte Carlo sims for the Frame Order theories.

For this, the following methods have been added:
__tensor_loop()
back_calc()
base_data_loop()
create_mc_data()
data_names()
model_loop()
return_error()
set_selected_sim()
sim_init_values()
sim_pack_data()
sim_return_param()
sim_return_selected()

Many other methods have also been modified.
........
r9137 | bugman | 2009-06-23 16:45:44 +0200 (Tue, 23 Jun 2009) | 3 lines

Updated the init() and set() method to allow alignment tensor errors to be input.
........
r9138 | bugman | 2009-06-23 17:41:52 +0200 (Tue, 23 Jun 2009) | 3 lines

More fixes for error setting in the set() function.
........
r9139 | bugman | 2009-06-23 17:52:07 +0200 (Tue, 23 Jun 2009) | 5 lines

Bug fix for the init() method.

Now errors are being placed in the pre-existing tensor, rather than a new tensor being added.
........
r9140 | bugman | 2009-06-23 18:19:49 +0200 (Tue, 23 Jun 2009) | 5 lines

Another bug fix for the init() method.

Errors are not properly handled for all input data types.
........
r9141 | bugman | 2009-06-23 19:23:11 +0200 (Tue, 23 Jun 2009) | 5 lines

Removed ambiguity from the align_tensor.reduction() user function.

The from_tensor and to_tensor args have been renamed to full_tensor and red_tensor respectively.
........
r9142 | bugman | 2009-06-25 12:00:41 +0200 (Thu, 25 Jun 2009) | 3 lines

Created the interface to the frame_order.cone_pdb() user function.
........
r9143 | bugman | 2009-06-25 13:17:53 +0200 (Thu, 25 Jun 2009) | 3 lines

Created the interface for the frame_order.pivot() user function.
........
r9144 | bugman | 2009-06-25 13:38:11 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fix for the R_2vect() function.

The rotation axis is not always of unit length!
........
r9145 | bugman | 2009-06-25 13:42:50 +0200 (Thu, 25 Jun 2009) | 3 lines

Spun out the cone axis generation code into generate_vector().
........
r9146 | bugman | 2009-06-25 13:45:54 +0200 (Thu, 25 Jun 2009) | 3 lines

Simplified compile_2nd_matrix_iso_cone() by using R_2vect().
........
r9147 | bugman | 2009-06-25 14:02:23 +0200 (Thu, 25 Jun 2009) | 3 lines

Bug fix for the generate_vector_residues() for numpy MC sim structures.
........
r9148 | bugman | 2009-06-25 14:03:36 +0200 (Thu, 25 Jun 2009) | 3 lines

Another bug fix for the generate_vector_residues() function for MC simulations.
........
r9149 | bugman | 2009-06-25 14:22:32 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fix for generate_vector_residues() when the neg flag is False.

The atoms were incorrectly numbered.
........
r9150 | bugman | 2009-06-25 14:24:51 +0200 (Thu, 25 Jun 2009) | 3 lines

Wrote the cone_pdb() and pivot() methods.
........
r9151 | bugman | 2009-06-25 15:02:34 +0200 (Thu, 25 Jun 2009) | 5 lines

Renaming and fixes for stitch_cone_to_edge().

This was stitch_cap_to_cone().
........
r9152 | bugman | 2009-06-25 15:24:01 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fixes for the write_pdb() method.

The Hetrogen section was failing with MC simulations.
........
r9153 | bugman | 2009-06-25 15:24:41 +0200 (Thu, 25 Jun 2009) | 3 lines

Fixes for the cone_pdb() method.
........
r9154 | bugman | 2009-06-25 15:58:39 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fixes for the generate_vector_dist() function.

The protons were not being correctly stitched together!
........
r9155 | bugman | 2009-06-25 16:02:26 +0200 (Thu, 25 Jun 2009) | 3 lines

Added a test for a loaded structure to the pymol.cartoon() user function.
........
r9156 | bugman | 2009-06-25 16:26:11 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fix for the pymol.cartoon() user function.

This was failing when multiple proteins were loaded.
........
r9157 | bugman | 2009-06-25 16:34:17 +0200 (Thu, 25 Jun 2009) | 3 lines

Changed the scaling arg to a direct size arg.
........
r9158 | bugman | 2009-06-25 16:36:00 +0200 (Thu, 25 Jun 2009) | 3 lines

cone_pdb() now handles the AXE residue.
........
r9159 | bugman | 2009-06-25 16:37:03 +0200 (Thu, 25 Jun 2009) | 3 lines

Renamed the axis atom from 'Axe' to 'Axis'.
........
r9160 | bugman | 2009-06-25 16:41:25 +0200 (Thu, 25 Jun 2009) | 3 lines

Made the cone_pdb() function less specific for the N-state model and added SIM as an axis to decorate.
........
r9161 | bugman | 2009-06-25 16:46:40 +0200 (Thu, 25 Jun 2009) | 3 lines

The user can now set the number of increments used to generate the cone PDB.
........
r9162 | bugman | 2009-06-29 10:24:03 +0200 (Mon, 29 Jun 2009) | 3 lines

Wrote the calculate() method for calculating the chi-squared value for the current parameters.
........
r9163 | bugman | 2009-06-29 10:25:13 +0200 (Mon, 29 Jun 2009) | 6 lines

Expansion of frame order to both the forward and reverse rotations.

reduce_alignment_tensor() was renamed to reduce_alignment_tensor_reverse(), and the new function
reduce_alignment_tensor() added.
........
r9164 | bugman | 2009-06-30 11:21:49 +0200 (Tue, 30 Jun 2009) | 3 lines

Added checks for the presence of the data structures necessary for frame_order.cone_pdb().
........
r9165 | bugman | 2009-06-30 11:24:12 +0200 (Tue, 30 Jun 2009) | 3 lines

Bug fix for frame_order.cone_pdb() for when no MC sims exist.
........
r9166 | bugman | 2009-06-30 11:43:31 +0200 (Tue, 30 Jun 2009) | 5 lines

Bug fix for the cone PDB generation.

If there were more than 1000 protons, the PDB file was corrupted by the proton name being too long.
........
r9167 | bugman | 2009-07-01 13:05:09 +0200 (Wed, 01 Jul 2009) | 6 lines

Reverted r9128 to r9133, the elimination of a Euler angle (maybe only temporarily).

The command used was:
svn merge -r9134:9127 .
........
r9168 | bugman | 2009-07-01 16:08:46 +0200 (Wed, 01 Jul 2009) | 3 lines

Renamed theta to theta cone (again due to the reversion).
........
r9169 | bugman | 2009-07-02 02:28:25 +0200 (Thu, 02 Jul 2009) | 3 lines

Missing import.
........
r9170 | bugman | 2009-07-02 02:33:45 +0200 (Thu, 02 Jul 2009) | 3 lines

The cone axis is back, and better support for the Euler angles.
........
r9171 | bugman | 2009-07-02 02:36:53 +0200 (Thu, 02 Jul 2009) | 3 lines

Return of the cone axis, and rotation of the reduced tensor.
........
r9172 | bugman | 2009-07-02 02:55:17 +0200 (Thu, 02 Jul 2009) | 6 lines

Partly reverted r9167 - the previous reversion.

The command used was:
svn merge -r9167:9166 generic_fns/monte_carlo.py
........
r9173 | bugman | 2009-07-02 02:58:54 +0200 (Thu, 02 Jul 2009) | 8 lines

Partly reverted r9167 - the previous revision.

The command used was:
svn merge -r9167:9166 maths_fns/frame_order_matrix_ops.py

This returns the cone axis.
........
r9174 | bugman | 2009-07-02 03:01:41 +0200 (Thu, 02 Jul 2009) | 6 lines

Partly reverted r9167 - the previous reversion.

The command used was:
svn merge -r9167:9166 maths_fns/frame_order_models.py
........
r9175 | bugman | 2009-07-02 03:02:12 +0200 (Thu, 02 Jul 2009) | 3 lines

Missing import.
........
r9176 | bugman | 2009-07-02 03:19:39 +0200 (Thu, 02 Jul 2009) | 3 lines

The Euler angles are now wrapped between 0 and 2pi.
........
r9177 | bugman | 2009-07-02 14:03:17 +0200 (Thu, 02 Jul 2009) | 3 lines

Added the new function R_to_axis_angle().
........
r9178 | bugman | 2009-07-02 15:25:08 +0200 (Thu, 02 Jul 2009) | 3 lines

Bug fix for the R_to_axis_angle() function. The axis needs to be normalised.
........
r9179 | bugman | 2009-07-02 15:25:40 +0200 (Thu, 02 Jul 2009) | 3 lines

Both the positive and negative cones are now made.
........
r9180 | bugman | 2009-07-02 16:50:51 +0200 (Thu, 02 Jul 2009) | 3 lines

Fixes for the negative cone.
........
r9181 | bugman | 2009-07-02 17:18:50 +0200 (Thu, 02 Jul 2009) | 3 lines

Fix for the N-state model arg checks.
........
r9182 | bugman | 2009-07-02 23:09:23 +0200 (Thu, 02 Jul 2009) | 3 lines

Bug fix for cone_pdb() for when no MC sims are run.
........
r9183 | bugman | 2009-07-02 23:13:13 +0200 (Thu, 02 Jul 2009) | 3 lines

Created and now using the full_in_ref_frame data structure (copy of N-state model).
........
r9184 | bugman | 2009-07-02 23:22:55 +0200 (Thu, 02 Jul 2009) | 3 lines

Added a check for the reference domain setup to __minimise_setup_tensors().
........
r9185 | bugman | 2009-07-02 23:25:33 +0200 (Thu, 02 Jul 2009) | 3 lines

Renamed n_state_model.set_domain() to align_tensor.set_domain().
........
r9186 | bugman | 2009-07-02 23:27:38 +0200 (Thu, 02 Jul 2009) | 3 lines

Shifted the set_domain() back-end from the N-state model to the alignment tensor.
........
r9187 | bugman | 2009-07-03 00:11:43 +0200 (Fri, 03 Jul 2009) | 3 lines

Added the interface for the frame_order.n_state_model() user function.
........
r9190 | bugman | 2009-07-12 23:31:31 +0200 (Sun, 12 Jul 2009) | 3 lines

Fixes for the unit tests of the user functions shifted from n_state_model to align_tensor.
........
r9191 | bugman | 2009-07-12 23:38:43 +0200 (Sun, 12 Jul 2009) | 3 lines

Fixes for the 5-state model system test.
........
r9192 | bugman | 2009-07-12 23:49:33 +0200 (Sun, 12 Jul 2009) | 3 lines

Modified the N-state model code to be more like the Frame Order matrix code.
........
r9193 | bugman | 2009-07-12 23:52:54 +0200 (Sun, 12 Jul 2009) | 3 lines

Copyright statement update.
........
................
r9200 | bugman | 2009-07-13 00:14:36 +0200 (Mon, 13 Jul 2009) | 3 lines

Removed merge properties.
................
r9202 | bugman | 2009-07-13 10:08:16 +0200 (Mon, 13 Jul 2009) | 7 lines

Removed all usages of float128, as this type is not present on all machines.

This was reported by Sebastian Morin in the post:
https://mail.gna.org/public/relax-devel/2009-07/msg00000.html (Message-id:
<4A5A7338.4030500@...>).
................
r9203 | bugman | 2009-07-13 15:16:27 +0200 (Mon, 13 Jul 2009) | 3 lines

Missing import.
................
r9204 | bugman | 2009-07-13 15:17:34 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fixes for the get_specific_fn() function.
................
r9205 | bugman | 2009-07-13 15:18:36 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fixes for the grace.write() user function.
................
r9206 | bugman | 2009-07-13 15:19:41 +0200 (Mon, 13 Jul 2009) | 5 lines

Bug fix for the molmol macro setup.

This was not being correctly retrieved.
................
r9207 | bugman | 2009-07-13 15:21:55 +0200 (Mon, 13 Jul 2009) | 3 lines

Changed the statistics ordering when running profiling.
................
r9208 | bugman | 2009-07-13 15:22:33 +0200 (Mon, 13 Jul 2009) | 3 lines

align_tensor.init() can now accept any type of float or int (python or numpy).
................
r9209 | bugman | 2009-07-13 16:28:58 +0200 (Mon, 13 Jul 2009) | 6 lines

Partial reversion of r9204.

The AttributeError should be checked for, not the NameError! NameError was only triggered by
another bug.
................
r9210 | bugman | 2009-07-13 18:29:31 +0200 (Mon, 13 Jul 2009) | 5 lines

Bug fixes for return_conversion_factor() and return_units() functions.

The spin and spin_id args are now accepted.
................
r9211 | bugman | 2009-07-13 18:30:04 +0200 (Mon, 13 Jul 2009) | 5 lines

Fix for the write_multi_header() function.

The spin_id variable now exists.
................
r9212 | bugman | 2009-07-13 18:30:45 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fix: The return_conversion_factor() method now accepts the spin arg.
................
r9213 | bugman | 2009-07-13 18:31:07 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fix: The return_units() method now accepts the spin_id keyword arg.
................
r9214 | bugman | 2009-07-13 18:32:32 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fix for the return_units() method, the spin_id keyword arg is now accepted.
................
r9215 | bugman | 2009-07-13 18:38:06 +0200 (Mon, 13 Jul 2009) | 5 lines

Fix for the return_units() method.

The spin and spin_id args are now accepted.
................
r9216 | bugman | 2009-07-14 11:04:22 +0200 (Tue, 14 Jul 2009) | 3 lines

Added a check for the chi-squared value for the 5-state model system test.
................
r9217 | bugman | 2009-07-14 11:26:12 +0200 (Tue, 14 Jul 2009) | 3 lines

Bug fix: The tensor reduction was specified back to front!
................
r9218 | bugman | 2009-07-14 11:26:55 +0200 (Tue, 14 Jul 2009) | 3 lines

Fix for the func_2domain() method for the N-state model tensor reduction code.
................
r9219 | bugman | 2009-07-14 11:27:30 +0200 (Tue, 14 Jul 2009) | 3 lines

Removed a debugging print out.
................
r9220 | bugman | 2009-07-14 11:31:51 +0200 (Tue, 14 Jul 2009) | 3 lines

Fixes for all the N-state model optimisation unit tests.
................
r9221 | bugman | 2009-07-14 11:49:22 +0200 (Tue, 14 Jul 2009) | 3 lines

Fix for the return_units() method. The spin and spin_id args are now accepted.
................
r9222 | bugman | 2009-07-14 12:02:38 +0200 (Tue, 14 Jul 2009) | 5 lines

Fixes for Tyler's peptide system test.

