svn+ssh://bugman@.../svn/relax/branches/rdc_analysis
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r6837 | bugman | 2008-07-08 16:23:35 +0200 (Tue, 08 Jul 2008) | 3 lines
Created the framework for a user function class for handling RDCs (by copying the relax_data code).
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r6839 | bugman | 2008-07-08 20:30:14 +0200 (Tue, 08 Jul 2008) | 3 lines
Removed a test for the model setup in the set_non_spin_params() method.
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r6841 | bugman | 2008-07-08 21:02:19 +0200 (Tue, 08 Jul 2008) | 3 lines
Fix for the return_data_name() method when no match occurs and the index flag is True.
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r6842 | bugman | 2008-07-08 21:03:21 +0200 (Tue, 08 Jul 2008) | 5 lines
Added a number of new parameters to the return_data_name() method.
This include the bond length, and heteronucleus and proton types.
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r6843 | bugman | 2008-07-08 21:12:31 +0200 (Tue, 08 Jul 2008) | 3 lines
Fix for the return_data_name() method when no match occurs and the index flag is True.
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r6844 | bugman | 2008-07-08 21:17:05 +0200 (Tue, 08 Jul 2008) | 3 lines
Removed some debugging code.
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r6845 | bugman | 2008-07-08 21:24:29 +0200 (Tue, 08 Jul 2008) | 3 lines
Converted the rdc.read() user function from the relax_data.read() code.
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r6846 | bugman | 2008-07-08 21:25:41 +0200 (Tue, 08 Jul 2008) | 3 lines
Converted all instances of 'ri_label' to 'id'.
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r6847 | bugman | 2008-07-08 21:26:26 +0200 (Tue, 08 Jul 2008) | 3 lines
Converted all instances of 'relax_data' to 'rdc'.
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r6848 | bugman | 2008-07-08 21:36:00 +0200 (Tue, 08 Jul 2008) | 3 lines
Converted all of the rdc user functions from the relax_data code.
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r6849 | bugman | 2008-07-08 21:37:46 +0200 (Tue, 08 Jul 2008) | 3 lines
Created a generic_fns rdc module by copying the relax_data module.
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r6850 | bugman | 2008-07-08 21:54:07 +0200 (Tue, 08 Jul 2008) | 3 lines
Created 2 new error classes, RelaxNoRDCError and RelaxRDCError.
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r6851 | bugman | 2008-07-08 22:03:09 +0200 (Tue, 08 Jul 2008) | 3 lines
Converted the read() function from the relax_data code.
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r6852 | bugman | 2008-07-08 22:20:28 +0200 (Tue, 08 Jul 2008) | 3 lines
Made the error column optional in the loading of RDCs.
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r6853 | bugman | 2008-07-08 22:25:44 +0200 (Tue, 08 Jul 2008) | 3 lines
Fixes for the read() function to allow the error column to be missing.
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r6854 | bugman | 2008-07-09 10:59:43 +0200 (Wed, 09 Jul 2008) | 8 lines
Split up the n_state_model.model() user function.
The new user functions are:
n_state_model.number_of_states()
n_state_model.ref_domain()
n_state_model.setup_model()
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r6855 | bugman | 2008-07-09 11:02:23 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixed the unit tests broken by the split up of n_state_model.model().
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r6856 | bugman | 2008-07-09 11:04:15 +0200 (Wed, 09 Jul 2008) | 3 lines
Wrote the model arg unit test for the n_state_model.setup_model() user function.
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r6857 | bugman | 2008-07-09 11:06:51 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixes for the N-state model system test.
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r6859 | bugman | 2008-07-09 11:18:53 +0200 (Wed, 09 Jul 2008) | 3 lines
Split up the model_setup() method into number_of_states(), ref_domain(), and setup_model().
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r6860 | bugman | 2008-07-09 11:20:29 +0200 (Wed, 09 Jul 2008) | 3 lines
Created the new error class RelaxNoModelError.
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r6861 | bugman | 2008-07-09 11:21:18 +0200 (Wed, 09 Jul 2008) | 3 lines
Fix for the n_state_model.select_model() user function.
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r6862 | bugman | 2008-07-09 11:23:36 +0200 (Wed, 09 Jul 2008) | 3 lines
Docstring and print out fixes for the n_state_model.select_model() user function.
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r6863 | bugman | 2008-07-09 11:26:09 +0200 (Wed, 09 Jul 2008) | 5 lines
Renamed the n_state_model.setup_model() user function to n_state_model.select_model().
This is to match the convention of the other analyses.
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r6864 | bugman | 2008-07-09 11:26:58 +0200 (Wed, 09 Jul 2008) | 3 lines
System test fix for the renaming of n_state_model.setup_model().
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r6865 | bugman | 2008-07-09 11:29:10 +0200 (Wed, 09 Jul 2008) | 3 lines
Added some error checking for the validity of the selected model type.
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r6866 | bugman | 2008-07-09 11:41:10 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixed the model checking in the minimise() method.
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r6867 | bugman | 2008-07-09 11:51:05 +0200 (Wed, 09 Jul 2008) | 3 lines
Created the setup_model() method so that the model parameters can be set up by numerous methods.
