svn+ssh://bugman@.../svn/relax/1.3
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r14819 | bugman | 2011-10-11 10:28:29 +0200 (Tue, 11 Oct 2011) | 6 lines
Added a truncated version of the CaM-KKalpha data from the BMRB 15183 entry for system tests.
This will be used to validate the Grace plotting when multiple types of spin are present.
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r14820 | bugman | 2011-10-11 10:53:51 +0200 (Tue, 11 Oct 2011) | 3 lines
Created the test_cam_kkalpha_plot1() system test for checking the grace plotting of mixed data.
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r14821 | bugman | 2011-10-11 10:58:18 +0200 (Tue, 11 Oct 2011) | 3 lines
Some small fixes for the new test_cam_kkalpha_plot1() system test.
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r14822 | bugman | 2011-10-11 10:59:39 +0200 (Tue, 11 Oct 2011) | 5 lines
Bug fix for the grace.write user function for when the spin ID is specified.
The spin ID was previously unused!
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r14823 | bugman | 2011-10-12 13:07:25 +0200 (Wed, 12 Oct 2011) | 6 lines
The alignment_tensor.fix user function is now tensor specific.
This will allow a subset of tensors to be optimised while the others are kept fixed. The specific
analysis code will need to be updated for this.
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r14824 | bugman | 2011-10-12 13:12:18 +0200 (Wed, 12 Oct 2011) | 3 lines
Created the generic_fns.align_tensor.all_fixed() fn for determining if all tensors are fixed.
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r14825 | bugman | 2011-10-12 13:16:14 +0200 (Wed, 12 Oct 2011) | 3 lines
Renamed all_fixed() to all_tensors_fixed().
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r14826 | bugman | 2011-10-12 13:23:23 +0200 (Wed, 12 Oct 2011) | 3 lines
Syntax fix in the all_tensors_fixed() function.
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r14827 | bugman | 2011-10-12 13:24:08 +0200 (Wed, 12 Oct 2011) | 3 lines
Syntax error in the align_tensor.fix user function front end.
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r14828 | bugman | 2011-10-12 13:34:05 +0200 (Wed, 12 Oct 2011) | 3 lines
Updated the relax data store alignment tensor objects to allow for the per-tensor fixed flag.
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r14829 | bugman | 2011-10-12 13:36:16 +0200 (Wed, 12 Oct 2011) | 5 lines
Updated the N-state model analysis code to handle the per-alignment tensor fixed flag.
This allows subsets of tensors to be optimised while the others are fixed.
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r14830 | bugman | 2011-10-12 13:54:33 +0200 (Wed, 12 Oct 2011) | 5 lines
Fixes for the N-state model optimisation for when a subset of tensors are fixed.
The RDC and PCS data was incorrectly assembled.
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r14831 | bugman | 2011-10-12 14:00:19 +0200 (Wed, 12 Oct 2011) | 5 lines
The RDC and PCS Q factor functions are now more robust when data is missing.
The data checks are now more extensive.
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r14832 | bugman | 2011-10-12 14:06:31 +0200 (Wed, 12 Oct 2011) | 3 lines
Fix for a divide by zero error in the PCS Q factor function.
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r14833 | bugman | 2011-10-12 14:21:02 +0200 (Wed, 12 Oct 2011) | 3 lines
The RDC and PCS Q factors for each alignment is now stored as a dictionary in the relax data store.
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r14834 | bugman | 2011-10-12 14:35:47 +0200 (Wed, 12 Oct 2011) | 3 lines
Fix for the storing of the N-state model back-calculated RDC and PCS data.
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r14835 | bugman | 2011-10-12 14:46:14 +0200 (Wed, 12 Oct 2011) | 5 lines
Fix for the N-state model _minimise_bc_data() method for when no alignments are present.
This fixes a recently introduced problem.
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r14836 | bugman | 2011-10-12 14:57:13 +0200 (Wed, 12 Oct 2011) | 3 lines
Another fix for a recent bug in _minimise_bc_data().
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r14837 | bugman | 2011-10-12 15:18:25 +0200 (Wed, 12 Oct 2011) | 3 lines
Created a system test script for checking one type of algorithm for Ln3+ position optimisation.
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r14838 | bugman | 2011-10-12 15:32:46 +0200 (Wed, 12 Oct 2011) | 5 lines
Created the test_metal_pos_opt() N-state model system test.
Specific RDC and PCS data for this test has also been generated.
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r14839 | bugman | 2011-10-12 15:40:08 +0200 (Wed, 12 Oct 2011) | 5 lines
Bug fix for the setup of the N-state model target function.
This is triggered by missing data.
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r14840 | bugman | 2011-10-12 16:30:00 +0200 (Wed, 12 Oct 2011) | 5 lines
The N-state model can now be optimised with a subset of the alignment tensors fixed.
This required a reworking of the data assembly and target function code.
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r14841 | bugman | 2011-10-12 16:30:24 +0200 (Wed, 12 Oct 2011) | 3 lines
Removed an empty line.
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r14842 | bugman | 2011-10-12 16:40:56 +0200 (Wed, 12 Oct 2011) | 3 lines
Updated the metal_pos_opt.py N-state model system test script to catch another code design problem.
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r14843 | bugman | 2011-10-12 16:47:53 +0200 (Wed, 12 Oct 2011) | 5 lines
Fixes for the population N-state model for when subsets of alignment tensors are fixed.
This is in the function, gradient, and Hessian code.
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r14844 | bugman | 2011-10-12 16:55:39 +0200 (Wed, 12 Oct 2011) | 3 lines
Fixes for the population N-state model target function.
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r14845 | bugman | 2011-10-12 17:00:24 +0200 (Wed, 12 Oct 2011) | 3 lines
Fix for the setup of the 2-domain N-state model.
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r14846 | bugman | 2011-10-12 17:19:36 +0200 (Wed, 12 Oct 2011) | 3 lines
Fixes for all of the N-state models - the indices were not being incremented!
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r14847 | bugman | 2011-10-12 17:28:48 +0200 (Wed, 12 Oct 2011) | 3 lines
One last fix for the setup of the N-state model target functions.
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r14848 | bugman | 2011-10-12 17:36:19 +0200 (Wed, 12 Oct 2011) | 5 lines
Added another check to the metal optimisation N-state model system test script.
This now catches if the metal has been optimised when the tensors are fixed.
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r14849 | bugman | 2011-10-12 17:40:47 +0200 (Wed, 12 Oct 2011) | 5 lines
Yet another fix for the N-state model target functions.