The residue was 111 in the PDB but 211 in the results file, and the spin was unnamed.
................
r9223 | bugman | 2009-07-14 13:24:30 +0200 (Tue, 14 Jul 2009) | 5 lines

Bug fix for the generate_vector_dist() function.

Now the diffusion tensor and cone geometric objects are correctly created!
................
r9224 | bugman | 2009-07-14 13:31:53 +0200 (Tue, 14 Jul 2009) | 5 lines

Bug fix for the generate_vector_residues() function.

Now the negative vector actually is negative! It was previously the same as the positive vector.
................
r9225 | bugman | 2009-07-14 14:10:30 +0200 (Tue, 14 Jul 2009) | 6 lines

Improvements for the reload_pdb() method.

Now the system path is searched for the PDB file. This allows the system tests to pass when not
running from the installation path.
................
r9226 | bugman | 2009-07-14 14:11:19 +0200 (Tue, 14 Jul 2009) | 3 lines

Extended the OMP model-free system test to run MC sims for the diffusion tensor.
................
r9227 | bugman | 2009-07-14 15:12:22 +0200 (Tue, 14 Jul 2009) | 5 lines

Bug fix for the setup of MC simulations of the diffusion tensor.

MC sims were not working when all parameters except for the diffusion tensor are fixed.
................
r9228 | bugman | 2009-07-14 15:26:28 +0200 (Tue, 14 Jul 2009) | 5 lines

Bug fixes for the OMP model-free system test.

The diffusion tensor MC simulation test was not functional.
................
r9229 | bugman | 2009-07-14 15:56:19 +0200 (Tue, 14 Jul 2009) | 5 lines

Fix for the checks in test_omp_analysis().

The wrong data pipe was being accessed.
................
r9230 | bugman | 2009-07-14 15:57:59 +0200 (Tue, 14 Jul 2009) | 5 lines

The diffusion and alignment tensor *_sim and *_err attributes are now listed as modifiable.

This means that this data is placed into the results file, and read back out again!
................

Merged revisions 9048-9066,9068-9069,9081,9194-9196,9198-9200,9202-9230 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

................
r9048 | bugman | 2009-05-12 10:47:02 +0200 (Tue, 12 May 2009) | 3 lines

Updated the pipes.hybridise() user function interface to the 1.3 line design.
................
r9049 | bugman | 2009-05-12 11:09:24 +0200 (Tue, 12 May 2009) | 3 lines

Added 3 new RelaxErrors for sequence matching.
................
r9050 | bugman | 2009-05-12 11:21:59 +0200 (Tue, 12 May 2009) | 3 lines

Added the pipe keyword to all the sequence counting functions.
................
r9051 | bugman | 2009-05-12 11:22:41 +0200 (Tue, 12 May 2009) | 3 lines

Renamed the hybridise() pipes keyword to pipe_list.
................
r9052 | bugman | 2009-05-12 11:25:38 +0200 (Tue, 12 May 2009) | 3 lines

Created the compare_sequence() for checking if 2 sequences are the same.
................
r9053 | bugman | 2009-05-12 11:28:49 +0200 (Tue, 12 May 2009) | 3 lines

Converted the hybridise() method to the 1.3 line design.
................
r9054 | bugman | 2009-05-12 11:31:08 +0200 (Tue, 12 May 2009) | 3 lines

Added the hybrid data pipe to the list of allowable data pipes.
................
r9055 | bugman | 2009-05-12 11:34:40 +0200 (Tue, 12 May 2009) | 3 lines

Added a check for the pipe type to hybridise().
................
r9056 | bugman | 2009-05-12 11:41:12 +0200 (Tue, 12 May 2009) | 3 lines

Converted the duplicate_data() method to the 1.3 line design.
................
r9057 | bugman | 2009-05-12 14:42:06 +0200 (Tue, 12 May 2009) | 3 lines

Removed a test that disallowed model selection between different pipe types.
................
r9058 | bugman | 2009-05-12 14:56:23 +0200 (Tue, 12 May 2009) | 5 lines

Converted all parts of the hybrid module to the 1.3 line design.

This includes the addition of many new, very simple methods and the translation of old code.
................
r9059 | bugman | 2009-05-15 10:47:59 +0200 (Fri, 15 May 2009) | 3 lines

Created the R_axis_angle() function to generate the rotation matrix from the axis-angle notation.
................
r9060 | bugman | 2009-05-15 11:58:55 +0200 (Fri, 15 May 2009) | 3 lines

Added the functions random_rot_axis() and random_R() to generate random rotations.
................
r9061 | bugman | 2009-05-25 13:45:14 +0200 (Mon, 25 May 2009) | 6 lines

Changed the precision of the te check in the model-free system tests.

This is in response to Sebastian's post at
https://mail.gna.org/public/relax-devel/2009-05/msg00003.html.
................
r9062 | bugman | 2009-05-28 15:37:08 +0200 (Thu, 28 May 2009) | 3 lines

Renamed random_R() to R_random_axis().
................
r9063 | bugman | 2009-05-28 15:57:48 +0200 (Thu, 28 May 2009) | 3 lines

Wrote 2 new functions, R_random_hypersphere() and quaternion_to_R().
................
r9064 | bugman | 2009-05-28 16:53:23 +0200 (Thu, 28 May 2009) | 3 lines

Bug fix for the quaternion_to_R() function.
................
r9065 | bugman | 2009-05-29 10:47:09 +0200 (Fri, 29 May 2009) | 3 lines

Fix for the align_tensor.init() user function docstring.
................
r9066 | bugman | 2009-06-02 13:54:11 +0200 (Tue, 02 Jun 2009) | 3 lines

Indentation fix.
................
r9068 | bugman | 2009-06-08 16:21:38 +0200 (Mon, 08 Jun 2009) | 3 lines

Added a function for calculating the Kronecker product.
................
r9069 | bugman | 2009-06-08 17:13:54 +0200 (Mon, 08 Jun 2009) | 3 lines

Added a copyright notice and spun out the T14 transpose into its own function.
................
r9081 | bugman | 2009-06-18 15:01:00 +0200 (Thu, 18 Jun 2009) | 3 lines

Added numpy int and float data types to the list of tested user function args.
................
r9194 | bugman | 2009-07-12 23:55:17 +0200 (Sun, 12 Jul 2009) | 3 lines

Commented out a data type temporarily until someone complains about int32 types.
................
r9195 | bugman | 2009-07-13 00:03:51 +0200 (Mon, 13 Jul 2009) | 5 lines

Created lists of number types (python and numpy).

These are in the prompt.num_types module and are now used by value.set() for argument checking.
................
r9196 | bugman | 2009-07-13 00:05:31 +0200 (Mon, 13 Jul 2009) | 6 lines

Reverted r9194, the temporary commenting out of a data type.

The command used was:
svn merge -r9194:9193 .
................
r9198 | bugman | 2009-07-13 00:07:41 +0200 (Mon, 13 Jul 2009) | 3 lines

Initialized merge tracking via "svnmerge" with revisions "1-9069" from
svn+ssh://bugman@.../svn/relax/branches/frame_order
................
r9199 | bugman | 2009-07-13 00:11:11 +0200 (Mon, 13 Jul 2009) | 566 lines

Merged revisions 9070-9187,9190-9196,9198 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order

........
r9070 | bugman | 2009-06-17 19:27:42 +0200 (Wed, 17 Jun 2009) | 3 lines

Created a branch for the new Frame Order theories.
........
r9071 | bugman | 2009-06-17 19:34:39 +0200 (Wed, 17 Jun 2009) | 3 lines

Added Frame Order to the list of allowable data pipes.
........
r9072 | bugman | 2009-06-17 19:36:36 +0200 (Wed, 17 Jun 2009) | 3 lines

Added a stub package for Frame Order related calculation code.
........
r9073 | bugman | 2009-06-17 20:03:58 +0200 (Wed, 17 Jun 2009) | 3 lines

Added a function for printing out the 2nd degree Frame Order matrix.
........
r9074 | bugman | 2009-06-17 20:05:50 +0200 (Wed, 17 Jun 2009) | 3 lines

Shifted the print_frame_order_2nd_degree() function to generic_fns.
........
r9075 | bugman | 2009-06-17 20:10:17 +0200 (Wed, 17 Jun 2009) | 3 lines

Added a missing import.
........
r9076 | bugman | 2009-06-17 20:30:26 +0200 (Wed, 17 Jun 2009) | 3 lines

Added functions for populating the Frame Order matrices for isotropic cones.
........
r9077 | bugman | 2009-06-18 10:41:27 +0200 (Thu, 18 Jun 2009) | 5 lines

Renamed the frame_order package to frame_order_matrix_ops.

This is to make way for the target function code.
........
r9078 | bugman | 2009-06-18 10:42:31 +0200 (Thu, 18 Jun 2009) | 6 lines

Added the Frame Order target function class.

It currently contains only one target function for an isotropic cone model directly optimised to the
Frame Order matrix elements.
........
r9079 | bugman | 2009-06-18 10:47:30 +0200 (Thu, 18 Jun 2009) | 3 lines

A few fixes for the Frame_order class.
........
r9080 | bugman | 2009-06-18 11:29:22 +0200 (Thu, 18 Jun 2009) | 3 lines

Aliased self.func_iso_cone_elements to self.func.
........
r9082 | bugman | 2009-06-18 22:04:39 +0200 (Thu, 18 Jun 2009) | 3 lines

Renamed the user function n_state_model.set_type() to align_tensor.reduction().
........
r9083 | bugman | 2009-06-18 22:15:18 +0200 (Thu, 18 Jun 2009) | 3 lines

Shifted the N-state model set_type() method to the align_tensor function reduction().
........
r9084 | bugman | 2009-06-19 10:18:35 +0200 (Fri, 19 Jun 2009) | 3 lines

Added the Frame Order theories to the setup of the specific code.
........
r9085 | bugman | 2009-06-19 10:30:00 +0200 (Fri, 19 Jun 2009) | 3 lines

Added the skeleton of the Frame Order specific code.
........
r9086 | bugman | 2009-06-19 10:31:03 +0200 (Fri, 19 Jun 2009) | 3 lines

Added the Frame Order type to get_string().
........
r9087 | bugman | 2009-06-19 10:43:37 +0200 (Fri, 19 Jun 2009) | 3 lines

Implemented most of the grid_search() method.
........
r9088 | bugman | 2009-06-19 10:50:19 +0200 (Fri, 19 Jun 2009) | 5 lines

Created the Frame Order user function class.

The only user function yet available is frame_order.select_model().
........
r9089 | bugman | 2009-06-19 10:51:59 +0200 (Fri, 19 Jun 2009) | 3 lines

Registered the Frame Order user function class into the interpreter.
........
r9090 | bugman | 2009-06-19 10:55:28 +0200 (Fri, 19 Jun 2009) | 3 lines

Wrote the select_model() method.
........
r9091 | bugman | 2009-06-19 10:58:47 +0200 (Fri, 19 Jun 2009) | 3 lines

Added the __update_model() method.
........
r9092 | bugman | 2009-06-19 11:01:22 +0200 (Fri, 19 Jun 2009) | 3 lines

Some fixed for the grid_search() method.
........
r9093 | bugman | 2009-06-19 11:29:00 +0200 (Fri, 19 Jun 2009) | 3 lines

Modifications to the __update_model() method.
........
r9094 | bugman | 2009-06-19 11:44:57 +0200 (Fri, 19 Jun 2009) | 5 lines

Wrote the minimise() and __unpack_opt_results() methods.

The minimise() method is rudimentary and will not work.
........
r9095 | bugman | 2009-06-19 11:50:26 +0200 (Fri, 19 Jun 2009) | 3 lines

Modified the __init__() method and spun of some code into __init_iso_cone_elements().
........
r9096 | bugman | 2009-06-19 11:51:24 +0200 (Fri, 19 Jun 2009) | 3 lines

Docstring update.
........
r9097 | bugman | 2009-06-19 11:52:00 +0200 (Fri, 19 Jun 2009) | 3 lines

Missing RelaxError import.
........
r9098 | bugman | 2009-06-19 15:27:08 +0200 (Fri, 19 Jun 2009) | 3 lines

Fixes for the minimise() method.
........
r9099 | bugman | 2009-06-19 15:57:11 +0200 (Fri, 19 Jun 2009) | 3 lines

Created the compile_2nd_matrix_iso_cone() function for building the 2nd degree Frame Order matrix.
........
r9100 | bugman | 2009-06-19 16:03:20 +0200 (Fri, 19 Jun 2009) | 3 lines

Shifted more code into the compile_2nd_matrix_iso_cone() function.
........
r9101 | bugman | 2009-06-19 16:05:14 +0200 (Fri, 19 Jun 2009) | 3 lines

Fixed the arguments of compile_2nd_matrix_iso_cone().
........
r9102 | bugman | 2009-06-19 16:06:39 +0200 (Fri, 19 Jun 2009) | 3 lines

Missing numpy imports.
........
r9103 | bugman | 2009-06-19 16:07:41 +0200 (Fri, 19 Jun 2009) | 5 lines

Preliminary support for optimisation against alignment tensors.

Added the func_iso_cone() and __init_iso_cone() methods.
........
r9104 | bugman | 2009-06-19 16:09:33 +0200 (Fri, 19 Jun 2009) | 3 lines

Added a check for incorrectly supplied arguments.
........
r9105 | bugman | 2009-06-19 16:35:47 +0200 (Fri, 19 Jun 2009) | 3 lines

Created the __minimise_setup_tensors() method to compile the data needed for optimisation.
........
r9106 | bugman | 2009-06-19 16:39:03 +0200 (Fri, 19 Jun 2009) | 3 lines

Modified the reduction() function to store alignment tensor indices rather than names.
........
r9107 | bugman | 2009-06-19 16:41:15 +0200 (Fri, 19 Jun 2009) | 3 lines

Fixed for the __minimise_setup_tensors() method.
........
r9108 | bugman | 2009-06-19 16:42:19 +0200 (Fri, 19 Jun 2009) | 3 lines

Fix for the frame_order_models.Frame_order setup within minimise().
........
r9109 | bugman | 2009-06-19 16:43:16 +0200 (Fri, 19 Jun 2009) | 3 lines

Removed an unused print statement.
........
r9110 | bugman | 2009-06-19 16:50:03 +0200 (Fri, 19 Jun 2009) | 3 lines

Docstring fixes and variable renaming in __minimise_setup_tensors().
........
r9111 | bugman | 2009-06-19 16:51:53 +0200 (Fri, 19 Jun 2009) | 3 lines

Docstring updates.
........
r9112 | bugman | 2009-06-19 16:52:04 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fix for the tensor optimisation.
........
r9113 | bugman | 2009-06-19 17:12:57 +0200 (Fri, 19 Jun 2009) | 3 lines

Temporary fix for func_iso_cone().
........
r9114 | bugman | 2009-06-19 17:15:33 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fixes for the __unpack_opt_results() method.
........
r9115 | bugman | 2009-06-19 17:21:56 +0200 (Fri, 19 Jun 2009) | 3 lines

Parameter values are initialised to zero so that a grid search is not necessary.
........
r9116 | bugman | 2009-06-19 17:31:41 +0200 (Fri, 19 Jun 2009) | 6 lines

Fix for the compilation of the Frame Order matrix.

