Author: bugman Date: Wed Jul 15 11:26:01 2009 New Revision: 9233 URL: http://svn.gna.org/viewcvs/relax?rev=9233&view=rev Log: Merged revisions 9048-9066,9068-9069,9081,9194-9196,9198-9200,9202-9230 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/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@xxxxxxxxxxx/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@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. ........ [... 505 lines stripped ...]