The Ln3+ optimisation with the tensors fixed was resulting in a chi2 value of 0 at all times!
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r14850 | bugman | 2011-10-12 17:50:04 +0200 (Wed, 12 Oct 2011) | 5 lines
Added some optimisation speed ups to the metal_pos_opt.py N-state model system test script.
These are to allow the test to complete in a reasonable time.
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r14851 | bugman | 2011-10-12 17:51:56 +0200 (Wed, 12 Oct 2011) | 3 lines
Fixes for the N-state model minimisation RDC and PCS setup methods.
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r14852 | bugman | 2011-10-12 17:56:04 +0200 (Wed, 12 Oct 2011) | 3 lines
Added some more checks into the metal_pos_opt.py N-state model system test script.
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r14853 | bugman | 2011-10-12 17:59:41 +0200 (Wed, 12 Oct 2011) | 16 lines
Reverted r14849 as this was not the correct solution to the problem!
The command used was:
svn merge -r14849:r14848 .
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r14849 | bugman | 2011-10-12 17:40:47 +0200 (Wed, 12 Oct 2011) | 5 lines
Changed paths:
M /1.3/maths_fns/n_state_model.py
Yet another fix for the N-state model target functions.
The Ln3+ optimisation with the tensors fixed was resulting in a chi2 value of 0 at all times!
.....
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r14854 | bugman | 2011-10-12 18:16:05 +0200 (Wed, 12 Oct 2011) | 5 lines
Fixes for the metal position optimisation test data.
The RDCs and PCSs were 3 times too large!
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r14855 | bugman | 2011-10-12 18:17:56 +0200 (Wed, 12 Oct 2011) | 3 lines
A fix for the previous fixes for the metal position optimisation test data!
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r14856 | bugman | 2011-10-12 18:19:28 +0200 (Wed, 12 Oct 2011) | 3 lines
The chi2 of zero test in the metal_pos_opt.py system test script is now not exact.
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r14857 | bugman | 2011-10-12 18:22:29 +0200 (Wed, 12 Oct 2011) | 3 lines
Added another chi2 of zero check to the metal_pos_opt.py system test script.
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r14858 | bugman | 2011-10-12 18:31:16 +0200 (Wed, 12 Oct 2011) | 3 lines
Added a check that the chi2 value is no longer zero if the Ln3+ is moved in the metal_pos_opt.py test.
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r14859 | bugman | 2011-10-12 18:54:15 +0200 (Wed, 12 Oct 2011) | 3 lines
More attempts at fixing the N-state model code.......
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r14860 | bugman | 2011-10-12 18:54:49 +0200 (Wed, 12 Oct 2011) | 3 lines
Fix for the position checking in the metal_pos_opt.py script.
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r14861 | bugman | 2011-10-12 18:57:31 +0200 (Wed, 12 Oct 2011) | 6 lines
Reverted the last revision (r14860) as the change was rubbish.
The command used was:
svn merge -r14860:r14859 .
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r14862 | bugman | 2011-10-12 19:01:27 +0200 (Wed, 12 Oct 2011) | 3 lines
More fixes and improvements to the test_metal_pos_opt() system test.
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r14863 | bugman | 2011-10-12 19:07:04 +0200 (Wed, 12 Oct 2011) | 23 lines
Revert the reversion of revision r14853 which was a reversion of r14849, as it was ok!
The command used was:
svn merge -r14853:r14852 .
.....
Reverted r14849 as this was not the correct solution to the problem!
The command used was:
svn merge -r14849:r14848 .
.....
r14849 | bugman | 2011-10-12 17:40:47 +0200 (Wed, 12 Oct 2011) | 5 lines
Changed paths:
M /1.3/maths_fns/n_state_model.py
Yet another fix for the N-state model target functions.
The Ln3+ optimisation with the tensors fixed was resulting in a chi2 value of 0 at all times!
.....
.....
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r14864 | bugman | 2011-10-12 19:12:19 +0200 (Wed, 12 Oct 2011) | 3 lines
Fixes for the N-state model optimisation set up if PCS or RDC data is not loaded.
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r14865 | bugman | 2011-10-12 19:16:18 +0200 (Wed, 12 Oct 2011) | 3 lines
Clean up of the metal_pos_opt.py system test script.
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r14866 | bugman | 2011-10-12 19:31:40 +0200 (Wed, 12 Oct 2011) | 3 lines
Removed the Q factor calculations from metal_pos_opt.py as they should already be calculated.
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r14867 | bugman | 2011-10-12 19:32:04 +0200 (Wed, 12 Oct 2011) | 3 lines
Some last fixes, hopefully, for the N-state model code.
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r14868 | bugman | 2011-10-13 18:31:08 +0200 (Thu, 13 Oct 2011) | 3 lines
Fix for the paramag.centre user function when a numpy array is used.
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r14869 | bugman | 2011-10-14 10:21:50 +0200 (Fri, 14 Oct 2011) | 6 lines
Fix for a problem introduced at r14810 - relax uses D and not 2D internally for the RDCs.
This is only a problem if the rdc.read 'data_type' argument is used. This is only a few days old so
will affect no one!
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r14870 | bugman | 2011-10-14 16:31:45 +0200 (Fri, 14 Oct 2011) | 6 lines
Bug fix allowing relax to be run in profiling mode.
This still does not work as the multi-processor branch has broken this coding and debugging
functionality.
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r14871 | bugman | 2011-10-14 16:37:52 +0200 (Fri, 14 Oct 2011) | 6 lines
Bug fix for the profiling!
This coding and debugging functionality now works again. This has been broken since the merger of
the multi-processor branch.
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r14872 | bugman | 2011-10-14 20:29:51 +0200 (Fri, 14 Oct 2011) | 5 lines
Increased the efficiency of the relax data store spin system creation.
This becomes noticeable when large numbers of structures are read into relax.
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r14873 | bugman | 2011-10-17 13:59:57 +0200 (Mon, 17 Oct 2011) | 6 lines
Added the bc flag to the RDC and PCS display and write user function front-ends.
This This will allow the back-calculated data to be displayed or written rather than the measured
values.
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r14874 | bugman | 2011-10-17 14:09:51 +0200 (Mon, 17 Oct 2011) | 5 lines
Updated the RDC and PCS display and write user function backends for the new bc flag.
This allows access to the back-calculated rather than measured data.
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r14875 | bugman | 2011-10-17 18:31:38 +0200 (Mon, 17 Oct 2011) | 3 lines
Created a system test with RDC data for loading RDCs from a file with spin ID strings at the start.