The compile_2nd_matrix_iso_cone() function now returns the matrix as it is now in a different
memory location.
........
r9117 | bugman | 2009-06-19 19:22:07 +0200 (Fri, 19 Jun 2009) | 5 lines

Added the function reduce_alignment_tensor().

This calculates how the Frame Order matrix reduces the alignment tensor.
........
r9118 | bugman | 2009-06-19 19:22:29 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fix for reduce_alignment_tensor().
........
r9119 | bugman | 2009-06-19 19:22:59 +0200 (Fri, 19 Jun 2009) | 3 lines

The reduced tensors are now back calculated.
........
r9120 | bugman | 2009-06-19 19:23:23 +0200 (Fri, 19 Jun 2009) | 3 lines

Simplification of func_iso_cone().
........
r9121 | bugman | 2009-06-19 19:23:48 +0200 (Fri, 19 Jun 2009) | 3 lines

Another bug fix for reduce_alignment_tensor().
........
r9122 | bugman | 2009-06-19 19:24:19 +0200 (Fri, 19 Jun 2009) | 3 lines

Imported reduce_alignment_tensor().
........
r9123 | bugman | 2009-06-19 19:25:09 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fix for func_iso_cone().
........
r9124 | bugman | 2009-06-19 19:25:33 +0200 (Fri, 19 Jun 2009) | 3 lines

Another bug fix for reduce_alignment_tensor().
........
r9125 | bugman | 2009-06-19 19:30:06 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fix for the initialisation of self.red_tensors_bc.
........
r9126 | bugman | 2009-06-19 19:42:51 +0200 (Fri, 19 Jun 2009) | 3 lines

Made the default errors more reasonable.
........
r9127 | bugman | 2009-06-22 19:52:00 +0200 (Mon, 22 Jun 2009) | 3 lines

Bug fix for the reduce_alignment_tensor() function.
........
r9128 | bugman | 2009-06-23 11:14:13 +0200 (Tue, 23 Jun 2009) | 5 lines

Elimination of an Euler angle from the isotropic cone model.

Only the cone axis theta and phi angles are now optimised.
........
r9129 | bugman | 2009-06-23 11:20:16 +0200 (Tue, 23 Jun 2009) | 3 lines

Set up the z-axis data structures.
........
r9130 | bugman | 2009-06-23 11:31:59 +0200 (Tue, 23 Jun 2009) | 3 lines

Added the cone axis storage structure.
........
r9131 | bugman | 2009-06-23 11:32:19 +0200 (Tue, 23 Jun 2009) | 3 lines

Updated the compile_2nd_matrix_iso_cone() function to use the cone axis angles rather than Euler.
........
r9132 | bugman | 2009-06-23 11:37:05 +0200 (Tue, 23 Jun 2009) | 5 lines

Bug fix for compile_2nd_matrix_iso_cone().

The rotation matrix uses the polar angle, not the cone angle.
........
r9133 | bugman | 2009-06-23 12:58:40 +0200 (Tue, 23 Jun 2009) | 5 lines

Bug fix for the compile_2nd_matrix_iso_cone() function.

The cross product of 2 normal vectors is not a normal vector!!!
........
r9134 | bugman | 2009-06-23 13:42:26 +0200 (Tue, 23 Jun 2009) | 5 lines

Removed the sequence test in the Monte Carlo create_data() function.

No all data pipes in relax require sequence info.
........
r9135 | bugman | 2009-06-23 14:23:53 +0200 (Tue, 23 Jun 2009) | 3 lines

Added a dummy eliminate() method.
........
r9136 | bugman | 2009-06-23 16:22:12 +0200 (Tue, 23 Jun 2009) | 19 lines

Added the ability to perform Monte Carlo sims for the Frame Order theories.

For this, the following methods have been added:
__tensor_loop()
back_calc()
base_data_loop()
create_mc_data()
data_names()
model_loop()
return_error()
set_selected_sim()
sim_init_values()
sim_pack_data()
sim_return_param()
sim_return_selected()

Many other methods have also been modified.
........
r9137 | bugman | 2009-06-23 16:45:44 +0200 (Tue, 23 Jun 2009) | 3 lines

Updated the init() and set() method to allow alignment tensor errors to be input.
........
r9138 | bugman | 2009-06-23 17:41:52 +0200 (Tue, 23 Jun 2009) | 3 lines

More fixes for error setting in the set() function.
........
r9139 | bugman | 2009-06-23 17:52:07 +0200 (Tue, 23 Jun 2009) | 5 lines

Bug fix for the init() method.

Now errors are being placed in the pre-existing tensor, rather than a new tensor being added.
........
r9140 | bugman | 2009-06-23 18:19:49 +0200 (Tue, 23 Jun 2009) | 5 lines

Another bug fix for the init() method.

Errors are not properly handled for all input data types.
........
r9141 | bugman | 2009-06-23 19:23:11 +0200 (Tue, 23 Jun 2009) | 5 lines

Removed ambiguity from the align_tensor.reduction() user function.

The from_tensor and to_tensor args have been renamed to full_tensor and red_tensor respectively.
........
r9142 | bugman | 2009-06-25 12:00:41 +0200 (Thu, 25 Jun 2009) | 3 lines

Created the interface to the frame_order.cone_pdb() user function.
........
r9143 | bugman | 2009-06-25 13:17:53 +0200 (Thu, 25 Jun 2009) | 3 lines

Created the interface for the frame_order.pivot() user function.
........
r9144 | bugman | 2009-06-25 13:38:11 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fix for the R_2vect() function.

The rotation axis is not always of unit length!
........
r9145 | bugman | 2009-06-25 13:42:50 +0200 (Thu, 25 Jun 2009) | 3 lines

Spun out the cone axis generation code into generate_vector().
........
r9146 | bugman | 2009-06-25 13:45:54 +0200 (Thu, 25 Jun 2009) | 3 lines

Simplified compile_2nd_matrix_iso_cone() by using R_2vect().
........
r9147 | bugman | 2009-06-25 14:02:23 +0200 (Thu, 25 Jun 2009) | 3 lines

Bug fix for the generate_vector_residues() for numpy MC sim structures.
........
r9148 | bugman | 2009-06-25 14:03:36 +0200 (Thu, 25 Jun 2009) | 3 lines

Another bug fix for the generate_vector_residues() function for MC simulations.
........
r9149 | bugman | 2009-06-25 14:22:32 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fix for generate_vector_residues() when the neg flag is False.

The atoms were incorrectly numbered.
........
r9150 | bugman | 2009-06-25 14:24:51 +0200 (Thu, 25 Jun 2009) | 3 lines

Wrote the cone_pdb() and pivot() methods.
........
r9151 | bugman | 2009-06-25 15:02:34 +0200 (Thu, 25 Jun 2009) | 5 lines

Renaming and fixes for stitch_cone_to_edge().

This was stitch_cap_to_cone().
........
r9152 | bugman | 2009-06-25 15:24:01 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fixes for the write_pdb() method.

The Hetrogen section was failing with MC simulations.
........
r9153 | bugman | 2009-06-25 15:24:41 +0200 (Thu, 25 Jun 2009) | 3 lines

Fixes for the cone_pdb() method.
........
r9154 | bugman | 2009-06-25 15:58:39 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fixes for the generate_vector_dist() function.

The protons were not being correctly stitched together!
........
r9155 | bugman | 2009-06-25 16:02:26 +0200 (Thu, 25 Jun 2009) | 3 lines

Added a test for a loaded structure to the pymol.cartoon() user function.
........
r9156 | bugman | 2009-06-25 16:26:11 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fix for the pymol.cartoon() user function.

This was failing when multiple proteins were loaded.
........
r9157 | bugman | 2009-06-25 16:34:17 +0200 (Thu, 25 Jun 2009) | 3 lines

Changed the scaling arg to a direct size arg.
........
r9158 | bugman | 2009-06-25 16:36:00 +0200 (Thu, 25 Jun 2009) | 3 lines

cone_pdb() now handles the AXE residue.
........
r9159 | bugman | 2009-06-25 16:37:03 +0200 (Thu, 25 Jun 2009) | 3 lines

Renamed the axis atom from 'Axe' to 'Axis'.
........
r9160 | bugman | 2009-06-25 16:41:25 +0200 (Thu, 25 Jun 2009) | 3 lines

Made the cone_pdb() function less specific for the N-state model and added SIM as an axis to decorate.
........
r9161 | bugman | 2009-06-25 16:46:40 +0200 (Thu, 25 Jun 2009) | 3 lines

The user can now set the number of increments used to generate the cone PDB.
........
r9162 | bugman | 2009-06-29 10:24:03 +0200 (Mon, 29 Jun 2009) | 3 lines

Wrote the calculate() method for calculating the chi-squared value for the current parameters.
........
r9163 | bugman | 2009-06-29 10:25:13 +0200 (Mon, 29 Jun 2009) | 6 lines

Expansion of frame order to both the forward and reverse rotations.

reduce_alignment_tensor() was renamed to reduce_alignment_tensor_reverse(), and the new function
reduce_alignment_tensor() added.
........
r9164 | bugman | 2009-06-30 11:21:49 +0200 (Tue, 30 Jun 2009) | 3 lines

Added checks for the presence of the data structures necessary for frame_order.cone_pdb().
........
r9165 | bugman | 2009-06-30 11:24:12 +0200 (Tue, 30 Jun 2009) | 3 lines

Bug fix for frame_order.cone_pdb() for when no MC sims exist.
........
r9166 | bugman | 2009-06-30 11:43:31 +0200 (Tue, 30 Jun 2009) | 5 lines

Bug fix for the cone PDB generation.

If there were more than 1000 protons, the PDB file was corrupted by the proton name being too long.
........
r9167 | bugman | 2009-07-01 13:05:09 +0200 (Wed, 01 Jul 2009) | 6 lines

Reverted r9128 to r9133, the elimination of a Euler angle (maybe only temporarily).

The command used was:
svn merge -r9134:9127 .
........
r9168 | bugman | 2009-07-01 16:08:46 +0200 (Wed, 01 Jul 2009) | 3 lines

Renamed theta to theta cone (again due to the reversion).
........
r9169 | bugman | 2009-07-02 02:28:25 +0200 (Thu, 02 Jul 2009) | 3 lines

Missing import.
........
r9170 | bugman | 2009-07-02 02:33:45 +0200 (Thu, 02 Jul 2009) | 3 lines

The cone axis is back, and better support for the Euler angles.
........
r9171 | bugman | 2009-07-02 02:36:53 +0200 (Thu, 02 Jul 2009) | 3 lines

Return of the cone axis, and rotation of the reduced tensor.
........
r9172 | bugman | 2009-07-02 02:55:17 +0200 (Thu, 02 Jul 2009) | 6 lines

Partly reverted r9167 - the previous reversion.

The command used was:
svn merge -r9167:9166 generic_fns/monte_carlo.py
........
r9173 | bugman | 2009-07-02 02:58:54 +0200 (Thu, 02 Jul 2009) | 8 lines

Partly reverted r9167 - the previous revision.

The command used was:
svn merge -r9167:9166 maths_fns/frame_order_matrix_ops.py

This returns the cone axis.
........
r9174 | bugman | 2009-07-02 03:01:41 +0200 (Thu, 02 Jul 2009) | 6 lines

Partly reverted r9167 - the previous reversion.

The command used was:
svn merge -r9167:9166 maths_fns/frame_order_models.py
........
r9175 | bugman | 2009-07-02 03:02:12 +0200 (Thu, 02 Jul 2009) | 3 lines

Missing import.
........
r9176 | bugman | 2009-07-02 03:19:39 +0200 (Thu, 02 Jul 2009) | 3 lines

The Euler angles are now wrapped between 0 and 2pi.
........
r9177 | bugman | 2009-07-02 14:03:17 +0200 (Thu, 02 Jul 2009) | 3 lines

Added the new function R_to_axis_angle().
........
r9178 | bugman | 2009-07-02 15:25:08 +0200 (Thu, 02 Jul 2009) | 3 lines

Bug fix for the R_to_axis_angle() function. The axis needs to be normalised.
........
r9179 | bugman | 2009-07-02 15:25:40 +0200 (Thu, 02 Jul 2009) | 3 lines

Both the positive and negative cones are now made.
........
r9180 | bugman | 2009-07-02 16:50:51 +0200 (Thu, 02 Jul 2009) | 3 lines

Fixes for the negative cone.
........
r9181 | bugman | 2009-07-02 17:18:50 +0200 (Thu, 02 Jul 2009) | 3 lines

Fix for the N-state model arg checks.
........
r9182 | bugman | 2009-07-02 23:09:23 +0200 (Thu, 02 Jul 2009) | 3 lines

Bug fix for cone_pdb() for when no MC sims are run.
........
r9183 | bugman | 2009-07-02 23:13:13 +0200 (Thu, 02 Jul 2009) | 3 lines

Created and now using the full_in_ref_frame data structure (copy of N-state model).
........
r9184 | bugman | 2009-07-02 23:22:55 +0200 (Thu, 02 Jul 2009) | 3 lines

Added a check for the reference domain setup to __minimise_setup_tensors().
........
r9185 | bugman | 2009-07-02 23:25:33 +0200 (Thu, 02 Jul 2009) | 3 lines

Renamed n_state_model.set_domain() to align_tensor.set_domain().
........
r9186 | bugman | 2009-07-02 23:27:38 +0200 (Thu, 02 Jul 2009) | 3 lines

Shifted the set_domain() back-end from the N-state model to the alignment tensor.
........
r9187 | bugman | 2009-07-03 00:11:43 +0200 (Fri, 03 Jul 2009) | 3 lines

Added the interface for the frame_order.n_state_model() user function.
........
r9190 | bugman | 2009-07-12 23:31:31 +0200 (Sun, 12 Jul 2009) | 3 lines

Fixes for the unit tests of the user functions shifted from n_state_model to align_tensor.
........
r9191 | bugman | 2009-07-12 23:38:43 +0200 (Sun, 12 Jul 2009) | 3 lines

Fixes for the 5-state model system test.
........
r9192 | bugman | 2009-07-12 23:49:33 +0200 (Sun, 12 Jul 2009) | 3 lines

Modified the N-state model code to be more like the Frame Order matrix code.
........
r9193 | bugman | 2009-07-12 23:52:54 +0200 (Sun, 12 Jul 2009) | 3 lines

Copyright statement update.
........
................
r9200 | bugman | 2009-07-13 00:14:36 +0200 (Mon, 13 Jul 2009) | 3 lines

Removed merge properties.
................
r9202 | bugman | 2009-07-13 10:08:16 +0200 (Mon, 13 Jul 2009) | 7 lines

Removed all usages of float128, as this type is not present on all machines.