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r6868 | bugman | 2008-07-09 11:52:45 +0200 (Wed, 09 Jul 2008) | 3 lines
Fix for the model arg of the n_state_model.select_model() user function.
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r6869 | bugman | 2008-07-09 13:29:21 +0200 (Wed, 09 Jul 2008) | 3 lines
Spun out some of the minimisation code into the minimise_setup_tensors() method.
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r6870 | bugman | 2008-07-09 13:33:29 +0200 (Wed, 09 Jul 2008) | 3 lines
Renamed setup_model() to the private __update_model() method.
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r6871 | bugman | 2008-07-09 13:34:46 +0200 (Wed, 09 Jul 2008) | 3 lines
Made a call to __update_model() from select_model().
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r6872 | bugman | 2008-07-09 13:37:45 +0200 (Wed, 09 Jul 2008) | 3 lines
Made the __update_model() method less fatal.
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r6873 | bugman | 2008-07-09 13:38:55 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixed the call to __update_model() from number_of_states().
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r6874 | bugman | 2008-07-09 13:39:18 +0200 (Wed, 09 Jul 2008) | 3 lines
Added a call to __update_model() from ref_domain().
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r6875 | bugman | 2008-07-09 13:40:26 +0200 (Wed, 09 Jul 2008) | 3 lines
Added an alias to the current data pipe in minimise_setup_tensors().
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r6876 | bugman | 2008-07-09 13:43:57 +0200 (Wed, 09 Jul 2008) | 3 lines
Passed the param_vector into minimise_setup_tensors() and fixed the variable of the returned data.
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r6877 | bugman | 2008-07-09 13:53:23 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixes for the __update_model() to prevent the model data being overwritten or too many params added.
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r6878 | bugman | 2008-07-09 14:40:41 +0200 (Wed, 09 Jul 2008) | 3 lines
Created the minimise_setup_rdcs() method.
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r6880 | bugman | 2008-07-09 15:05:46 +0200 (Wed, 09 Jul 2008) | 3 lines
Modified minimise_setup_rdcs() to throw a warning if RDCs exist but XH bond vectors are missing.
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r6882 | bugman | 2008-07-09 15:11:47 +0200 (Wed, 09 Jul 2008) | 3 lines
Fix for minimise_setup_rdcs(). The spin id is now generated for the warning.
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r6883 | bugman | 2008-07-09 15:18:36 +0200 (Wed, 09 Jul 2008) | 3 lines
The N_state_opt class now accepts the model, rdcs, and xh_vect arguments.
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r6884 | bugman | 2008-07-09 15:35:23 +0200 (Wed, 09 Jul 2008) | 3 lines
Modified the N_state_opt class to handle both alignment tensor and RDC optimisation.
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r6885 | bugman | 2008-07-09 15:40:54 +0200 (Wed, 09 Jul 2008) | 6 lines
Changed the N_state_opt functions to be model dependent.
The func_rdcs() method is now func_population(), and the func_tensors() method is now
func_2domain().
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r6886 | bugman | 2008-07-09 15:42:16 +0200 (Wed, 09 Jul 2008) | 3 lines
Fix for the N_state_opt class set up for the tensor optimisation.
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r6887 | bugman | 2008-07-09 15:49:39 +0200 (Wed, 09 Jul 2008) | 3 lines
Created an empty module to dump RDC related computational functions into.
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r6888 | bugman | 2008-07-09 16:13:45 +0200 (Wed, 09 Jul 2008) | 6 lines
Created the average_rdc_5D() function.
This calculates the average RDC for an ensemble set of XH bond vectors, using the 5D alignment
tensor notation.
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r6889 | bugman | 2008-07-09 16:19:13 +0200 (Wed, 09 Jul 2008) | 6 lines
Created the average_rdc_tensor() function.
This is equivalent to the average_rdc_5D() function but takes the full tensor in numpy matrix form
rather than the elements of the 5D vector.
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r6890 | bugman | 2008-07-09 16:20:01 +0200 (Wed, 09 Jul 2008) | 3 lines
Docstring fix for average_rdc_5D(). The XH vectors must be unit vectors!
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r6891 | bugman | 2008-07-09 16:25:57 +0200 (Wed, 09 Jul 2008) | 3 lines
Created the to_tensor() function to convert from 5D vector to 3D matrix.
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r6892 | bugman | 2008-07-09 16:28:49 +0200 (Wed, 09 Jul 2008) | 3 lines
Some fixes for the to_tensor() function. The elements Ayx, Azx, and Azy were being referenced!
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r6893 | bugman | 2008-07-09 16:36:25 +0200 (Wed, 09 Jul 2008) | 3 lines
Created the to_5D() function for converting from matrix form to 5D vector form.
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r6894 | bugman | 2008-07-09 16:39:11 +0200 (Wed, 09 Jul 2008) | 3 lines
Modified the to_tensor() to be more efficient by working only with numpy arrays.
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r6895 | bugman | 2008-07-09 16:42:14 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixes for the to_tensor() function. The tensor was completely wrong.