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r14876 | bugman | 2011-10-18 08:51:59 +0200 (Tue, 18 Oct 2011) | 5 lines
Bug fix for the relax_io.read_spin_data() function for spin IDs.
Spin IDs can now be handled if they are the first column in the data file!
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r14877 | bugman | 2011-10-18 09:13:22 +0200 (Tue, 18 Oct 2011) | 7 lines
The rdc and pcs display and write user functions now output mol, res, and spin name and num cols.
Instead of the spin ID column, these user functions now output the molecule name, residue name,
residue number, spin name and spin number columns. This is better to read back into relax as info
such as the spin number can be ignored to allow different PDB files to be used.
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r14878 | bugman | 2011-10-18 10:39:11 +0200 (Tue, 18 Oct 2011) | 5 lines
Created the alignment tensor module num_tensors() method for counting tensors.
This excludes fixed tensors by default.
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r14879 | bugman | 2011-10-18 10:47:58 +0200 (Tue, 18 Oct 2011) | 5 lines
Created the alignment tensor module return_tensor() function for returning tensors.
This takes fixed tensors into account, skipping them if the skip_fixed flag is set.
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r14880 | bugman | 2011-10-18 11:09:31 +0200 (Tue, 18 Oct 2011) | 3 lines
The N-state model Monte Carlo simulations can now handle fixed alignment tensors.
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r14881 | bugman | 2011-10-18 15:46:27 +0200 (Tue, 18 Oct 2011) | 6 lines
Fix for the set up of Monte Carlo data for fixed alignment tensors in the N-state model.
The _minimise_setup_fixed_tensors() method has been fixed to return the actual tensor rather than
simulation for the fixed tensors, as there is no simulation tensor in that case.
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r14882 | bugman | 2011-10-21 11:12:39 +0200 (Fri, 21 Oct 2011) | 5 lines
Fix for the frame_order.cone_pdb user function.
The create_cone_pdb was referencing a non-existent variable!
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r14883 | bugman | 2011-10-23 18:51:42 +0200 (Sun, 23 Oct 2011) | 11 lines
Added a few new RelaxError classes.
These include:
RelaxNoneListFloatError
RelaxMatrixFloatError
RelaxNoneMatrixFloatError
The BaseArgError class was also modified to handle the length arg (now the size arg) being a tuple
for matrix sizes.
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r14884 | bugman | 2011-10-23 18:55:01 +0200 (Sun, 23 Oct 2011) | 7 lines
Added a few new argument checks for arrays and matrices of floats.
These are:
is_float_array()
is_float_matrix()
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r14885 | bugman | 2011-10-23 18:56:36 +0200 (Sun, 23 Oct 2011) | 6 lines
Created the front end for the new structure.rotate user function.
The purpose of this user function is to apply arbitrary rotations to the structures loaded into
relax about a given origin.
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r14886 | bugman | 2011-10-23 18:58:00 +0200 (Sun, 23 Oct 2011) | 3 lines
Created the back end for the structure.rotate user function.
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r14887 | bugman | 2011-10-23 19:03:51 +0200 (Sun, 23 Oct 2011) | 5 lines
Started to create some data for testing the frame order theory.
This will be used to generate synthetic data for all 9 models currently in relax.
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r14888 | bugman | 2011-10-23 19:05:50 +0200 (Sun, 23 Oct 2011) | 3 lines
Created the RDC and PCS test data for the rigid frame order model.
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r14889 | bugman | 2011-10-23 22:08:25 +0200 (Sun, 23 Oct 2011) | 3 lines
Errors are now set on the RDCs and PCSs.
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r14890 | bugman | 2011-10-24 00:29:08 +0200 (Mon, 24 Oct 2011) | 3 lines
Updated the alignment tensor fitting script.
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r14891 | bugman | 2011-10-24 09:35:29 +0200 (Mon, 24 Oct 2011) | 3 lines
Small fix for the tensor fitting script, and addition of the log file and output tensors.
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r14892 | bugman | 2011-10-24 11:59:51 +0200 (Mon, 24 Oct 2011) | 5 lines
Added a script for optimising the rigid frame order CaM test data.
The resultant average position PDB file and relax save file have also been added for reference.
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r14893 | bugman | 2011-10-24 12:11:07 +0200 (Mon, 24 Oct 2011) | 3 lines
Created the Frame_order.test_cam_rigid system test and optimisation script.
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r14894 | bugman | 2011-10-24 12:24:51 +0200 (Mon, 24 Oct 2011) | 6 lines
Modified the rigid frame order CaM test model script to properly test the PyMOL representation.
This is not a system test, but is to be used manually and visually to check that the PyMOL
representation created by relax of the average position, eigenframe, and cone is correct!
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r14895 | bugman | 2011-10-24 12:25:32 +0200 (Mon, 24 Oct 2011) | 3 lines
Created a data directory for the free rotor CaM test model.
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r14896 | bugman | 2011-10-24 14:58:21 +0200 (Mon, 24 Oct 2011) | 5 lines
Created a PDB distribution of CaM orientations for the free rotor frame order model.
This is a uniform set of rotations about the pivot-CoM axis.
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r14897 | bugman | 2011-10-24 15:01:05 +0200 (Mon, 24 Oct 2011) | 5 lines
The structure.rotate user function can now operate in individual structural models.
The model keyword argument has been added to allow this.
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r14898 | bugman | 2011-10-24 15:01:47 +0200 (Mon, 24 Oct 2011) | 3 lines
The structure.write_pdb user function can now create compressed (bzip2 or gzip) PDB files.
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r14899 | bugman | 2011-10-24 15:10:52 +0200 (Mon, 24 Oct 2011) | 3 lines
Back calculated the RDC and PCS test data from the CaM free rotor frame order model.
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r14900 | bugman | 2011-10-24 15:31:02 +0200 (Mon, 24 Oct 2011) | 3 lines
Calculated the pure RDC tensors for the free rotor CaM frame order model.
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r14901 | bugman | 2011-10-24 15:34:04 +0200 (Mon, 24 Oct 2011) | 3 lines
The structure.read_pdb user function can now handle bzip2 or gzip compressed PDB files.
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r14902 | bugman | 2011-10-24 15:44:36 +0200 (Mon, 24 Oct 2011) | 3 lines
Added the frame order free rotor optimisation script and its results.
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r14903 | bugman | 2011-10-24 16:09:00 +0200 (Mon, 24 Oct 2011) | 3 lines
Created a script for animating the CaM free rotor frame order model test data in PyMOL.