This was reported by Sebastian Morin in the post:
https://mail.gna.org/public/relax-devel/2009-07/msg00000.html (Message-id:
<4A5A7338.4030500@...>).
................
r9203 | bugman | 2009-07-13 15:16:27 +0200 (Mon, 13 Jul 2009) | 3 lines

Missing import.
................
r9204 | bugman | 2009-07-13 15:17:34 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fixes for the get_specific_fn() function.
................
r9205 | bugman | 2009-07-13 15:18:36 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fixes for the grace.write() user function.
................
r9206 | bugman | 2009-07-13 15:19:41 +0200 (Mon, 13 Jul 2009) | 5 lines

Bug fix for the molmol macro setup.

This was not being correctly retrieved.
................
r9207 | bugman | 2009-07-13 15:21:55 +0200 (Mon, 13 Jul 2009) | 3 lines

Changed the statistics ordering when running profiling.
................
r9208 | bugman | 2009-07-13 15:22:33 +0200 (Mon, 13 Jul 2009) | 3 lines

align_tensor.init() can now accept any type of float or int (python or numpy).
................
r9209 | bugman | 2009-07-13 16:28:58 +0200 (Mon, 13 Jul 2009) | 6 lines

Partial reversion of r9204.

The AttributeError should be checked for, not the NameError! NameError was only triggered by
another bug.
................
r9210 | bugman | 2009-07-13 18:29:31 +0200 (Mon, 13 Jul 2009) | 5 lines

Bug fixes for return_conversion_factor() and return_units() functions.

The spin and spin_id args are now accepted.
................
r9211 | bugman | 2009-07-13 18:30:04 +0200 (Mon, 13 Jul 2009) | 5 lines

Fix for the write_multi_header() function.

The spin_id variable now exists.
................
r9212 | bugman | 2009-07-13 18:30:45 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fix: The return_conversion_factor() method now accepts the spin arg.
................
r9213 | bugman | 2009-07-13 18:31:07 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fix: The return_units() method now accepts the spin_id keyword arg.
................
r9214 | bugman | 2009-07-13 18:32:32 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fix for the return_units() method, the spin_id keyword arg is now accepted.
................
r9215 | bugman | 2009-07-13 18:38:06 +0200 (Mon, 13 Jul 2009) | 5 lines

Fix for the return_units() method.

The spin and spin_id args are now accepted.
................
r9216 | bugman | 2009-07-14 11:04:22 +0200 (Tue, 14 Jul 2009) | 3 lines

Added a check for the chi-squared value for the 5-state model system test.
................
r9217 | bugman | 2009-07-14 11:26:12 +0200 (Tue, 14 Jul 2009) | 3 lines

Bug fix: The tensor reduction was specified back to front!
................
r9218 | bugman | 2009-07-14 11:26:55 +0200 (Tue, 14 Jul 2009) | 3 lines

Fix for the func_2domain() method for the N-state model tensor reduction code.
................
r9219 | bugman | 2009-07-14 11:27:30 +0200 (Tue, 14 Jul 2009) | 3 lines

Removed a debugging print out.
................
r9220 | bugman | 2009-07-14 11:31:51 +0200 (Tue, 14 Jul 2009) | 3 lines

Fixes for all the N-state model optimisation unit tests.
................
r9221 | bugman | 2009-07-14 11:49:22 +0200 (Tue, 14 Jul 2009) | 3 lines

Fix for the return_units() method. The spin and spin_id args are now accepted.
................
r9222 | bugman | 2009-07-14 12:02:38 +0200 (Tue, 14 Jul 2009) | 5 lines

Fixes for Tyler's peptide system test.

The residue was 111 in the PDB but 211 in the results file, and the spin was unnamed.
................
r9223 | bugman | 2009-07-14 13:24:30 +0200 (Tue, 14 Jul 2009) | 5 lines

Bug fix for the generate_vector_dist() function.

Now the diffusion tensor and cone geometric objects are correctly created!
................
r9224 | bugman | 2009-07-14 13:31:53 +0200 (Tue, 14 Jul 2009) | 5 lines

Bug fix for the generate_vector_residues() function.

Now the negative vector actually is negative! It was previously the same as the positive vector.
................
r9225 | bugman | 2009-07-14 14:10:30 +0200 (Tue, 14 Jul 2009) | 6 lines

Improvements for the reload_pdb() method.

Now the system path is searched for the PDB file. This allows the system tests to pass when not
running from the installation path.
................
r9226 | bugman | 2009-07-14 14:11:19 +0200 (Tue, 14 Jul 2009) | 3 lines

Extended the OMP model-free system test to run MC sims for the diffusion tensor.
................
r9227 | bugman | 2009-07-14 15:12:22 +0200 (Tue, 14 Jul 2009) | 5 lines

Bug fix for the setup of MC simulations of the diffusion tensor.

MC sims were not working when all parameters except for the diffusion tensor are fixed.
................
r9228 | bugman | 2009-07-14 15:26:28 +0200 (Tue, 14 Jul 2009) | 5 lines

Bug fixes for the OMP model-free system test.

The diffusion tensor MC simulation test was not functional.
................
r9229 | bugman | 2009-07-14 15:56:19 +0200 (Tue, 14 Jul 2009) | 5 lines

Fix for the checks in test_omp_analysis().

The wrong data pipe was being accessed.
................
r9230 | bugman | 2009-07-14 15:57:59 +0200 (Tue, 14 Jul 2009) | 5 lines

The diffusion and alignment tensor *_sim and *_err attributes are now listed as modifiable.

This means that this data is placed into the results file, and read back out again!
................

Merged revisions 9048-9066,9068-9069,9081,9194-9196,9198-9200,9202-9230 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

................
r9048 | bugman | 2009-05-12 10:47:02 +0200 (Tue, 12 May 2009) | 3 lines

Updated the pipes.hybridise() user function interface to the 1.3 line design.
................
r9049 | bugman | 2009-05-12 11:09:24 +0200 (Tue, 12 May 2009) | 3 lines

Added 3 new RelaxErrors for sequence matching.
................
r9050 | bugman | 2009-05-12 11:21:59 +0200 (Tue, 12 May 2009) | 3 lines

Added the pipe keyword to all the sequence counting functions.
................
r9051 | bugman | 2009-05-12 11:22:41 +0200 (Tue, 12 May 2009) | 3 lines

Renamed the hybridise() pipes keyword to pipe_list.
................
r9052 | bugman | 2009-05-12 11:25:38 +0200 (Tue, 12 May 2009) | 3 lines

Created the compare_sequence() for checking if 2 sequences are the same.
................
r9053 | bugman | 2009-05-12 11:28:49 +0200 (Tue, 12 May 2009) | 3 lines

Converted the hybridise() method to the 1.3 line design.
................
r9054 | bugman | 2009-05-12 11:31:08 +0200 (Tue, 12 May 2009) | 3 lines

Added the hybrid data pipe to the list of allowable data pipes.
................
r9055 | bugman | 2009-05-12 11:34:40 +0200 (Tue, 12 May 2009) | 3 lines

Added a check for the pipe type to hybridise().
................
r9056 | bugman | 2009-05-12 11:41:12 +0200 (Tue, 12 May 2009) | 3 lines

Converted the duplicate_data() method to the 1.3 line design.
................
r9057 | bugman | 2009-05-12 14:42:06 +0200 (Tue, 12 May 2009) | 3 lines

Removed a test that disallowed model selection between different pipe types.
................
r9058 | bugman | 2009-05-12 14:56:23 +0200 (Tue, 12 May 2009) | 5 lines

Converted all parts of the hybrid module to the 1.3 line design.

This includes the addition of many new, very simple methods and the translation of old code.
................
r9059 | bugman | 2009-05-15 10:47:59 +0200 (Fri, 15 May 2009) | 3 lines

Created the R_axis_angle() function to generate the rotation matrix from the axis-angle notation.
................
r9060 | bugman | 2009-05-15 11:58:55 +0200 (Fri, 15 May 2009) | 3 lines

Added the functions random_rot_axis() and random_R() to generate random rotations.
................
r9061 | bugman | 2009-05-25 13:45:14 +0200 (Mon, 25 May 2009) | 6 lines

Changed the precision of the te check in the model-free system tests.

This is in response to Sebastian's post at
https://mail.gna.org/public/relax-devel/2009-05/msg00003.html.
................
r9062 | bugman | 2009-05-28 15:37:08 +0200 (Thu, 28 May 2009) | 3 lines

Renamed random_R() to R_random_axis().
................
r9063 | bugman | 2009-05-28 15:57:48 +0200 (Thu, 28 May 2009) | 3 lines

Wrote 2 new functions, R_random_hypersphere() and quaternion_to_R().
................
r9064 | bugman | 2009-05-28 16:53:23 +0200 (Thu, 28 May 2009) | 3 lines

Bug fix for the quaternion_to_R() function.
................
r9065 | bugman | 2009-05-29 10:47:09 +0200 (Fri, 29 May 2009) | 3 lines

Fix for the align_tensor.init() user function docstring.
................
r9066 | bugman | 2009-06-02 13:54:11 +0200 (Tue, 02 Jun 2009) | 3 lines

Indentation fix.
................
r9068 | bugman | 2009-06-08 16:21:38 +0200 (Mon, 08 Jun 2009) | 3 lines

Added a function for calculating the Kronecker product.
................
r9069 | bugman | 2009-06-08 17:13:54 +0200 (Mon, 08 Jun 2009) | 3 lines

Added a copyright notice and spun out the T14 transpose into its own function.
................
r9081 | bugman | 2009-06-18 15:01:00 +0200 (Thu, 18 Jun 2009) | 3 lines

Added numpy int and float data types to the list of tested user function args.
................
r9194 | bugman | 2009-07-12 23:55:17 +0200 (Sun, 12 Jul 2009) | 3 lines

Commented out a data type temporarily until someone complains about int32 types.
................
r9195 | bugman | 2009-07-13 00:03:51 +0200 (Mon, 13 Jul 2009) | 5 lines

Created lists of number types (python and numpy).

These are in the prompt.num_types module and are now used by value.set() for argument checking.
................
r9196 | bugman | 2009-07-13 00:05:31 +0200 (Mon, 13 Jul 2009) | 6 lines

Reverted r9194, the temporary commenting out of a data type.

The command used was:
svn merge -r9194:9193 .
................
r9198 | bugman | 2009-07-13 00:07:41 +0200 (Mon, 13 Jul 2009) | 3 lines

Initialized merge tracking via "svnmerge" with revisions "1-9069" from
svn+ssh://bugman@.../svn/relax/branches/frame_order
................
r9199 | bugman | 2009-07-13 00:11:11 +0200 (Mon, 13 Jul 2009) | 566 lines

Merged revisions 9070-9187,9190-9196,9198 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order

........
r9070 | bugman | 2009-06-17 19:27:42 +0200 (Wed, 17 Jun 2009) | 3 lines

Created a branch for the new Frame Order theories.
........
r9071 | bugman | 2009-06-17 19:34:39 +0200 (Wed, 17 Jun 2009) | 3 lines

Added Frame Order to the list of allowable data pipes.
........
r9072 | bugman | 2009-06-17 19:36:36 +0200 (Wed, 17 Jun 2009) | 3 lines

Added a stub package for Frame Order related calculation code.
........
r9073 | bugman | 2009-06-17 20:03:58 +0200 (Wed, 17 Jun 2009) | 3 lines

Added a function for printing out the 2nd degree Frame Order matrix.
........
r9074 | bugman | 2009-06-17 20:05:50 +0200 (Wed, 17 Jun 2009) | 3 lines

Shifted the print_frame_order_2nd_degree() function to generic_fns.
........
r9075 | bugman | 2009-06-17 20:10:17 +0200 (Wed, 17 Jun 2009) | 3 lines

Added a missing import.
........
r9076 | bugman | 2009-06-17 20:30:26 +0200 (Wed, 17 Jun 2009) | 3 lines

Added functions for populating the Frame Order matrices for isotropic cones.
........
r9077 | bugman | 2009-06-18 10:41:27 +0200 (Thu, 18 Jun 2009) | 5 lines

Renamed the frame_order package to frame_order_matrix_ops.

This is to make way for the target function code.
........
r9078 | bugman | 2009-06-18 10:42:31 +0200 (Thu, 18 Jun 2009) | 6 lines

Added the Frame Order target function class.

It currently contains only one target function for an isotropic cone model directly optimised to the
Frame Order matrix elements.
........
r9079 | bugman | 2009-06-18 10:47:30 +0200 (Thu, 18 Jun 2009) | 3 lines

A few fixes for the Frame_order class.
........
r9080 | bugman | 2009-06-18 11:29:22 +0200 (Thu, 18 Jun 2009) | 3 lines

Aliased self.func_iso_cone_elements to self.func.
........
r9082 | bugman | 2009-06-18 22:04:39 +0200 (Thu, 18 Jun 2009) | 3 lines

Renamed the user function n_state_model.set_type() to align_tensor.reduction().
........
r9083 | bugman | 2009-06-18 22:15:18 +0200 (Thu, 18 Jun 2009) | 3 lines

Shifted the N-state model set_type() method to the align_tensor function reduction().
........
r9084 | bugman | 2009-06-19 10:18:35 +0200 (Fri, 19 Jun 2009) | 3 lines

Added the Frame Order theories to the setup of the specific code.
........
r9085 | bugman | 2009-06-19 10:30:00 +0200 (Fri, 19 Jun 2009) | 3 lines

Added the skeleton of the Frame Order specific code.
........
r9086 | bugman | 2009-06-19 10:31:03 +0200 (Fri, 19 Jun 2009) | 3 lines

Added the Frame Order type to get_string().
........
r9087 | bugman | 2009-06-19 10:43:37 +0200 (Fri, 19 Jun 2009) | 3 lines

Implemented most of the grid_search() method.
........
r9088 | bugman | 2009-06-19 10:50:19 +0200 (Fri, 19 Jun 2009) | 5 lines

Created the Frame Order user function class.

