Author: bugman
Date: Wed Jul 15 11:28:19 2009
New Revision: 9234
URL: http://svn.gna.org/viewcvs/relax?rev=9234&view=rev
Log:
Merged revisions 9068-9069,9081,9194-9196,9198-9200,9202-9230 via svnmerge
from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r9068 | bugman | 2009-06-08 16:21:38 +0200 (Mon, 08 Jun 2009) | 3 lines
Added a function for calculating the Kronecker product.
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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.
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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.
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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.
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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.
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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 .
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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
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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
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r9070 | bugman | 2009-06-17 19:27:42 +0200 (Wed, 17 Jun 2009) | 3 lines
Created a branch for the new Frame Order theories.
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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.
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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.
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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.
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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.
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r9075 | bugman | 2009-06-17 20:10:17 +0200 (Wed, 17 Jun 2009) | 3 lines
Added a missing import.
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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.
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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.
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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.
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r9079 | bugman | 2009-06-18 10:47:30 +0200 (Thu, 18 Jun 2009) | 3 lines
A few fixes for the Frame_order class.
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r9080 | bugman | 2009-06-18 11:29:22 +0200 (Thu, 18 Jun 2009) | 3 lines
Aliased self.func_iso_cone_elements to self.func.
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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().
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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().
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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.
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r9085 | bugman | 2009-06-19 10:30:00 +0200 (Fri, 19 Jun 2009) | 3 lines
Added the skeleton of the Frame Order specific code.
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r9086 | bugman | 2009-06-19 10:31:03 +0200 (Fri, 19 Jun 2009) | 3 lines
Added the Frame Order type to get_string().
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r9087 | bugman | 2009-06-19 10:43:37 +0200 (Fri, 19 Jun 2009) | 3 lines
Implemented most of the grid_search() method.
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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().
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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.
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r9090 | bugman | 2009-06-19 10:55:28 +0200 (Fri, 19 Jun 2009) | 3 lines
Wrote the select_model() method.
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r9091 | bugman | 2009-06-19 10:58:47 +0200 (Fri, 19 Jun 2009) | 3 lines
Added the __update_model() method.
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r9092 | bugman | 2009-06-19 11:01:22 +0200 (Fri, 19 Jun 2009) | 3 lines
Some fixed for the grid_search() method.
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r9093 | bugman | 2009-06-19 11:29:00 +0200 (Fri, 19 Jun 2009) | 3 lines
Modifications to the __update_model() method.
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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.
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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().
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r9096 | bugman | 2009-06-19 11:51:24 +0200 (Fri, 19 Jun 2009) | 3 lines
Docstring update.
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r9097 | bugman | 2009-06-19 11:52:00 +0200 (Fri, 19 Jun 2009) | 3 lines
Missing RelaxError import.
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r9098 | bugman | 2009-06-19 15:27:08 +0200 (Fri, 19 Jun 2009) | 3 lines
Fixes for the minimise() method.
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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.
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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.
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r9101 | bugman | 2009-06-19 16:05:14 +0200 (Fri, 19 Jun 2009) | 3 lines
Fixed the arguments of compile_2nd_matrix_iso_cone().
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r9102 | bugman | 2009-06-19 16:06:39 +0200 (Fri, 19 Jun 2009) | 3 lines
Missing numpy imports.
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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.
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r9104 | bugman | 2009-06-19 16:09:33 +0200 (Fri, 19 Jun 2009) | 3 lines
Added a check for incorrectly supplied arguments.
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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.
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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.
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r9107 | bugman | 2009-06-19 16:41:15 +0200 (Fri, 19 Jun 2009) | 3 lines
Fixed for the __minimise_setup_tensors() method.
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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().
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r9109 | bugman | 2009-06-19 16:43:16 +0200 (Fri, 19 Jun 2009) | 3 lines
Removed an unused print statement.
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r9110 | bugman | 2009-06-19 16:50:03 +0200 (Fri, 19 Jun 2009) | 3 lines
Docstring fixes and variable renaming in __minimise_setup_tensors().
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r9111 | bugman | 2009-06-19 16:51:53 +0200 (Fri, 19 Jun 2009) | 3 lines
Docstring updates.