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r14904 | bugman | 2011-10-24 16:35:42 +0200 (Mon, 24 Oct 2011) | 3 lines
Created the Frame_order.test_cam_free_rotor system test for the CaM synthetic data.
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r14905 | bugman | 2011-10-24 17:52:04 +0200 (Mon, 24 Oct 2011) | 3 lines
Added checks for the n_state_model.cone_pdb user fn in the N_state_model.test_5_state_xz system test.
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r14906 | bugman | 2011-10-24 17:52:47 +0200 (Mon, 24 Oct 2011) | 5 lines
Bug fixes for the n_state_model.cone_pdb user function.
The code was old and not functional any more.
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r14907 | bugman | 2011-10-24 17:55:26 +0200 (Mon, 24 Oct 2011) | 5 lines
Bug fix for the pymol.cone_pdb user function for when there is no average domain position.
This is necessary for the old 2-domain N-state model analysis type.
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r14908 | bugman | 2011-10-24 23:35:10 +0200 (Mon, 24 Oct 2011) | 3 lines
Extended the N-state model analysis to allow a separate paramagnetic centre per state.
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r14909 | bugman | 2011-10-25 11:02:49 +0200 (Tue, 25 Oct 2011) | 5 lines
Created the front end for the new structure.displacement user function.
This is used to calculate the rotational and translational displacement between two models.
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r14910 | bugman | 2011-10-25 11:08:47 +0200 (Tue, 25 Oct 2011) | 5 lines
Added the atom_id arg to the new structure.displacement user function front end.
This will be used to restrict the calculation to subsets of all atoms.
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r14911 | bugman | 2011-10-25 11:55:00 +0200 (Tue, 25 Oct 2011) | 3 lines
Created the Structure.test_displacement() system test for checking the structure.displacement uf.
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r14912 | bugman | 2011-10-25 14:20:22 +0200 (Tue, 25 Oct 2011) | 6 lines
Implemented the back end of the structure.displacement user function.
This will still require some debugging, and the data objects will need to be stored in the XML save
files.
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r14913 | bugman | 2011-10-25 14:43:10 +0200 (Tue, 25 Oct 2011) | 3 lines
The structural model displacement objects are now stored in the relax XML save files.
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r14914 | bugman | 2011-10-25 14:58:38 +0200 (Tue, 25 Oct 2011) | 3 lines
Expanded the Structure.test_displacement() system test to test the XML save files.
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r14915 | bugman | 2011-10-25 16:24:30 +0200 (Tue, 25 Oct 2011) | 5 lines
The structural model displacement data structure is now restored from the XML save files.
There are a few fixes for the to_xml() methods as well.
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r14916 | bugman | 2011-10-25 16:41:43 +0200 (Tue, 25 Oct 2011) | 6 lines
Fixes for the structure.displacement user function.
The rotations are now correctly calculated - the problem was that the numpy SVD is not transposing
the last matrix v. The technique is now labelled as the Kabsch algorithm.
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r14917 | bugman | 2011-10-25 16:49:29 +0200 (Tue, 25 Oct 2011) | 3 lines
The Structure.test_displacement() system test is now checking all of the numerical results.
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r14918 | bugman | 2011-10-26 10:25:23 +0200 (Wed, 26 Oct 2011) | 6 lines
Added the centroid arg to the structure.displacement user function for pivoted motions.
By specifying the centroid position for all structures, a pivoted motion is assumed. All
displacements will be zero, and the angles will be that of the pivoting motion.
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r14919 | bugman | 2011-10-26 10:38:16 +0200 (Wed, 26 Oct 2011) | 3 lines
Shifted out the Kabsch superimposition code into its own module.
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r14920 | bugman | 2011-10-26 10:49:27 +0200 (Wed, 26 Oct 2011) | 6 lines
Created the Structure.test_superimpose_fit_to_first system test.
The structure.superimpose user function doesn't exist yet, but all the necessary algorithms are
already in relax.
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r14921 | bugman | 2011-10-26 11:25:07 +0200 (Wed, 26 Oct 2011) | 3 lines
The Structure.test_superimpose_fit_to_first system test is now testing the backbone heavy atom fit.
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r14922 | bugman | 2011-10-26 11:25:27 +0200 (Wed, 26 Oct 2011) | 3 lines
Implemented the front end of the structure.superimpose user function.
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r14923 | bugman | 2011-10-26 11:40:17 +0200 (Wed, 26 Oct 2011) | 3 lines
Created the arg_check.is_int_list() function for checking for lists of integers.
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r14924 | bugman | 2011-10-26 11:51:44 +0200 (Wed, 26 Oct 2011) | 3 lines
Shifted the structural API calc_displacement() method into the main module.
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r14925 | bugman | 2011-10-26 12:24:24 +0200 (Wed, 26 Oct 2011) | 5 lines
Implemented the back end of the structure.superimpose user function.
This only implements the 'fit to first' algorithm. The 'fit to mean' is yet to be implemented.
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r14926 | bugman | 2011-10-26 12:25:19 +0200 (Wed, 26 Oct 2011) | 3 lines
Added a 3rd structure to the Structure.test_superimpose_fit_to_first system test and loosened the checks.
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r14927 | bugman | 2011-10-26 12:26:53 +0200 (Wed, 26 Oct 2011) | 5 lines
Created the Structure.test_superimpose_fit_to_mean system test.
This is to test the 'fit to mean' algorithm of the structure.superimpose user function.
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r14928 | bugman | 2011-10-26 14:47:24 +0200 (Wed, 26 Oct 2011) | 5 lines
Rearranged the back end of the structure.superimpose user function.
This is just to shift more code into the 'superimpose' module.
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r14929 | bugman | 2011-10-26 15:43:14 +0200 (Wed, 26 Oct 2011) | 3 lines
Implemented the 'fit to mean' algorithm for the structure.superimpose user function.
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r14930 | bugman | 2011-10-26 15:47:53 +0200 (Wed, 26 Oct 2011) | 6 lines
Created a second system test for the structure.superimpose user function using 'fit to mean'.
This translates one model, superimposes it to the original, and checks to see if the structures
shift correctly.
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r14931 | bugman | 2011-10-26 15:50:58 +0200 (Wed, 26 Oct 2011) | 3 lines
Created the structure.translate user function front end.
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r14932 | bugman | 2011-10-26 15:52:36 +0200 (Wed, 26 Oct 2011) | 3 lines
Small fix for the new Structure.test_superimpose_fit_to_mean2 system test.
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r14933 | bugman | 2011-10-26 15:54:58 +0200 (Wed, 26 Oct 2011) | 5 lines
Fix for the structure.translate user function front end.