The only user function yet available is frame_order.select_model().
........
r9089 | bugman | 2009-06-19 10:51:59 +0200 (Fri, 19 Jun 2009) | 3 lines

Registered the Frame Order user function class into the interpreter.
........
r9090 | bugman | 2009-06-19 10:55:28 +0200 (Fri, 19 Jun 2009) | 3 lines

Wrote the select_model() method.
........
r9091 | bugman | 2009-06-19 10:58:47 +0200 (Fri, 19 Jun 2009) | 3 lines

Added the __update_model() method.
........
r9092 | bugman | 2009-06-19 11:01:22 +0200 (Fri, 19 Jun 2009) | 3 lines

Some fixed for the grid_search() method.
........
r9093 | bugman | 2009-06-19 11:29:00 +0200 (Fri, 19 Jun 2009) | 3 lines

Modifications to the __update_model() method.
........
r9094 | bugman | 2009-06-19 11:44:57 +0200 (Fri, 19 Jun 2009) | 5 lines

Wrote the minimise() and __unpack_opt_results() methods.

The minimise() method is rudimentary and will not work.
........
r9095 | bugman | 2009-06-19 11:50:26 +0200 (Fri, 19 Jun 2009) | 3 lines

Modified the __init__() method and spun of some code into __init_iso_cone_elements().
........
r9096 | bugman | 2009-06-19 11:51:24 +0200 (Fri, 19 Jun 2009) | 3 lines

Docstring update.
........
r9097 | bugman | 2009-06-19 11:52:00 +0200 (Fri, 19 Jun 2009) | 3 lines

Missing RelaxError import.
........
r9098 | bugman | 2009-06-19 15:27:08 +0200 (Fri, 19 Jun 2009) | 3 lines

Fixes for the minimise() method.
........
r9099 | bugman | 2009-06-19 15:57:11 +0200 (Fri, 19 Jun 2009) | 3 lines

Created the compile_2nd_matrix_iso_cone() function for building the 2nd degree Frame Order matrix.
........
r9100 | bugman | 2009-06-19 16:03:20 +0200 (Fri, 19 Jun 2009) | 3 lines

Shifted more code into the compile_2nd_matrix_iso_cone() function.
........
r9101 | bugman | 2009-06-19 16:05:14 +0200 (Fri, 19 Jun 2009) | 3 lines

Fixed the arguments of compile_2nd_matrix_iso_cone().
........
r9102 | bugman | 2009-06-19 16:06:39 +0200 (Fri, 19 Jun 2009) | 3 lines

Missing numpy imports.
........
r9103 | bugman | 2009-06-19 16:07:41 +0200 (Fri, 19 Jun 2009) | 5 lines

Preliminary support for optimisation against alignment tensors.

Added the func_iso_cone() and __init_iso_cone() methods.
........
r9104 | bugman | 2009-06-19 16:09:33 +0200 (Fri, 19 Jun 2009) | 3 lines

Added a check for incorrectly supplied arguments.
........
r9105 | bugman | 2009-06-19 16:35:47 +0200 (Fri, 19 Jun 2009) | 3 lines

Created the __minimise_setup_tensors() method to compile the data needed for optimisation.
........
r9106 | bugman | 2009-06-19 16:39:03 +0200 (Fri, 19 Jun 2009) | 3 lines

Modified the reduction() function to store alignment tensor indices rather than names.
........
r9107 | bugman | 2009-06-19 16:41:15 +0200 (Fri, 19 Jun 2009) | 3 lines

Fixed for the __minimise_setup_tensors() method.
........
r9108 | bugman | 2009-06-19 16:42:19 +0200 (Fri, 19 Jun 2009) | 3 lines

Fix for the frame_order_models.Frame_order setup within minimise().
........
r9109 | bugman | 2009-06-19 16:43:16 +0200 (Fri, 19 Jun 2009) | 3 lines

Removed an unused print statement.
........
r9110 | bugman | 2009-06-19 16:50:03 +0200 (Fri, 19 Jun 2009) | 3 lines

Docstring fixes and variable renaming in __minimise_setup_tensors().
........
r9111 | bugman | 2009-06-19 16:51:53 +0200 (Fri, 19 Jun 2009) | 3 lines

Docstring updates.
........
r9112 | bugman | 2009-06-19 16:52:04 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fix for the tensor optimisation.
........
r9113 | bugman | 2009-06-19 17:12:57 +0200 (Fri, 19 Jun 2009) | 3 lines

Temporary fix for func_iso_cone().
........
r9114 | bugman | 2009-06-19 17:15:33 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fixes for the __unpack_opt_results() method.
........
r9115 | bugman | 2009-06-19 17:21:56 +0200 (Fri, 19 Jun 2009) | 3 lines

Parameter values are initialised to zero so that a grid search is not necessary.
........
r9116 | bugman | 2009-06-19 17:31:41 +0200 (Fri, 19 Jun 2009) | 6 lines

Fix for the compilation of the Frame Order matrix.

The compile_2nd_matrix_iso_cone() function now returns the matrix as it is now in a different
memory location.
........
r9117 | bugman | 2009-06-19 19:22:07 +0200 (Fri, 19 Jun 2009) | 5 lines

Added the function reduce_alignment_tensor().

This calculates how the Frame Order matrix reduces the alignment tensor.
........
r9118 | bugman | 2009-06-19 19:22:29 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fix for reduce_alignment_tensor().
........
r9119 | bugman | 2009-06-19 19:22:59 +0200 (Fri, 19 Jun 2009) | 3 lines

The reduced tensors are now back calculated.
........
r9120 | bugman | 2009-06-19 19:23:23 +0200 (Fri, 19 Jun 2009) | 3 lines

Simplification of func_iso_cone().
........
r9121 | bugman | 2009-06-19 19:23:48 +0200 (Fri, 19 Jun 2009) | 3 lines

Another bug fix for reduce_alignment_tensor().
........
r9122 | bugman | 2009-06-19 19:24:19 +0200 (Fri, 19 Jun 2009) | 3 lines

Imported reduce_alignment_tensor().
........
r9123 | bugman | 2009-06-19 19:25:09 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fix for func_iso_cone().
........
r9124 | bugman | 2009-06-19 19:25:33 +0200 (Fri, 19 Jun 2009) | 3 lines

Another bug fix for reduce_alignment_tensor().
........
r9125 | bugman | 2009-06-19 19:30:06 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fix for the initialisation of self.red_tensors_bc.
........
r9126 | bugman | 2009-06-19 19:42:51 +0200 (Fri, 19 Jun 2009) | 3 lines

Made the default errors more reasonable.
........
r9127 | bugman | 2009-06-22 19:52:00 +0200 (Mon, 22 Jun 2009) | 3 lines

Bug fix for the reduce_alignment_tensor() function.
........
r9128 | bugman | 2009-06-23 11:14:13 +0200 (Tue, 23 Jun 2009) | 5 lines

Elimination of an Euler angle from the isotropic cone model.

Only the cone axis theta and phi angles are now optimised.
........
r9129 | bugman | 2009-06-23 11:20:16 +0200 (Tue, 23 Jun 2009) | 3 lines

Set up the z-axis data structures.
........
r9130 | bugman | 2009-06-23 11:31:59 +0200 (Tue, 23 Jun 2009) | 3 lines

Added the cone axis storage structure.
........
r9131 | bugman | 2009-06-23 11:32:19 +0200 (Tue, 23 Jun 2009) | 3 lines

Updated the compile_2nd_matrix_iso_cone() function to use the cone axis angles rather than Euler.
........
r9132 | bugman | 2009-06-23 11:37:05 +0200 (Tue, 23 Jun 2009) | 5 lines

Bug fix for compile_2nd_matrix_iso_cone().

The rotation matrix uses the polar angle, not the cone angle.
........
r9133 | bugman | 2009-06-23 12:58:40 +0200 (Tue, 23 Jun 2009) | 5 lines

Bug fix for the compile_2nd_matrix_iso_cone() function.

The cross product of 2 normal vectors is not a normal vector!!!
........
r9134 | bugman | 2009-06-23 13:42:26 +0200 (Tue, 23 Jun 2009) | 5 lines

Removed the sequence test in the Monte Carlo create_data() function.

No all data pipes in relax require sequence info.
........
r9135 | bugman | 2009-06-23 14:23:53 +0200 (Tue, 23 Jun 2009) | 3 lines

Added a dummy eliminate() method.
........
r9136 | bugman | 2009-06-23 16:22:12 +0200 (Tue, 23 Jun 2009) | 19 lines

Added the ability to perform Monte Carlo sims for the Frame Order theories.

For this, the following methods have been added:
__tensor_loop()
back_calc()
base_data_loop()
create_mc_data()
data_names()
model_loop()
return_error()
set_selected_sim()
sim_init_values()
sim_pack_data()
sim_return_param()
sim_return_selected()

Many other methods have also been modified.
........
r9137 | bugman | 2009-06-23 16:45:44 +0200 (Tue, 23 Jun 2009) | 3 lines

Updated the init() and set() method to allow alignment tensor errors to be input.
........
r9138 | bugman | 2009-06-23 17:41:52 +0200 (Tue, 23 Jun 2009) | 3 lines

More fixes for error setting in the set() function.
........
r9139 | bugman | 2009-06-23 17:52:07 +0200 (Tue, 23 Jun 2009) | 5 lines

Bug fix for the init() method.

Now errors are being placed in the pre-existing tensor, rather than a new tensor being added.
........
r9140 | bugman | 2009-06-23 18:19:49 +0200 (Tue, 23 Jun 2009) | 5 lines

Another bug fix for the init() method.

Errors are not properly handled for all input data types.
........
r9141 | bugman | 2009-06-23 19:23:11 +0200 (Tue, 23 Jun 2009) | 5 lines

Removed ambiguity from the align_tensor.reduction() user function.

The from_tensor and to_tensor args have been renamed to full_tensor and red_tensor respectively.
........
r9142 | bugman | 2009-06-25 12:00:41 +0200 (Thu, 25 Jun 2009) | 3 lines

Created the interface to the frame_order.cone_pdb() user function.
........
r9143 | bugman | 2009-06-25 13:17:53 +0200 (Thu, 25 Jun 2009) | 3 lines

Created the interface for the frame_order.pivot() user function.
........
r9144 | bugman | 2009-06-25 13:38:11 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fix for the R_2vect() function.

The rotation axis is not always of unit length!
........
r9145 | bugman | 2009-06-25 13:42:50 +0200 (Thu, 25 Jun 2009) | 3 lines

Spun out the cone axis generation code into generate_vector().
........
r9146 | bugman | 2009-06-25 13:45:54 +0200 (Thu, 25 Jun 2009) | 3 lines

Simplified compile_2nd_matrix_iso_cone() by using R_2vect().
........
r9147 | bugman | 2009-06-25 14:02:23 +0200 (Thu, 25 Jun 2009) | 3 lines

Bug fix for the generate_vector_residues() for numpy MC sim structures.
........
r9148 | bugman | 2009-06-25 14:03:36 +0200 (Thu, 25 Jun 2009) | 3 lines

Another bug fix for the generate_vector_residues() function for MC simulations.
........
r9149 | bugman | 2009-06-25 14:22:32 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fix for generate_vector_residues() when the neg flag is False.

The atoms were incorrectly numbered.
........
r9150 | bugman | 2009-06-25 14:24:51 +0200 (Thu, 25 Jun 2009) | 3 lines

Wrote the cone_pdb() and pivot() methods.
........
r9151 | bugman | 2009-06-25 15:02:34 +0200 (Thu, 25 Jun 2009) | 5 lines

Renaming and fixes for stitch_cone_to_edge().

This was stitch_cap_to_cone().
........
r9152 | bugman | 2009-06-25 15:24:01 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fixes for the write_pdb() method.

The Hetrogen section was failing with MC simulations.
........
r9153 | bugman | 2009-06-25 15:24:41 +0200 (Thu, 25 Jun 2009) | 3 lines

Fixes for the cone_pdb() method.
........
r9154 | bugman | 2009-06-25 15:58:39 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fixes for the generate_vector_dist() function.

The protons were not being correctly stitched together!
........
r9155 | bugman | 2009-06-25 16:02:26 +0200 (Thu, 25 Jun 2009) | 3 lines

Added a test for a loaded structure to the pymol.cartoon() user function.
........
r9156 | bugman | 2009-06-25 16:26:11 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fix for the pymol.cartoon() user function.

This was failing when multiple proteins were loaded.
........
r9157 | bugman | 2009-06-25 16:34:17 +0200 (Thu, 25 Jun 2009) | 3 lines

Changed the scaling arg to a direct size arg.
........
r9158 | bugman | 2009-06-25 16:36:00 +0200 (Thu, 25 Jun 2009) | 3 lines

cone_pdb() now handles the AXE residue.
........
r9159 | bugman | 2009-06-25 16:37:03 +0200 (Thu, 25 Jun 2009) | 3 lines

Renamed the axis atom from 'Axe' to 'Axis'.
........
r9160 | bugman | 2009-06-25 16:41:25 +0200 (Thu, 25 Jun 2009) | 3 lines

Made the cone_pdb() function less specific for the N-state model and added SIM as an axis to decorate.
........
r9161 | bugman | 2009-06-25 16:46:40 +0200 (Thu, 25 Jun 2009) | 3 lines

The user can now set the number of increments used to generate the cone PDB.
........
r9162 | bugman | 2009-06-29 10:24:03 +0200 (Mon, 29 Jun 2009) | 3 lines

Wrote the calculate() method for calculating the chi-squared value for the current parameters.
........
r9163 | bugman | 2009-06-29 10:25:13 +0200 (Mon, 29 Jun 2009) | 6 lines

Expansion of frame order to both the forward and reverse rotations.

reduce_alignment_tensor() was renamed to reduce_alignment_tensor_reverse(), and the new function
reduce_alignment_tensor() added.
........
r9164 | bugman | 2009-06-30 11:21:49 +0200 (Tue, 30 Jun 2009) | 3 lines

Added checks for the presence of the data structures necessary for frame_order.cone_pdb().
........
r9165 | bugman | 2009-06-30 11:24:12 +0200 (Tue, 30 Jun 2009) | 3 lines

Bug fix for frame_order.cone_pdb() for when no MC sims exist.
........
r9166 | bugman | 2009-06-30 11:43:31 +0200 (Tue, 30 Jun 2009) | 5 lines

Bug fix for the cone PDB generation.

If there were more than 1000 protons, the PDB file was corrupted by the proton name being too long.
........
r9167 | bugman | 2009-07-01 13:05:09 +0200 (Wed, 01 Jul 2009) | 6 lines

Reverted r9128 to r9133, the elimination of a Euler angle (maybe only temporarily).

The command used was:
svn merge -r9134:9127 .
........
r9168 | bugman | 2009-07-01 16:08:46 +0200 (Wed, 01 Jul 2009) | 3 lines

Renamed theta to theta cone (again due to the reversion).
........
r9169 | bugman | 2009-07-02 02:28:25 +0200 (Thu, 02 Jul 2009) | 3 lines

Missing import.
........
r9170 | bugman | 2009-07-02 02:33:45 +0200 (Thu, 02 Jul 2009) | 3 lines

The cone axis is back, and better support for the Euler angles.
........
r9171 | bugman | 2009-07-02 02:36:53 +0200 (Thu, 02 Jul 2009) | 3 lines

Return of the cone axis, and rotation of the reduced tensor.
........
r9172 | bugman | 2009-07-02 02:55:17 +0200 (Thu, 02 Jul 2009) | 6 lines

Partly reverted r9167 - the previous reversion.