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r9112 | bugman | 2009-06-19 16:52:04 +0200 (Fri, 19 Jun 2009) | 3 lines
Bug fix for the tensor optimisation.
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r9113 | bugman | 2009-06-19 17:12:57 +0200 (Fri, 19 Jun 2009) | 3 lines
Temporary fix for func_iso_cone().
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r9114 | bugman | 2009-06-19 17:15:33 +0200 (Fri, 19 Jun 2009) | 3 lines
Bug fixes for the __unpack_opt_results() method.
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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.
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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.
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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.
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r9118 | bugman | 2009-06-19 19:22:29 +0200 (Fri, 19 Jun 2009) | 3 lines
Bug fix for reduce_alignment_tensor().
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r9119 | bugman | 2009-06-19 19:22:59 +0200 (Fri, 19 Jun 2009) | 3 lines
The reduced tensors are now back calculated.
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r9120 | bugman | 2009-06-19 19:23:23 +0200 (Fri, 19 Jun 2009) | 3 lines
Simplification of func_iso_cone().
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r9121 | bugman | 2009-06-19 19:23:48 +0200 (Fri, 19 Jun 2009) | 3 lines
Another bug fix for reduce_alignment_tensor().
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r9122 | bugman | 2009-06-19 19:24:19 +0200 (Fri, 19 Jun 2009) | 3 lines
Imported reduce_alignment_tensor().
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r9123 | bugman | 2009-06-19 19:25:09 +0200 (Fri, 19 Jun 2009) | 3 lines
Bug fix for func_iso_cone().
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r9124 | bugman | 2009-06-19 19:25:33 +0200 (Fri, 19 Jun 2009) | 3 lines
Another bug fix for reduce_alignment_tensor().
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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.
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r9126 | bugman | 2009-06-19 19:42:51 +0200 (Fri, 19 Jun 2009) | 3 lines
Made the default errors more reasonable.
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r9127 | bugman | 2009-06-22 19:52:00 +0200 (Mon, 22 Jun 2009) | 3 lines
Bug fix for the reduce_alignment_tensor() function.
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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.
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r9129 | bugman | 2009-06-23 11:20:16 +0200 (Tue, 23 Jun 2009) | 3 lines
Set up the z-axis data structures.
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r9130 | bugman | 2009-06-23 11:31:59 +0200 (Tue, 23 Jun 2009) | 3 lines
Added the cone axis storage structure.
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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.
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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.
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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!!!
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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.
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r9135 | bugman | 2009-06-23 14:23:53 +0200 (Tue, 23 Jun 2009) | 3 lines
Added a dummy eliminate() method.
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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.
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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.
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r9138 | bugman | 2009-06-23 17:41:52 +0200 (Tue, 23 Jun 2009) | 3 lines
More fixes for error setting in the set() function.
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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.
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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.
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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.
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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.
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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.
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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!
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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().
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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().
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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.
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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.
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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.
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r9150 | bugman | 2009-06-25 14:24:51 +0200 (Thu, 25 Jun 2009) | 3 lines
Wrote the cone_pdb() and pivot() methods.
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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().
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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.
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r9153 | bugman | 2009-06-25 15:24:41 +0200 (Thu, 25 Jun 2009) | 3 lines
Fixes for the cone_pdb() method.
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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!
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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.
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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.
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r9157 | bugman | 2009-06-25 16:34:17 +0200 (Thu, 25 Jun 2009) | 3 lines
Changed the scaling arg to a direct size arg.
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r9158 | bugman | 2009-06-25 16:36:00 +0200 (Thu, 25 Jun 2009) | 3 lines
cone_pdb() now handles the AXE residue.
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r9159 | bugman | 2009-06-25 16:37:03 +0200 (Thu, 25 Jun 2009) | 3 lines
Renamed the axis atom from 'Axe' to 'Axis'.
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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.
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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.
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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.
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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.
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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().
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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.
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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.
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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 .
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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).
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r9169 | bugman | 2009-07-02 02:28:25 +0200 (Thu, 02 Jul 2009) | 3 lines
Missing import.
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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.
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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.
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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
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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.
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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:
[... 400 lines stripped ...]
r9234 - in /branches/relax_disp: ./ data/ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ specific_fns/ specific_fns/...