The back end already exists, so this is now functional.
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r14934 | bugman | 2011-10-26 16:52:12 +0200 (Wed, 26 Oct 2011) | 3 lines
Updated the generic_fns.structure package __all__ list to include the superimposition module.
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r14935 | bugman | 2011-10-26 16:54:59 +0200 (Wed, 26 Oct 2011) | 3 lines
Synchronised the atom_loop() method args in the structural API.
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r14936 | bugman | 2011-10-26 16:57:34 +0200 (Wed, 26 Oct 2011) | 3 lines
Added the translate method to the structural API.
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r14937 | bugman | 2011-10-26 17:28:40 +0200 (Wed, 26 Oct 2011) | 5 lines
Fix for the structure.displacement user function.
The kabsch() function now returns the pivot of the rotation as well.
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r14938 | bugman | 2011-10-26 18:06:33 +0200 (Wed, 26 Oct 2011) | 6 lines
Created a second test model for the free rotor frame order model.
In this case, the C-domain does not rotate about the pivot-CoM axis, but an axis tilted 30 degrees
from the pivot-CoM axis.
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r14939 | bugman | 2011-10-27 12:48:01 +0200 (Thu, 27 Oct 2011) | 6 lines
Created the Frame_order.test_cam_free_rotor2 system test.
This tests the free rotor frame order CaM test model where the axis is tilted from the pivot-CoM
axis.
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r14940 | bugman | 2011-10-28 16:10:16 +0200 (Fri, 28 Oct 2011) | 6 lines
Created the structure.add_atom user function.
This simply exposes some of the functionality of the structural API to the user. The get_molecule()
API method has also been added to return molecule containers.
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r14941 | bugman | 2011-10-28 16:12:15 +0200 (Fri, 28 Oct 2011) | 5 lines
The internal structural object no longer requires the 'ATOM' PDB record for creating PDB files.
This affects the structure.write_pdb user function.
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r14942 | bugman | 2011-10-28 18:21:19 +0200 (Fri, 28 Oct 2011) | 3 lines
Slight changes to the pivot-CoM PDB representation for the frame order test data.
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r14943 | bugman | 2011-10-31 10:45:33 +0100 (Mon, 31 Oct 2011) | 6 lines
Created the structure.connect_atom user function to expose the back-end functionality.
This works with atom indices, so is not ideal for a user function. In the future this should be
modified to handle atom ID strings instead.
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r14944 | bugman | 2011-10-31 11:27:08 +0100 (Mon, 31 Oct 2011) | 5 lines
The internal structural reader can now create PDB files if atom numbers are missing.
This fixes the structure.write_pdb user function in certain edge cases.
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r14945 | bugman | 2011-10-31 11:53:56 +0100 (Mon, 31 Oct 2011) | 6 lines
The generation script for the free rotor frame order test model 2 creates a PDB for the axis system.
The generate_distribution.py now creates the axis.pdb file which encoded the rotation axis of the
domain distribution. The animate.py will also display this rotation axis.
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r14946 | bugman | 2011-10-31 14:50:28 +0100 (Mon, 31 Oct 2011) | 5 lines
Fixes for the free rotor frame order 2nd test model data.
The rotation axes were not normalised, so the data was not correct!
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r14947 | bugman | 2011-10-31 15:30:39 +0100 (Mon, 31 Oct 2011) | 6 lines
Fixes and speed up for the 2nd frame order free rotor model system test.
The grid search has been replaced by the setting of values to that after a high resolution grid
search, decreasing the test time from ~39 seconds to ~0.8 seconds.
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r14948 | bugman | 2011-10-31 17:06:51 +0100 (Mon, 31 Oct 2011) | 3 lines
Properly added the add_atom() and connect_atom() methods to the structural API.
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r14949 | bugman | 2011-10-31 17:40:02 +0100 (Mon, 31 Oct 2011) | 7 lines
Created a frame order rotor test model whereby the rotation axis is perpendicular to the domain.
The rotation is a total of 60 degrees about an axis perpendicular to the pivot-CoM vector. The
'rotor' test model directory is reserved for a model whereby the rotation axis is the pivot-CoM
vector.
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r14950 | bugman | 2011-11-02 10:22:14 +0100 (Wed, 02 Nov 2011) | 6 lines
Created the Frame_order.test_cam_rotor2 system test.
This checks the frame order rotor model whereby the rotation axis is perpendicular to the pivot-CoM
vector.
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r14951 | bugman | 2011-11-02 10:46:22 +0100 (Wed, 02 Nov 2011) | 3 lines
Added a check to prevent the frame order grid search from being too big causing out of memory errors.
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r14952 | bugman | 2011-11-02 11:59:28 +0100 (Wed, 02 Nov 2011) | 5 lines
Created a frame order rotor test model whereby the rotation axis is the pivot-CoM vector.
The rotation is a total of 60 degrees about the pivot-CoM vector.
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r14953 | bugman | 2011-11-02 12:06:48 +0100 (Wed, 02 Nov 2011) | 5 lines
Created the Frame_order.test_cam_rotor system test.
This is the rotor model with the rotation axis being the pivot-CoM vector.
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r14954 | bugman | 2011-11-02 14:27:06 +0100 (Wed, 02 Nov 2011) | 3 lines
Created a frame order test model for the rotor model when there are only two states.
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r14955 | bugman | 2011-11-02 14:45:40 +0100 (Wed, 02 Nov 2011) | 3 lines
Fixes for the test data committed previously (r14954).
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r14956 | bugman | 2011-11-02 15:17:19 +0100 (Wed, 02 Nov 2011) | 7 lines
The frame order torsion angle cone_sigma_max is now forced to be positive.
Optimisation sometimes comes up with the negative of the angle, as both the negative and positive
angles give the same result, so now the angle is always unpacked after optimisation as the absolute
value.
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r14957 | bugman | 2011-11-02 15:19:14 +0100 (Wed, 02 Nov 2011) | 5 lines
Fixes for the rotor frame order system test data.
The first structure of the distribution was missing!
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r14958 | bugman | 2011-11-02 16:30:48 +0100 (Wed, 02 Nov 2011) | 7 lines
Eliminated one of the eigenframe parameters from the rotor frame order model.
In the rotor frame order model, the x and y axes of the eigenframe of the motion are not defined.
Therefore the 3 eigenframe Euler angles have been replaced by 2 spherical angles defining the
rotation axis. This removes a lot of optimisation issues with this model.