The command used was:
svn merge -r9167:9166 generic_fns/monte_carlo.py
........
r9173 | bugman | 2009-07-02 02:58:54 +0200 (Thu, 02 Jul 2009) | 8 lines

Partly reverted r9167 - the previous revision.

The command used was:
svn merge -r9167:9166 maths_fns/frame_order_matrix_ops.py

This returns the cone axis.
........
r9174 | bugman | 2009-07-02 03:01:41 +0200 (Thu, 02 Jul 2009) | 6 lines

Partly reverted r9167 - the previous reversion.

The command used was:
svn merge -r9167:9166 maths_fns/frame_order_models.py
........
r9175 | bugman | 2009-07-02 03:02:12 +0200 (Thu, 02 Jul 2009) | 3 lines

Missing import.
........
r9176 | bugman | 2009-07-02 03:19:39 +0200 (Thu, 02 Jul 2009) | 3 lines

The Euler angles are now wrapped between 0 and 2pi.
........
r9177 | bugman | 2009-07-02 14:03:17 +0200 (Thu, 02 Jul 2009) | 3 lines

Added the new function R_to_axis_angle().
........
r9178 | bugman | 2009-07-02 15:25:08 +0200 (Thu, 02 Jul 2009) | 3 lines

Bug fix for the R_to_axis_angle() function. The axis needs to be normalised.
........
r9179 | bugman | 2009-07-02 15:25:40 +0200 (Thu, 02 Jul 2009) | 3 lines

Both the positive and negative cones are now made.
........
r9180 | bugman | 2009-07-02 16:50:51 +0200 (Thu, 02 Jul 2009) | 3 lines

Fixes for the negative cone.
........
r9181 | bugman | 2009-07-02 17:18:50 +0200 (Thu, 02 Jul 2009) | 3 lines

Fix for the N-state model arg checks.
........
r9182 | bugman | 2009-07-02 23:09:23 +0200 (Thu, 02 Jul 2009) | 3 lines

Bug fix for cone_pdb() for when no MC sims are run.
........
r9183 | bugman | 2009-07-02 23:13:13 +0200 (Thu, 02 Jul 2009) | 3 lines

Created and now using the full_in_ref_frame data structure (copy of N-state model).
........
r9184 | bugman | 2009-07-02 23:22:55 +0200 (Thu, 02 Jul 2009) | 3 lines

Added a check for the reference domain setup to __minimise_setup_tensors().
........
r9185 | bugman | 2009-07-02 23:25:33 +0200 (Thu, 02 Jul 2009) | 3 lines

Renamed n_state_model.set_domain() to align_tensor.set_domain().
........
r9186 | bugman | 2009-07-02 23:27:38 +0200 (Thu, 02 Jul 2009) | 3 lines

Shifted the set_domain() back-end from the N-state model to the alignment tensor.
........
r9187 | bugman | 2009-07-03 00:11:43 +0200 (Fri, 03 Jul 2009) | 3 lines

Added the interface for the frame_order.n_state_model() user function.
........
r9190 | bugman | 2009-07-12 23:31:31 +0200 (Sun, 12 Jul 2009) | 3 lines

Fixes for the unit tests of the user functions shifted from n_state_model to align_tensor.
........
r9191 | bugman | 2009-07-12 23:38:43 +0200 (Sun, 12 Jul 2009) | 3 lines

Fixes for the 5-state model system test.
........
r9192 | bugman | 2009-07-12 23:49:33 +0200 (Sun, 12 Jul 2009) | 3 lines

Modified the N-state model code to be more like the Frame Order matrix code.
........
r9193 | bugman | 2009-07-12 23:52:54 +0200 (Sun, 12 Jul 2009) | 3 lines

Copyright statement update.
........
................
r9200 | bugman | 2009-07-13 00:14:36 +0200 (Mon, 13 Jul 2009) | 3 lines

Removed merge properties.
................
r9202 | bugman | 2009-07-13 10:08:16 +0200 (Mon, 13 Jul 2009) | 7 lines

Removed all usages of float128, as this type is not present on all machines.

This was reported by Sebastian Morin in the post:
https://mail.gna.org/public/relax-devel/2009-07/msg00000.html (Message-id:
<4A5A7338.4030500@...>).
................
r9203 | bugman | 2009-07-13 15:16:27 +0200 (Mon, 13 Jul 2009) | 3 lines

Missing import.
................
r9204 | bugman | 2009-07-13 15:17:34 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fixes for the get_specific_fn() function.
................
r9205 | bugman | 2009-07-13 15:18:36 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fixes for the grace.write() user function.
................
r9206 | bugman | 2009-07-13 15:19:41 +0200 (Mon, 13 Jul 2009) | 5 lines

Bug fix for the molmol macro setup.

This was not being correctly retrieved.
................
r9207 | bugman | 2009-07-13 15:21:55 +0200 (Mon, 13 Jul 2009) | 3 lines

Changed the statistics ordering when running profiling.
................
r9208 | bugman | 2009-07-13 15:22:33 +0200 (Mon, 13 Jul 2009) | 3 lines

align_tensor.init() can now accept any type of float or int (python or numpy).
................
r9209 | bugman | 2009-07-13 16:28:58 +0200 (Mon, 13 Jul 2009) | 6 lines

Partial reversion of r9204.

The AttributeError should be checked for, not the NameError! NameError was only triggered by
another bug.
................
r9210 | bugman | 2009-07-13 18:29:31 +0200 (Mon, 13 Jul 2009) | 5 lines

Bug fixes for return_conversion_factor() and return_units() functions.

The spin and spin_id args are now accepted.
................
r9211 | bugman | 2009-07-13 18:30:04 +0200 (Mon, 13 Jul 2009) | 5 lines

Fix for the write_multi_header() function.

The spin_id variable now exists.
................
r9212 | bugman | 2009-07-13 18:30:45 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fix: The return_conversion_factor() method now accepts the spin arg.
................
r9213 | bugman | 2009-07-13 18:31:07 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fix: The return_units() method now accepts the spin_id keyword arg.
................
r9214 | bugman | 2009-07-13 18:32:32 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fix for the return_units() method, the spin_id keyword arg is now accepted.
................
r9215 | bugman | 2009-07-13 18:38:06 +0200 (Mon, 13 Jul 2009) | 5 lines

Fix for the return_units() method.

The spin and spin_id args are now accepted.
................
r9216 | bugman | 2009-07-14 11:04:22 +0200 (Tue, 14 Jul 2009) | 3 lines

Added a check for the chi-squared value for the 5-state model system test.
................
r9217 | bugman | 2009-07-14 11:26:12 +0200 (Tue, 14 Jul 2009) | 3 lines

Bug fix: The tensor reduction was specified back to front!
................
r9218 | bugman | 2009-07-14 11:26:55 +0200 (Tue, 14 Jul 2009) | 3 lines

Fix for the func_2domain() method for the N-state model tensor reduction code.
................
r9219 | bugman | 2009-07-14 11:27:30 +0200 (Tue, 14 Jul 2009) | 3 lines

Removed a debugging print out.
................
r9220 | bugman | 2009-07-14 11:31:51 +0200 (Tue, 14 Jul 2009) | 3 lines

Fixes for all the N-state model optimisation unit tests.
................
r9221 | bugman | 2009-07-14 11:49:22 +0200 (Tue, 14 Jul 2009) | 3 lines

Fix for the return_units() method. The spin and spin_id args are now accepted.
................
r9222 | bugman | 2009-07-14 12:02:38 +0200 (Tue, 14 Jul 2009) | 5 lines

Fixes for Tyler's peptide system test.

The residue was 111 in the PDB but 211 in the results file, and the spin was unnamed.
................
r9223 | bugman | 2009-07-14 13:24:30 +0200 (Tue, 14 Jul 2009) | 5 lines

Bug fix for the generate_vector_dist() function.

Now the diffusion tensor and cone geometric objects are correctly created!
................
r9224 | bugman | 2009-07-14 13:31:53 +0200 (Tue, 14 Jul 2009) | 5 lines

Bug fix for the generate_vector_residues() function.

Now the negative vector actually is negative! It was previously the same as the positive vector.
................
r9225 | bugman | 2009-07-14 14:10:30 +0200 (Tue, 14 Jul 2009) | 6 lines

Improvements for the reload_pdb() method.

Now the system path is searched for the PDB file. This allows the system tests to pass when not
running from the installation path.
................
r9226 | bugman | 2009-07-14 14:11:19 +0200 (Tue, 14 Jul 2009) | 3 lines

Extended the OMP model-free system test to run MC sims for the diffusion tensor.
................
r9227 | bugman | 2009-07-14 15:12:22 +0200 (Tue, 14 Jul 2009) | 5 lines

Bug fix for the setup of MC simulations of the diffusion tensor.

MC sims were not working when all parameters except for the diffusion tensor are fixed.
................
r9228 | bugman | 2009-07-14 15:26:28 +0200 (Tue, 14 Jul 2009) | 5 lines

Bug fixes for the OMP model-free system test.

The diffusion tensor MC simulation test was not functional.
................
r9229 | bugman | 2009-07-14 15:56:19 +0200 (Tue, 14 Jul 2009) | 5 lines

Fix for the checks in test_omp_analysis().

The wrong data pipe was being accessed.
................
r9230 | bugman | 2009-07-14 15:57:59 +0200 (Tue, 14 Jul 2009) | 5 lines

The diffusion and alignment tensor *_sim and *_err attributes are now listed as modifiable.

This means that this data is placed into the results file, and read back out again!
................

Merged revisions 9048-9066,9068-9069,9081,9194-9196,9198-9200,9202-9230 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

................
r9048 | bugman | 2009-05-12 10:47:02 +0200 (Tue, 12 May 2009) | 3 lines

Updated the pipes.hybridise() user function interface to the 1.3 line design.
................
r9049 | bugman | 2009-05-12 11:09:24 +0200 (Tue, 12 May 2009) | 3 lines

Added 3 new RelaxErrors for sequence matching.
................
r9050 | bugman | 2009-05-12 11:21:59 +0200 (Tue, 12 May 2009) | 3 lines

Added the pipe keyword to all the sequence counting functions.
................
r9051 | bugman | 2009-05-12 11:22:41 +0200 (Tue, 12 May 2009) | 3 lines

Renamed the hybridise() pipes keyword to pipe_list.
................
r9052 | bugman | 2009-05-12 11:25:38 +0200 (Tue, 12 May 2009) | 3 lines

Created the compare_sequence() for checking if 2 sequences are the same.
................
r9053 | bugman | 2009-05-12 11:28:49 +0200 (Tue, 12 May 2009) | 3 lines

Converted the hybridise() method to the 1.3 line design.
................
r9054 | bugman | 2009-05-12 11:31:08 +0200 (Tue, 12 May 2009) | 3 lines

Added the hybrid data pipe to the list of allowable data pipes.
................
r9055 | bugman | 2009-05-12 11:34:40 +0200 (Tue, 12 May 2009) | 3 lines

Added a check for the pipe type to hybridise().
................
r9056 | bugman | 2009-05-12 11:41:12 +0200 (Tue, 12 May 2009) | 3 lines

Converted the duplicate_data() method to the 1.3 line design.
................
r9057 | bugman | 2009-05-12 14:42:06 +0200 (Tue, 12 May 2009) | 3 lines

Removed a test that disallowed model selection between different pipe types.
................
r9058 | bugman | 2009-05-12 14:56:23 +0200 (Tue, 12 May 2009) | 5 lines

Converted all parts of the hybrid module to the 1.3 line design.

This includes the addition of many new, very simple methods and the translation of old code.
................
r9059 | bugman | 2009-05-15 10:47:59 +0200 (Fri, 15 May 2009) | 3 lines

Created the R_axis_angle() function to generate the rotation matrix from the axis-angle notation.
................
r9060 | bugman | 2009-05-15 11:58:55 +0200 (Fri, 15 May 2009) | 3 lines

Added the functions random_rot_axis() and random_R() to generate random rotations.
................
r9061 | bugman | 2009-05-25 13:45:14 +0200 (Mon, 25 May 2009) | 6 lines

Changed the precision of the te check in the model-free system tests.

This is in response to Sebastian's post at
https://mail.gna.org/public/relax-devel/2009-05/msg00003.html.
................
r9062 | bugman | 2009-05-28 15:37:08 +0200 (Thu, 28 May 2009) | 3 lines

Renamed random_R() to R_random_axis().
................
r9063 | bugman | 2009-05-28 15:57:48 +0200 (Thu, 28 May 2009) | 3 lines

Wrote 2 new functions, R_random_hypersphere() and quaternion_to_R().
................
r9064 | bugman | 2009-05-28 16:53:23 +0200 (Thu, 28 May 2009) | 3 lines

Bug fix for the quaternion_to_R() function.
................
r9065 | bugman | 2009-05-29 10:47:09 +0200 (Fri, 29 May 2009) | 3 lines

Fix for the align_tensor.init() user function docstring.
................
r9066 | bugman | 2009-06-02 13:54:11 +0200 (Tue, 02 Jun 2009) | 3 lines

Indentation fix.
................
r9068 | bugman | 2009-06-08 16:21:38 +0200 (Mon, 08 Jun 2009) | 3 lines

Added a function for calculating the Kronecker product.
................
r9069 | bugman | 2009-06-08 17:13:54 +0200 (Mon, 08 Jun 2009) | 3 lines

Added a copyright notice and spun out the T14 transpose into its own function.
................
r9081 | bugman | 2009-06-18 15:01:00 +0200 (Thu, 18 Jun 2009) | 3 lines

Added numpy int and float data types to the list of tested user function args.
................
r9194 | bugman | 2009-07-12 23:55:17 +0200 (Sun, 12 Jul 2009) | 3 lines

Commented out a data type temporarily until someone complains about int32 types.
................
r9195 | bugman | 2009-07-13 00:03:51 +0200 (Mon, 13 Jul 2009) | 5 lines

Created lists of number types (python and numpy).

These are in the prompt.num_types module and are now used by value.set() for argument checking.
................
r9196 | bugman | 2009-07-13 00:05:31 +0200 (Mon, 13 Jul 2009) | 6 lines

Reverted r9194, the temporary commenting out of a data type.

