Author: bugman Date: Mon Jul 13 00:11:11 2009 New Revision: 9199 URL: http://svn.gna.org/viewcvs/relax?rev=9199&view=rev Log: Merged revisions 9070-9187,9190-9196,9198 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/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. ........ Added: 1.3/generic_fns/frame_order.py - copied unchanged [... 86 lines stripped ...]