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r14959 | bugman | 2011-11-02 17:21:15 +0100 (Wed, 02 Nov 2011) | 3 lines
Monte Carlo simulations are now implemented for the frame order analysis.
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r14960 | bugman | 2011-11-02 17:36:51 +0100 (Wed, 02 Nov 2011) | 6 lines
Added Monte Carlo simulations to the second rotor frame order model testing script.
This is to check that the PyMOL representations are correct, as this cannot be done in a system
test.
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r14961 | bugman | 2011-11-02 17:41:51 +0100 (Wed, 02 Nov 2011) | 5 lines
Added MC sims to the Frame_order.test_cam_rotor system test.
This is just a quick check with 3 simulations to make sure the code is functional.
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r14962 | bugman | 2011-11-03 10:28:09 +0100 (Thu, 03 Nov 2011) | 3 lines
All private methods have been renamed by replacing '__*()' with '_*()'.
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r14963 | bugman | 2011-11-03 10:29:12 +0100 (Thu, 03 Nov 2011) | 3 lines
Shifted the add_molecule() method to the correct position.
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r14964 | bugman | 2011-11-03 10:42:14 +0100 (Thu, 03 Nov 2011) | 3 lines
Created the test data for the iso cone, free rotor frame order model.
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r14965 | bugman | 2011-11-03 11:17:43 +0100 (Thu, 03 Nov 2011) | 5 lines
Created the add_model() structural API method.
This is implemented within the internal structural object.
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r14966 | bugman | 2011-11-03 11:30:19 +0100 (Thu, 03 Nov 2011) | 3 lines
Fixes for all the renamed private methods in the internal structural object.
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r14967 | bugman | 2011-11-03 17:20:30 +0100 (Thu, 03 Nov 2011) | 3 lines
Clean up of a RelaxError print out.
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r14968 | bugman | 2011-11-03 17:32:37 +0100 (Thu, 03 Nov 2011) | 3 lines
The positive and negative cones from the frame order theory are now different PDB models.
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r14969 | bugman | 2011-11-03 17:33:30 +0100 (Thu, 03 Nov 2011) | 3 lines
A lot of fixes for the internal structural object for handling multiple models.
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r14970 | bugman | 2011-11-03 17:50:39 +0100 (Thu, 03 Nov 2011) | 3 lines
More use of the structural API in the create_diff_tensor_pdb() function.
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r14971 | bugman | 2011-11-03 17:51:46 +0100 (Thu, 03 Nov 2011) | 5 lines
Fix for the internal structural object add_molecule() method for when no models exist.
Now a model is created if none currently exist.
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r14972 | bugman | 2011-11-03 17:52:36 +0100 (Thu, 03 Nov 2011) | 3 lines
Fixes for the add_molecule() structural API method.
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r14973 | bugman | 2011-11-03 17:53:53 +0100 (Thu, 03 Nov 2011) | 5 lines
Fix for the test___parse_pdb_record unit test.
The private methods have been renamed.
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r14974 | bugman | 2011-11-03 18:34:27 +0100 (Thu, 03 Nov 2011) | 3 lines
Updates for the new cone PDB file where the negative image is in a second model.
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r14975 | bugman | 2011-11-07 11:07:33 +0100 (Mon, 07 Nov 2011) | 3 lines
Fix for the internal structural object add_atom() method for when no models or molecules are present.
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r14976 | bugman | 2011-11-07 15:38:34 +0100 (Mon, 07 Nov 2011) | 6 lines
Fixes for the Monte Carlo simulations of the iso cone, free rotor frame order model.
The derivative cone_theta parameter (calculated from cone_s1) now is handled in the Monte Carlo
simulations and an error analysis on it is performed.
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r14977 | bugman | 2011-11-07 16:22:17 +0100 (Mon, 07 Nov 2011) | 7 lines
Changes for the isotropic cone, free rotor frame order test data.
The distribution of structures consists of 5000 rather than 500 models now, so the PDB file is no
longer stored. This number is needed to properly sample the space. Monte Carlo simulations have
also been added.
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r14978 | bugman | 2011-11-07 16:23:05 +0100 (Mon, 07 Nov 2011) | 3 lines
Removed the back_calc.bz2 save file as it is far, far too big!
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r14979 | bugman | 2011-11-07 16:51:14 +0100 (Mon, 07 Nov 2011) | 6 lines
Fix for the pymol.cone_pdb user function for frame order models with no alpha average pos angle.
This is specifically for the isotropic cone, free rotor model. But other models might also be
affected by this fix.
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r14980 | bugman | 2011-11-08 11:13:25 +0100 (Tue, 08 Nov 2011) | 5 lines
Created a second iso cone, free rotor frame order model - this time with a tilted axis.
The centre of the distribution is an axis tilted 15 degrees from the pivot-CoM vector.
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r14981 | bugman | 2011-11-08 11:20:17 +0100 (Tue, 08 Nov 2011) | 3 lines
Added Monte Carlo simulations to all the frame order model optimisation test scripts.
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r14982 | bugman | 2011-11-08 11:20:57 +0100 (Tue, 08 Nov 2011) | 3 lines
Added a system test script for the iso cone, free rotor frame order test data.
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r14983 | bugman | 2011-11-08 11:23:48 +0100 (Tue, 08 Nov 2011) | 5 lines
Fixes for the free rotor frame order model system test scripts.
The average position alpha Euler angle is not defined in these models!
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r14984 | bugman | 2011-11-08 11:45:36 +0100 (Tue, 08 Nov 2011) | 5 lines
Fix for the iso_cone_free_rotor.py system test script.
The average position alpha Euler angle is not defined in this model.
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r14985 | bugman | 2011-11-08 11:45:56 +0100 (Tue, 08 Nov 2011) | 3 lines
Implemented the Frame_order.test_cam_iso_cone_free_rotor system test.
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r14986 | bugman | 2011-11-08 12:06:30 +0100 (Tue, 08 Nov 2011) | 5 lines
Created the Frame_order.test_cam_iso_cone_free_rotor2 system test.
This is the isotropic cone, free rotor frame order model with a tilted central axis.
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r14987 | bugman | 2011-11-08 17:23:57 +0100 (Tue, 08 Nov 2011) | 3 lines
Fixes for the negative cone creation in the frame_order.cone_pdb user function.
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r14988 | bugman | 2011-11-08 19:05:24 +0100 (Tue, 08 Nov 2011) | 3 lines
Fix for the negative cone PDB representation in the frame order theory.
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r14989 | bugman | 2011-11-09 11:38:56 +0100 (Wed, 09 Nov 2011) | 5 lines
The generic_fns.structure.mass.centre_of_mass() function now accepts the atom ID arg.