The command used was:
svn merge -r9194:9193 .
................
r9198 | bugman | 2009-07-13 00:07:41 +0200 (Mon, 13 Jul 2009) | 3 lines

Initialized merge tracking via "svnmerge" with revisions "1-9069" from
svn+ssh://bugman@.../svn/relax/branches/frame_order
................
r9199 | bugman | 2009-07-13 00:11:11 +0200 (Mon, 13 Jul 2009) | 566 lines

Merged revisions 9070-9187,9190-9196,9198 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order

........
r9070 | bugman | 2009-06-17 19:27:42 +0200 (Wed, 17 Jun 2009) | 3 lines

Created a branch for the new Frame Order theories.
........
r9071 | bugman | 2009-06-17 19:34:39 +0200 (Wed, 17 Jun 2009) | 3 lines

Added Frame Order to the list of allowable data pipes.
........
r9072 | bugman | 2009-06-17 19:36:36 +0200 (Wed, 17 Jun 2009) | 3 lines

Added a stub package for Frame Order related calculation code.
........
r9073 | bugman | 2009-06-17 20:03:58 +0200 (Wed, 17 Jun 2009) | 3 lines

Added a function for printing out the 2nd degree Frame Order matrix.
........
r9074 | bugman | 2009-06-17 20:05:50 +0200 (Wed, 17 Jun 2009) | 3 lines

Shifted the print_frame_order_2nd_degree() function to generic_fns.
........
r9075 | bugman | 2009-06-17 20:10:17 +0200 (Wed, 17 Jun 2009) | 3 lines

Added a missing import.
........
r9076 | bugman | 2009-06-17 20:30:26 +0200 (Wed, 17 Jun 2009) | 3 lines

Added functions for populating the Frame Order matrices for isotropic cones.
........
r9077 | bugman | 2009-06-18 10:41:27 +0200 (Thu, 18 Jun 2009) | 5 lines

Renamed the frame_order package to frame_order_matrix_ops.

This is to make way for the target function code.
........
r9078 | bugman | 2009-06-18 10:42:31 +0200 (Thu, 18 Jun 2009) | 6 lines

Added the Frame Order target function class.

It currently contains only one target function for an isotropic cone model directly optimised to the
Frame Order matrix elements.
........
r9079 | bugman | 2009-06-18 10:47:30 +0200 (Thu, 18 Jun 2009) | 3 lines

A few fixes for the Frame_order class.
........
r9080 | bugman | 2009-06-18 11:29:22 +0200 (Thu, 18 Jun 2009) | 3 lines

Aliased self.func_iso_cone_elements to self.func.
........
r9082 | bugman | 2009-06-18 22:04:39 +0200 (Thu, 18 Jun 2009) | 3 lines

Renamed the user function n_state_model.set_type() to align_tensor.reduction().
........
r9083 | bugman | 2009-06-18 22:15:18 +0200 (Thu, 18 Jun 2009) | 3 lines

Shifted the N-state model set_type() method to the align_tensor function reduction().
........
r9084 | bugman | 2009-06-19 10:18:35 +0200 (Fri, 19 Jun 2009) | 3 lines

Added the Frame Order theories to the setup of the specific code.
........
r9085 | bugman | 2009-06-19 10:30:00 +0200 (Fri, 19 Jun 2009) | 3 lines

Added the skeleton of the Frame Order specific code.
........
r9086 | bugman | 2009-06-19 10:31:03 +0200 (Fri, 19 Jun 2009) | 3 lines

Added the Frame Order type to get_string().
........
r9087 | bugman | 2009-06-19 10:43:37 +0200 (Fri, 19 Jun 2009) | 3 lines

Implemented most of the grid_search() method.
........
r9088 | bugman | 2009-06-19 10:50:19 +0200 (Fri, 19 Jun 2009) | 5 lines

Created the Frame Order user function class.

The only user function yet available is frame_order.select_model().
........
r9089 | bugman | 2009-06-19 10:51:59 +0200 (Fri, 19 Jun 2009) | 3 lines

Registered the Frame Order user function class into the interpreter.
........
r9090 | bugman | 2009-06-19 10:55:28 +0200 (Fri, 19 Jun 2009) | 3 lines

Wrote the select_model() method.
........
r9091 | bugman | 2009-06-19 10:58:47 +0200 (Fri, 19 Jun 2009) | 3 lines

Added the __update_model() method.
........
r9092 | bugman | 2009-06-19 11:01:22 +0200 (Fri, 19 Jun 2009) | 3 lines

Some fixed for the grid_search() method.
........
r9093 | bugman | 2009-06-19 11:29:00 +0200 (Fri, 19 Jun 2009) | 3 lines

Modifications to the __update_model() method.
........
r9094 | bugman | 2009-06-19 11:44:57 +0200 (Fri, 19 Jun 2009) | 5 lines

Wrote the minimise() and __unpack_opt_results() methods.

The minimise() method is rudimentary and will not work.
........
r9095 | bugman | 2009-06-19 11:50:26 +0200 (Fri, 19 Jun 2009) | 3 lines

Modified the __init__() method and spun of some code into __init_iso_cone_elements().
........
r9096 | bugman | 2009-06-19 11:51:24 +0200 (Fri, 19 Jun 2009) | 3 lines

Docstring update.
........
r9097 | bugman | 2009-06-19 11:52:00 +0200 (Fri, 19 Jun 2009) | 3 lines

Missing RelaxError import.
........
r9098 | bugman | 2009-06-19 15:27:08 +0200 (Fri, 19 Jun 2009) | 3 lines

Fixes for the minimise() method.
........
r9099 | bugman | 2009-06-19 15:57:11 +0200 (Fri, 19 Jun 2009) | 3 lines

Created the compile_2nd_matrix_iso_cone() function for building the 2nd degree Frame Order matrix.
........
r9100 | bugman | 2009-06-19 16:03:20 +0200 (Fri, 19 Jun 2009) | 3 lines

Shifted more code into the compile_2nd_matrix_iso_cone() function.
........
r9101 | bugman | 2009-06-19 16:05:14 +0200 (Fri, 19 Jun 2009) | 3 lines

Fixed the arguments of compile_2nd_matrix_iso_cone().
........
r9102 | bugman | 2009-06-19 16:06:39 +0200 (Fri, 19 Jun 2009) | 3 lines

Missing numpy imports.
........
r9103 | bugman | 2009-06-19 16:07:41 +0200 (Fri, 19 Jun 2009) | 5 lines

Preliminary support for optimisation against alignment tensors.

Added the func_iso_cone() and __init_iso_cone() methods.
........
r9104 | bugman | 2009-06-19 16:09:33 +0200 (Fri, 19 Jun 2009) | 3 lines

Added a check for incorrectly supplied arguments.
........
r9105 | bugman | 2009-06-19 16:35:47 +0200 (Fri, 19 Jun 2009) | 3 lines

Created the __minimise_setup_tensors() method to compile the data needed for optimisation.
........
r9106 | bugman | 2009-06-19 16:39:03 +0200 (Fri, 19 Jun 2009) | 3 lines

Modified the reduction() function to store alignment tensor indices rather than names.
........
r9107 | bugman | 2009-06-19 16:41:15 +0200 (Fri, 19 Jun 2009) | 3 lines

Fixed for the __minimise_setup_tensors() method.
........
r9108 | bugman | 2009-06-19 16:42:19 +0200 (Fri, 19 Jun 2009) | 3 lines

Fix for the frame_order_models.Frame_order setup within minimise().
........
r9109 | bugman | 2009-06-19 16:43:16 +0200 (Fri, 19 Jun 2009) | 3 lines

Removed an unused print statement.
........
r9110 | bugman | 2009-06-19 16:50:03 +0200 (Fri, 19 Jun 2009) | 3 lines

Docstring fixes and variable renaming in __minimise_setup_tensors().
........
r9111 | bugman | 2009-06-19 16:51:53 +0200 (Fri, 19 Jun 2009) | 3 lines

Docstring updates.
........
r9112 | bugman | 2009-06-19 16:52:04 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fix for the tensor optimisation.
........
r9113 | bugman | 2009-06-19 17:12:57 +0200 (Fri, 19 Jun 2009) | 3 lines

Temporary fix for func_iso_cone().
........
r9114 | bugman | 2009-06-19 17:15:33 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fixes for the __unpack_opt_results() method.
........
r9115 | bugman | 2009-06-19 17:21:56 +0200 (Fri, 19 Jun 2009) | 3 lines

Parameter values are initialised to zero so that a grid search is not necessary.
........
r9116 | bugman | 2009-06-19 17:31:41 +0200 (Fri, 19 Jun 2009) | 6 lines

Fix for the compilation of the Frame Order matrix.

The compile_2nd_matrix_iso_cone() function now returns the matrix as it is now in a different
memory location.
........
r9117 | bugman | 2009-06-19 19:22:07 +0200 (Fri, 19 Jun 2009) | 5 lines

Added the function reduce_alignment_tensor().

This calculates how the Frame Order matrix reduces the alignment tensor.
........
r9118 | bugman | 2009-06-19 19:22:29 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fix for reduce_alignment_tensor().
........
r9119 | bugman | 2009-06-19 19:22:59 +0200 (Fri, 19 Jun 2009) | 3 lines

The reduced tensors are now back calculated.
........
r9120 | bugman | 2009-06-19 19:23:23 +0200 (Fri, 19 Jun 2009) | 3 lines

Simplification of func_iso_cone().
........
r9121 | bugman | 2009-06-19 19:23:48 +0200 (Fri, 19 Jun 2009) | 3 lines

Another bug fix for reduce_alignment_tensor().
........
r9122 | bugman | 2009-06-19 19:24:19 +0200 (Fri, 19 Jun 2009) | 3 lines

Imported reduce_alignment_tensor().
........
r9123 | bugman | 2009-06-19 19:25:09 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fix for func_iso_cone().
........
r9124 | bugman | 2009-06-19 19:25:33 +0200 (Fri, 19 Jun 2009) | 3 lines

Another bug fix for reduce_alignment_tensor().
........
r9125 | bugman | 2009-06-19 19:30:06 +0200 (Fri, 19 Jun 2009) | 3 lines

Bug fix for the initialisation of self.red_tensors_bc.
........
r9126 | bugman | 2009-06-19 19:42:51 +0200 (Fri, 19 Jun 2009) | 3 lines

Made the default errors more reasonable.
........
r9127 | bugman | 2009-06-22 19:52:00 +0200 (Mon, 22 Jun 2009) | 3 lines

Bug fix for the reduce_alignment_tensor() function.
........
r9128 | bugman | 2009-06-23 11:14:13 +0200 (Tue, 23 Jun 2009) | 5 lines

Elimination of an Euler angle from the isotropic cone model.

Only the cone axis theta and phi angles are now optimised.
........
r9129 | bugman | 2009-06-23 11:20:16 +0200 (Tue, 23 Jun 2009) | 3 lines

Set up the z-axis data structures.
........
r9130 | bugman | 2009-06-23 11:31:59 +0200 (Tue, 23 Jun 2009) | 3 lines

Added the cone axis storage structure.
........
r9131 | bugman | 2009-06-23 11:32:19 +0200 (Tue, 23 Jun 2009) | 3 lines

Updated the compile_2nd_matrix_iso_cone() function to use the cone axis angles rather than Euler.
........
r9132 | bugman | 2009-06-23 11:37:05 +0200 (Tue, 23 Jun 2009) | 5 lines

Bug fix for compile_2nd_matrix_iso_cone().

The rotation matrix uses the polar angle, not the cone angle.
........
r9133 | bugman | 2009-06-23 12:58:40 +0200 (Tue, 23 Jun 2009) | 5 lines

Bug fix for the compile_2nd_matrix_iso_cone() function.

The cross product of 2 normal vectors is not a normal vector!!!
........
r9134 | bugman | 2009-06-23 13:42:26 +0200 (Tue, 23 Jun 2009) | 5 lines

Removed the sequence test in the Monte Carlo create_data() function.

No all data pipes in relax require sequence info.
........
r9135 | bugman | 2009-06-23 14:23:53 +0200 (Tue, 23 Jun 2009) | 3 lines

Added a dummy eliminate() method.
........
r9136 | bugman | 2009-06-23 16:22:12 +0200 (Tue, 23 Jun 2009) | 19 lines

Added the ability to perform Monte Carlo sims for the Frame Order theories.

For this, the following methods have been added:
__tensor_loop()
back_calc()
base_data_loop()
create_mc_data()
data_names()
model_loop()
return_error()
set_selected_sim()
sim_init_values()
sim_pack_data()
sim_return_param()
sim_return_selected()

Many other methods have also been modified.
........
r9137 | bugman | 2009-06-23 16:45:44 +0200 (Tue, 23 Jun 2009) | 3 lines

Updated the init() and set() method to allow alignment tensor errors to be input.
........
r9138 | bugman | 2009-06-23 17:41:52 +0200 (Tue, 23 Jun 2009) | 3 lines

More fixes for error setting in the set() function.
........
r9139 | bugman | 2009-06-23 17:52:07 +0200 (Tue, 23 Jun 2009) | 5 lines

Bug fix for the init() method.

Now errors are being placed in the pre-existing tensor, rather than a new tensor being added.
........
r9140 | bugman | 2009-06-23 18:19:49 +0200 (Tue, 23 Jun 2009) | 5 lines

Another bug fix for the init() method.

Errors are not properly handled for all input data types.
........
r9141 | bugman | 2009-06-23 19:23:11 +0200 (Tue, 23 Jun 2009) | 5 lines

Removed ambiguity from the align_tensor.reduction() user function.

The from_tensor and to_tensor args have been renamed to full_tensor and red_tensor respectively.
........
r9142 | bugman | 2009-06-25 12:00:41 +0200 (Thu, 25 Jun 2009) | 3 lines

Created the interface to the frame_order.cone_pdb() user function.
........
r9143 | bugman | 2009-06-25 13:17:53 +0200 (Thu, 25 Jun 2009) | 3 lines

Created the interface for the frame_order.pivot() user function.
........
r9144 | bugman | 2009-06-25 13:38:11 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fix for the R_2vect() function.

The rotation axis is not always of unit length!
........
r9145 | bugman | 2009-06-25 13:42:50 +0200 (Thu, 25 Jun 2009) | 3 lines

Spun out the cone axis generation code into generate_vector().
........
r9146 | bugman | 2009-06-25 13:45:54 +0200 (Thu, 25 Jun 2009) | 3 lines

Simplified compile_2nd_matrix_iso_cone() by using R_2vect().
........
r9147 | bugman | 2009-06-25 14:02:23 +0200 (Thu, 25 Jun 2009) | 3 lines

Bug fix for the generate_vector_residues() for numpy MC sim structures.
........
r9148 | bugman | 2009-06-25 14:03:36 +0200 (Thu, 25 Jun 2009) | 3 lines

Another bug fix for the generate_vector_residues() function for MC simulations.
........
r9149 | bugman | 2009-06-25 14:22:32 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fix for generate_vector_residues() when the neg flag is False.