This allows the centre of mass of subsets of the structure to be calculated.
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r14990 | bugman | 2011-11-09 11:45:33 +0100 (Wed, 09 Nov 2011) | 5 lines
The generic_fns.structure.mass.centre_of_mass() function now accepts the model number arg.
This allows specific models to be isolated.
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r14991 | bugman | 2011-11-09 11:55:34 +0100 (Wed, 09 Nov 2011) | 5 lines
Added the atom ID argument to the structure.rotate and structure.translate user functions.
This allows subsets of molecules or models to be translated and rotated.
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r14992 | bugman | 2011-11-09 11:59:33 +0100 (Wed, 09 Nov 2011) | 3 lines
Changed the name of the model_num arg to model in the centre_of_mass() function.
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r14993 | bugman | 2011-11-10 11:29:58 +0100 (Thu, 10 Nov 2011) | 6 lines
Fix for the precision of the chi2 value check in the N_state_model.test_monte_carlo_sims system test.
This affects 32-bit GNU/Linux and not 64-bit GNU/Linux. Other operating systems are unknown if this
test previously passed or not.
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r14996 | bugman | 2011-11-14 16:54:14 +0100 (Mon, 14 Nov 2011) | 6 lines
Merged the CHANGES file for relax version 1.3.13 back into the main 1.3 line.
The command used was:
svn merge -r14994:14995 svn+ssh://bugman@.../svn/relax/tags/1.3.13
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r14998 | bugman | 2011-11-14 17:13:07 +0100 (Mon, 14 Nov 2011) | 6 lines
Bug fix for the compilation of the user manual.
The molecule user function class used the temporary variable i, which was causing the
fetch_docstrings script to fail.
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r15002 | bugman | 2011-11-14 20:17:16 +0100 (Mon, 14 Nov 2011) | 6 lines
Modified the release checklist for large files!
The Mac OS X DMG file is ~120 Mb, so the uploading command for the distribution files has been
updated to show the progress.
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r15007 | bugman | 2011-11-22 14:20:41 +0100 (Tue, 22 Nov 2011) | 3 lines
Fix for the structure.superimpose user function print outs - the angle is now in degrees.
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r15008 | bugman | 2011-11-22 14:31:24 +0100 (Tue, 22 Nov 2011) | 6 lines
Another fix for the print out of the structure.superimpose user function.
The final step of calculating the displacements to the final mean structure was incorrectly output.
This has no effect on the algorithm.
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r15009 | bugman | 2011-11-22 18:27:21 +0100 (Tue, 22 Nov 2011) | 5 lines
Added the centroid argument to the structure.superimpose user function.
This allows for the superimposition of structures assuming a pivoted motion.
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r15010 | bugman | 2011-11-23 10:42:13 +0100 (Wed, 23 Nov 2011) | 5 lines
Added the validate_models() method to the structural API.
This is used to check that the models are 100% consistent.
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r15011 | bugman | 2011-11-23 13:52:58 +0100 (Wed, 23 Nov 2011) | 6 lines
Fix for the numbering of the TER record and subsequence HETATM records in the PDB file creation.
The structure.write_pdb user function now creates the correct TER record after the ATOM records,
and the HETATM records are renumbered if needed.
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r15012 | bugman | 2011-11-24 14:04:42 +0100 (Thu, 24 Nov 2011) | 5 lines
Created a new algorithm for finding the pivot of motion between different structural models.
This is available through the structure.find_pivot user function.
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r15016 | bugman | 2011-12-02 12:40:44 +0100 (Fri, 02 Dec 2011) | 3 lines
Bug fix for the arg_check.is_none() function - the RelaxNoneError was not imported!
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r15018 | bugman | 2011-12-02 12:44:50 +0100 (Fri, 02 Dec 2011) | 5 lines
Another fix for the arg_check.is_none() function.
This time, the RelaxNoneError was incorrectly called.
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r15165 | bugman | 2012-01-18 10:47:04 +0100 (Wed, 18 Jan 2012) | 3 lines
Updated the relax copyrights for 2012.
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r15205 | bugman | 2012-01-20 14:40:44 +0100 (Fri, 20 Jan 2012) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-15167" from
svn+ssh://bugman@.../svn/relax/branches/spec_api
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r15206 | bugman | 2012-01-20 14:42:30 +0100 (Fri, 20 Jan 2012) | 200 lines
Merged revisions 15168-15203 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/spec_api
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r15168 | bugman | 2012-01-18 15:17:34 +0100 (Wed, 18 Jan 2012) | 9 lines
Created a special specific API object called SPIN_PARAMS.
This will be used to handle all operations to do with model parameters. This is initialised in the
base class, and can be set up in the specific __init__() methods. The object Param_list has methods
for parameter initialisation (where all info is specified such as Grace string, units, default
value, etc) and for determining if a parameter exists. More methods will be added in the future to
expand the usability of this object and to simplify the specific API methods.
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r15169 | bugman | 2012-01-18 15:36:59 +0100 (Wed, 18 Jan 2012) | 3 lines
Created the Param_list.get_grace_string() method for returning the Grace string.
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r15170 | bugman | 2012-01-18 15:38:17 +0100 (Wed, 18 Jan 2012) | 6 lines
Some of the specific API common methods now use the new SPIN_PARAM structure.
Some are now spin specific, and a few new spin specific methods have been added for the specific
code to alias.
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r15171 | bugman | 2012-01-18 15:40:06 +0100 (Wed, 18 Jan 2012) | 5 lines
Fix for the frame order analysis as one of the common API methods has been renamed.
_return_data_name() is now _return_data_name_spin().
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r15172 | bugman | 2012-01-18 15:40:42 +0100 (Wed, 18 Jan 2012) | 3 lines
The reduced spectral density analysis code now uses the SPIN_PARAMS API object.
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r15173 | bugman | 2012-01-18 16:00:27 +0100 (Wed, 18 Jan 2012) | 3 lines
Updated the consistency testing code to use the new SPIN_PARAMS specific API structure.
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r15174 | bugman | 2012-01-18 16:43:54 +0100 (Wed, 18 Jan 2012) | 3 lines
Created the Param_list.get_units() method for returning the units corresponding to the parameter.
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r15175 | bugman | 2012-01-18 16:44:42 +0100 (Wed, 18 Jan 2012) | 3 lines
The internal objects of the Param_list object are now private.
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r15176 | bugman | 2012-01-18 16:46:00 +0100 (Wed, 18 Jan 2012) | 5 lines
Created the structural API GLOBAL_PARAMS structure.
This is also based on the Param_list object and is initialised in the base class for all analyses.
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r15177 | bugman | 2012-01-18 17:02:34 +0100 (Wed, 18 Jan 2012) | 8 lines
Created a few additional specific API common methods.
These include:
_return_data_name()
_return_data_name_global()
_return_units_global()
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r15178 | bugman | 2012-01-18 17:09:59 +0100 (Wed, 18 Jan 2012) | 3 lines
Started to migrate the frame order analysis to use the SPIN_PARAMS and GLOBAL_PARAMS specific API objects.
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r15179 | bugman | 2012-01-18 17:13:00 +0100 (Wed, 18 Jan 2012) | 5 lines
Removed the spin_id set to None check in the _set_param_values_global() specific API common method.
This check was not functioning correctly.
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r15180 | bugman | 2012-01-18 18:15:26 +0100 (Wed, 18 Jan 2012) | 6 lines
Removed the spin and spin_id args from the specific API return_units() method.
This was needed for the model-free Rex parameter where the first field strength was part of the
units. This has been replaced by the first global frequency value.
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r15181 | bugman | 2012-01-19 09:24:04 +0100 (Thu, 19 Jan 2012) | 3 lines
Removed the spin arg from the return_data_desc() specific function API method.
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r15182 | bugman | 2012-01-19 09:25:04 +0100 (Thu, 19 Jan 2012) | 3 lines
Created the Param_list.get_desc() method for returning the parameter description.
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r15183 | bugman | 2012-01-19 09:30:22 +0100 (Thu, 19 Jan 2012) | 3 lines
Created the specific function API common method _return_data_desc_spin().
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r15184 | bugman | 2012-01-19 09:46:45 +0100 (Thu, 19 Jan 2012) | 3 lines
The Param_list.get_desc() method now returns None rather than a RelaxError if the param is missing.
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r15185 | bugman | 2012-01-19 09:48:14 +0100 (Thu, 19 Jan 2012) | 3 lines
Added the 'select' and 'fixed' objects to the base SPIN_PARAM list.
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r15186 | bugman | 2012-01-19 09:48:54 +0100 (Thu, 19 Jan 2012) | 3 lines
Converted the NOE specific analysis to use the new SPIN_PARAM list API structure.
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r15187 | bugman | 2012-01-19 10:53:32 +0100 (Thu, 19 Jan 2012) | 3 lines
The relaxation curve-fitting specific analysis now uses the new SPIN_PARAMS list API object.
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r15188 | bugman | 2012-01-19 11:20:08 +0100 (Thu, 19 Jan 2012) | 5 lines
Added the ability to store and return conversion factors in the Param_list specific API object.
This includes accepting functions so that factors requiring user loaded data can be supported.
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r15189 | bugman | 2012-01-19 11:32:54 +0100 (Thu, 19 Jan 2012) | 3 lines
Fix for the Param_list.get_conv_factor() method - the function type was not properly handled.
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r15190 | bugman | 2012-01-19 11:33:48 +0100 (Thu, 19 Jan 2012) | 5 lines
The Param_list.get_units() method can now handle function type objects.
This is needed for the model-free Rex parameter.
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r15191 | bugman | 2012-01-19 11:35:16 +0100 (Thu, 19 Jan 2012) | 3 lines
Created the specific function API _return_conversion_factor_spin() method.
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r15192 | bugman | 2012-01-19 11:36:30 +0100 (Thu, 19 Jan 2012) | 5 lines
Removed spin args from return_conversion_factor() and added optimisation parameters.
The global and spin specific optimisation parameters are now set up for all specific analyses.
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r15193 | bugman | 2012-01-19 11:37:50 +0100 (Thu, 19 Jan 2012) | 3 lines
Fix for the initialisation of the conversion factor storage in Param_list.
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r15194 | bugman | 2012-01-19 12:21:06 +0100 (Thu, 19 Jan 2012) | 5 lines
Fix for the specific API _return_conversion_factor_spin() method.
The wrong variable was being used.
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r15195 | bugman | 2012-01-19 13:29:47 +0100 (Thu, 19 Jan 2012) | 5 lines
Fix for the function checking in the specific API Param_list objects.
Class methods were not being detected!
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r15196 | bugman | 2012-01-19 13:58:04 +0100 (Thu, 19 Jan 2012) | 3 lines
Updated the arg_check.is_func() function for handling class methods.
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r15197 | bugman | 2012-01-19 18:06:36 +0100 (Thu, 19 Jan 2012) | 5 lines
Fix for the specific API common method _return_value_general() for when spectrum IDs are not present.
Not sure why this change is necessary! This could introduce future bugs, or hide a new bug!
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r15198 | bugman | 2012-01-20 11:31:09 +0100 (Fri, 20 Jan 2012) | 15 lines
Mass conversion to the new GLOBAL_PARAMS and SPIN_PARAMS specific API data structures.
This involves mainly the conversion of the model-free analysis to these new objects, and the
subsequent changes to how model-free parameters are handled. The parameters are now all lowercase,
for example ['S2', 'te', 'Rex'] is now ['s2', 'te', 'rex']. The follow parameters are now converted
throughout relax:
'bond_length' to 'r',
'CSA' to 'csa',
'heteronucleus' to 'heteronuc_type',
'proton' to 'proton_type'.
The regularisation of the specific analysis parameters via GLOBAL_PARAMS and SPIN_PARAMS has
significantly simplified the current code and make it much easier to introduce new analyses.
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r15199 | bugman | 2012-01-20 11:45:13 +0100 (Fri, 20 Jan 2012) | 3 lines
Reintroduced the specific API default_value() method to most of the analyses.
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r15200 | bugman | 2012-01-20 11:48:39 +0100 (Fri, 20 Jan 2012) | 3 lines
Fix for the model-free specific API default_value() method.
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r15201 | bugman | 2012-01-20 11:52:45 +0100 (Fri, 20 Jan 2012) | 5 lines
Fix for the specific API common _default_value_spin() method.
The value is now returned!
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r15202 | bugman | 2012-01-20 12:11:59 +0100 (Fri, 20 Jan 2012) | 3 lines
Added the api_objects module to the package __all__ list.
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r15203 | bugman | 2012-01-20 13:42:50 +0100 (Fri, 20 Jan 2012) | 5 lines
Fixes for all of the value.set user function back end unit tests.
The parameter names are now regularised.
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r15207 | bugman | 2012-01-20 14:42:50 +0100 (Fri, 20 Jan 2012) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/spec_api
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