The atoms were incorrectly numbered.
........
r9150 | bugman | 2009-06-25 14:24:51 +0200 (Thu, 25 Jun 2009) | 3 lines

Wrote the cone_pdb() and pivot() methods.
........
r9151 | bugman | 2009-06-25 15:02:34 +0200 (Thu, 25 Jun 2009) | 5 lines

Renaming and fixes for stitch_cone_to_edge().

This was stitch_cap_to_cone().
........
r9152 | bugman | 2009-06-25 15:24:01 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fixes for the write_pdb() method.

The Hetrogen section was failing with MC simulations.
........
r9153 | bugman | 2009-06-25 15:24:41 +0200 (Thu, 25 Jun 2009) | 3 lines

Fixes for the cone_pdb() method.
........
r9154 | bugman | 2009-06-25 15:58:39 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fixes for the generate_vector_dist() function.

The protons were not being correctly stitched together!
........
r9155 | bugman | 2009-06-25 16:02:26 +0200 (Thu, 25 Jun 2009) | 3 lines

Added a test for a loaded structure to the pymol.cartoon() user function.
........
r9156 | bugman | 2009-06-25 16:26:11 +0200 (Thu, 25 Jun 2009) | 5 lines

Bug fix for the pymol.cartoon() user function.

This was failing when multiple proteins were loaded.
........
r9157 | bugman | 2009-06-25 16:34:17 +0200 (Thu, 25 Jun 2009) | 3 lines

Changed the scaling arg to a direct size arg.
........
r9158 | bugman | 2009-06-25 16:36:00 +0200 (Thu, 25 Jun 2009) | 3 lines

cone_pdb() now handles the AXE residue.
........
r9159 | bugman | 2009-06-25 16:37:03 +0200 (Thu, 25 Jun 2009) | 3 lines

Renamed the axis atom from 'Axe' to 'Axis'.
........
r9160 | bugman | 2009-06-25 16:41:25 +0200 (Thu, 25 Jun 2009) | 3 lines

Made the cone_pdb() function less specific for the N-state model and added SIM as an axis to decorate.
........
r9161 | bugman | 2009-06-25 16:46:40 +0200 (Thu, 25 Jun 2009) | 3 lines

The user can now set the number of increments used to generate the cone PDB.
........
r9162 | bugman | 2009-06-29 10:24:03 +0200 (Mon, 29 Jun 2009) | 3 lines

Wrote the calculate() method for calculating the chi-squared value for the current parameters.
........
r9163 | bugman | 2009-06-29 10:25:13 +0200 (Mon, 29 Jun 2009) | 6 lines

Expansion of frame order to both the forward and reverse rotations.

reduce_alignment_tensor() was renamed to reduce_alignment_tensor_reverse(), and the new function
reduce_alignment_tensor() added.
........
r9164 | bugman | 2009-06-30 11:21:49 +0200 (Tue, 30 Jun 2009) | 3 lines

Added checks for the presence of the data structures necessary for frame_order.cone_pdb().
........
r9165 | bugman | 2009-06-30 11:24:12 +0200 (Tue, 30 Jun 2009) | 3 lines

Bug fix for frame_order.cone_pdb() for when no MC sims exist.
........
r9166 | bugman | 2009-06-30 11:43:31 +0200 (Tue, 30 Jun 2009) | 5 lines

Bug fix for the cone PDB generation.

If there were more than 1000 protons, the PDB file was corrupted by the proton name being too long.
........
r9167 | bugman | 2009-07-01 13:05:09 +0200 (Wed, 01 Jul 2009) | 6 lines

Reverted r9128 to r9133, the elimination of a Euler angle (maybe only temporarily).

The command used was:
svn merge -r9134:9127 .
........
r9168 | bugman | 2009-07-01 16:08:46 +0200 (Wed, 01 Jul 2009) | 3 lines

Renamed theta to theta cone (again due to the reversion).
........
r9169 | bugman | 2009-07-02 02:28:25 +0200 (Thu, 02 Jul 2009) | 3 lines

Missing import.
........
r9170 | bugman | 2009-07-02 02:33:45 +0200 (Thu, 02 Jul 2009) | 3 lines

The cone axis is back, and better support for the Euler angles.
........
r9171 | bugman | 2009-07-02 02:36:53 +0200 (Thu, 02 Jul 2009) | 3 lines

Return of the cone axis, and rotation of the reduced tensor.
........
r9172 | bugman | 2009-07-02 02:55:17 +0200 (Thu, 02 Jul 2009) | 6 lines

Partly reverted r9167 - the previous reversion.

The command used was:
svn merge -r9167:9166 generic_fns/monte_carlo.py
........
r9173 | bugman | 2009-07-02 02:58:54 +0200 (Thu, 02 Jul 2009) | 8 lines

Partly reverted r9167 - the previous revision.

The command used was:
svn merge -r9167:9166 maths_fns/frame_order_matrix_ops.py

This returns the cone axis.
........
r9174 | bugman | 2009-07-02 03:01:41 +0200 (Thu, 02 Jul 2009) | 6 lines

Partly reverted r9167 - the previous reversion.

The command used was:
svn merge -r9167:9166 maths_fns/frame_order_models.py
........
r9175 | bugman | 2009-07-02 03:02:12 +0200 (Thu, 02 Jul 2009) | 3 lines

Missing import.
........
r9176 | bugman | 2009-07-02 03:19:39 +0200 (Thu, 02 Jul 2009) | 3 lines

The Euler angles are now wrapped between 0 and 2pi.
........
r9177 | bugman | 2009-07-02 14:03:17 +0200 (Thu, 02 Jul 2009) | 3 lines

Added the new function R_to_axis_angle().
........
r9178 | bugman | 2009-07-02 15:25:08 +0200 (Thu, 02 Jul 2009) | 3 lines

Bug fix for the R_to_axis_angle() function. The axis needs to be normalised.
........
r9179 | bugman | 2009-07-02 15:25:40 +0200 (Thu, 02 Jul 2009) | 3 lines

Both the positive and negative cones are now made.
........
r9180 | bugman | 2009-07-02 16:50:51 +0200 (Thu, 02 Jul 2009) | 3 lines

Fixes for the negative cone.
........
r9181 | bugman | 2009-07-02 17:18:50 +0200 (Thu, 02 Jul 2009) | 3 lines

Fix for the N-state model arg checks.
........
r9182 | bugman | 2009-07-02 23:09:23 +0200 (Thu, 02 Jul 2009) | 3 lines

Bug fix for cone_pdb() for when no MC sims are run.
........
r9183 | bugman | 2009-07-02 23:13:13 +0200 (Thu, 02 Jul 2009) | 3 lines

Created and now using the full_in_ref_frame data structure (copy of N-state model).
........
r9184 | bugman | 2009-07-02 23:22:55 +0200 (Thu, 02 Jul 2009) | 3 lines

Added a check for the reference domain setup to __minimise_setup_tensors().
........
r9185 | bugman | 2009-07-02 23:25:33 +0200 (Thu, 02 Jul 2009) | 3 lines

Renamed n_state_model.set_domain() to align_tensor.set_domain().
........
r9186 | bugman | 2009-07-02 23:27:38 +0200 (Thu, 02 Jul 2009) | 3 lines

Shifted the set_domain() back-end from the N-state model to the alignment tensor.
........
r9187 | bugman | 2009-07-03 00:11:43 +0200 (Fri, 03 Jul 2009) | 3 lines

Added the interface for the frame_order.n_state_model() user function.
........
r9190 | bugman | 2009-07-12 23:31:31 +0200 (Sun, 12 Jul 2009) | 3 lines

Fixes for the unit tests of the user functions shifted from n_state_model to align_tensor.
........
r9191 | bugman | 2009-07-12 23:38:43 +0200 (Sun, 12 Jul 2009) | 3 lines

Fixes for the 5-state model system test.
........
r9192 | bugman | 2009-07-12 23:49:33 +0200 (Sun, 12 Jul 2009) | 3 lines

Modified the N-state model code to be more like the Frame Order matrix code.
........
r9193 | bugman | 2009-07-12 23:52:54 +0200 (Sun, 12 Jul 2009) | 3 lines

Copyright statement update.
........
................
r9200 | bugman | 2009-07-13 00:14:36 +0200 (Mon, 13 Jul 2009) | 3 lines

Removed merge properties.
................
r9202 | bugman | 2009-07-13 10:08:16 +0200 (Mon, 13 Jul 2009) | 7 lines

Removed all usages of float128, as this type is not present on all machines.

This was reported by Sebastian Morin in the post:
https://mail.gna.org/public/relax-devel/2009-07/msg00000.html (Message-id:
<4A5A7338.4030500@...>).
................
r9203 | bugman | 2009-07-13 15:16:27 +0200 (Mon, 13 Jul 2009) | 3 lines

Missing import.
................
r9204 | bugman | 2009-07-13 15:17:34 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fixes for the get_specific_fn() function.
................
r9205 | bugman | 2009-07-13 15:18:36 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fixes for the grace.write() user function.
................
r9206 | bugman | 2009-07-13 15:19:41 +0200 (Mon, 13 Jul 2009) | 5 lines

Bug fix for the molmol macro setup.

This was not being correctly retrieved.
................
r9207 | bugman | 2009-07-13 15:21:55 +0200 (Mon, 13 Jul 2009) | 3 lines

Changed the statistics ordering when running profiling.
................
r9208 | bugman | 2009-07-13 15:22:33 +0200 (Mon, 13 Jul 2009) | 3 lines

align_tensor.init() can now accept any type of float or int (python or numpy).
................
r9209 | bugman | 2009-07-13 16:28:58 +0200 (Mon, 13 Jul 2009) | 6 lines

Partial reversion of r9204.

The AttributeError should be checked for, not the NameError! NameError was only triggered by
another bug.
................
r9210 | bugman | 2009-07-13 18:29:31 +0200 (Mon, 13 Jul 2009) | 5 lines

Bug fixes for return_conversion_factor() and return_units() functions.

The spin and spin_id args are now accepted.
................
r9211 | bugman | 2009-07-13 18:30:04 +0200 (Mon, 13 Jul 2009) | 5 lines

Fix for the write_multi_header() function.

The spin_id variable now exists.
................
r9212 | bugman | 2009-07-13 18:30:45 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fix: The return_conversion_factor() method now accepts the spin arg.
................
r9213 | bugman | 2009-07-13 18:31:07 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fix: The return_units() method now accepts the spin_id keyword arg.
................
r9214 | bugman | 2009-07-13 18:32:32 +0200 (Mon, 13 Jul 2009) | 3 lines

Bug fix for the return_units() method, the spin_id keyword arg is now accepted.
................
r9215 | bugman | 2009-07-13 18:38:06 +0200 (Mon, 13 Jul 2009) | 5 lines

Fix for the return_units() method.

The spin and spin_id args are now accepted.
................
r9216 | bugman | 2009-07-14 11:04:22 +0200 (Tue, 14 Jul 2009) | 3 lines

Added a check for the chi-squared value for the 5-state model system test.
................
r9217 | bugman | 2009-07-14 11:26:12 +0200 (Tue, 14 Jul 2009) | 3 lines

Bug fix: The tensor reduction was specified back to front!
................
r9218 | bugman | 2009-07-14 11:26:55 +0200 (Tue, 14 Jul 2009) | 3 lines

Fix for the func_2domain() method for the N-state model tensor reduction code.
................
r9219 | bugman | 2009-07-14 11:27:30 +0200 (Tue, 14 Jul 2009) | 3 lines

Removed a debugging print out.
................
r9220 | bugman | 2009-07-14 11:31:51 +0200 (Tue, 14 Jul 2009) | 3 lines

Fixes for all the N-state model optimisation unit tests.
................
r9221 | bugman | 2009-07-14 11:49:22 +0200 (Tue, 14 Jul 2009) | 3 lines

Fix for the return_units() method. The spin and spin_id args are now accepted.
................
r9222 | bugman | 2009-07-14 12:02:38 +0200 (Tue, 14 Jul 2009) | 5 lines

Fixes for Tyler's peptide system test.

The residue was 111 in the PDB but 211 in the results file, and the spin was unnamed.
................
r9223 | bugman | 2009-07-14 13:24:30 +0200 (Tue, 14 Jul 2009) | 5 lines

Bug fix for the generate_vector_dist() function.

Now the diffusion tensor and cone geometric objects are correctly created!
................
r9224 | bugman | 2009-07-14 13:31:53 +0200 (Tue, 14 Jul 2009) | 5 lines

Bug fix for the generate_vector_residues() function.

Now the negative vector actually is negative! It was previously the same as the positive vector.
................
r9225 | bugman | 2009-07-14 14:10:30 +0200 (Tue, 14 Jul 2009) | 6 lines

Improvements for the reload_pdb() method.

Now the system path is searched for the PDB file. This allows the system tests to pass when not
running from the installation path.
................
r9226 | bugman | 2009-07-14 14:11:19 +0200 (Tue, 14 Jul 2009) | 3 lines

Extended the OMP model-free system test to run MC sims for the diffusion tensor.
................
r9227 | bugman | 2009-07-14 15:12:22 +0200 (Tue, 14 Jul 2009) | 5 lines

Bug fix for the setup of MC simulations of the diffusion tensor.

MC sims were not working when all parameters except for the diffusion tensor are fixed.
................
r9228 | bugman | 2009-07-14 15:26:28 +0200 (Tue, 14 Jul 2009) | 5 lines

Bug fixes for the OMP model-free system test.

The diffusion tensor MC simulation test was not functional.
................
r9229 | bugman | 2009-07-14 15:56:19 +0200 (Tue, 14 Jul 2009) | 5 lines

Fix for the checks in test_omp_analysis().

The wrong data pipe was being accessed.
................
r9230 | bugman | 2009-07-14 15:57:59 +0200 (Tue, 14 Jul 2009) | 5 lines

The diffusion and alignment tensor *_sim and *_err attributes are now listed as modifiable.

This means that this data is placed into the results file, and read back out again!
................

The diffusion and alignment tensor *_sim and *_err attributes are now listed as modifiable.

This means that this data is placed into the results file, and read back out again!

Fix for the checks in test_omp_analysis().

The wrong data pipe was being accessed.

Bug fixes for the OMP model-free system test.

The diffusion tensor MC simulation test was not functional.

Bug fix for the setup of MC simulations of the diffusion tensor.

MC sims were not working when all parameters except for the diffusion tensor are fixed.

Extended the OMP model-free system test to run MC sims for the diffusion tensor.

Improvements for the reload_pdb() method.

Now the system path is searched for the PDB file. This allows the system tests to pass when not
running from the installation path.