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r6896 | bugman | 2008-07-09 16:49:43 +0200 (Wed, 09 Jul 2008) | 3 lines
Created maxA() for finding the maximal alignment or the Azz component in the alignment frame.
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r6897 | bugman | 2008-07-09 16:50:31 +0200 (Wed, 09 Jul 2008) | 3 lines
Imported some of the RDC functions.
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r6898 | bugman | 2008-07-09 16:54:09 +0200 (Wed, 09 Jul 2008) | 3 lines
Renamed the invalid variable name 5D_vector to vector_5D.
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r6899 | bugman | 2008-07-09 17:28:28 +0200 (Wed, 09 Jul 2008) | 3 lines
Implemented the core of the func_population() method.
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r6900 | bugman | 2008-07-09 17:35:01 +0200 (Wed, 09 Jul 2008) | 3 lines
Fix for the average_rdc_5D() function. The unit XH bond vector indecies were still in Mathematica format.
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r6901 | bugman | 2008-07-09 17:40:12 +0200 (Wed, 09 Jul 2008) | 6 lines
Fix for the func_population() method.
The RDC errors are now set to 1.0 if no errors are supplied, converting the chi2 value to a SSE
value.
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r6902 | bugman | 2008-07-09 18:03:07 +0200 (Wed, 09 Jul 2008) | 5 lines
Fixes for the __update_model() method.
The probabilities and Euler angle parameter arrays are only created for the relevant N-state model.
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r6903 | bugman | 2008-07-09 18:09:14 +0200 (Wed, 09 Jul 2008) | 3 lines
Spun out some of the minimise() code to create the __determine_data_type() method.
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r6904 | bugman | 2008-07-09 18:22:10 +0200 (Wed, 09 Jul 2008) | 3 lines
Updated the assemble_param_vector() method to return the correct parameter vector.
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r6905 | bugman | 2008-07-09 18:23:04 +0200 (Wed, 09 Jul 2008) | 3 lines
Fix for a missing cdp alias.
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r6906 | bugman | 2008-07-09 18:26:09 +0200 (Wed, 09 Jul 2008) | 5 lines
Complete change of the __determine_data_type() method.
The alignment tensors should be present when RDCs are loaded - they are part of the optimised model!
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r6907 | bugman | 2008-07-09 18:33:20 +0200 (Wed, 09 Jul 2008) | 5 lines
Modified the __update_model() method to create empty alignment tensors as necessary.
This is for the RDC based analysis were the tensors are optimised.
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r6908 | bugman | 2008-07-09 18:35:38 +0200 (Wed, 09 Jul 2008) | 5 lines
Fix for the __determine_data_type() method.
The flags were not correctly checked.
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r6909 | bugman | 2008-07-09 18:41:40 +0200 (Wed, 09 Jul 2008) | 3 lines
Created the tensor_5D automatically generated object to AlignTensorData.
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r6910 | bugman | 2008-07-09 18:43:34 +0200 (Wed, 09 Jul 2008) | 3 lines
Fix for the addition of alignment tensor parameters in assemble_param_vector().
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r6911 | bugman | 2008-07-09 18:55:11 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixes for the func_population() method.
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r6912 | bugman | 2008-07-09 19:04:20 +0200 (Wed, 09 Jul 2008) | 6 lines
Changed the initialisation of the N_state_opt class.
The rdcs, rdc_errors, and xh_vect args are now all expected to be numpy matricies. The rdcs and
rdc_errors matricies have also been transposed!
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r6913 | bugman | 2008-07-09 19:13:45 +0200 (Wed, 09 Jul 2008) | 3 lines
Converted the RDC and unit vector lists in minimise_setup_rdcs() to numpy matrices.
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r6914 | bugman | 2008-07-09 19:15:11 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixed the incorrect testing for the presence of RDC errors.
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r6915 | bugman | 2008-07-09 19:15:33 +0200 (Wed, 09 Jul 2008) | 3 lines
Missing import.
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r6916 | bugman | 2008-07-09 19:16:32 +0200 (Wed, 09 Jul 2008) | 3 lines
Initialised the back calculated RDC array.
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r6917 | bugman | 2008-07-09 19:18:04 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixed all the broken references to self.rdcs_back_calc.
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r6918 | bugman | 2008-07-09 19:21:47 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixed the calculation of the total number of spins and alignments.
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r6919 | bugman | 2008-07-09 19:23:48 +0200 (Wed, 09 Jul 2008) | 3 lines
Fixed the setting up of RDC errors when missing. These should be 1.0, not 0.0!
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r6920 | bugman | 2008-07-09 19:35:48 +0200 (Wed, 09 Jul 2008) | 5 lines
Fixed the setting up of self.rdc_errors when no errors are present.
Retard, 1.0 times another matrix does not make a matrix of ones!
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r6921 | bugman | 2008-07-09 19:40:11 +0200 (Wed, 09 Jul 2008) | 3 lines
The population weights are now taken into account in the func_population() target function.
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r6922 | bugman | 2008-07-09 19:40:53 +0200 (Wed, 09 Jul 2008) | 3 lines
Added some more comments.
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r6923 | bugman | 2008-07-09 19:41:54 +0200 (Wed, 09 Jul 2008) | 3 lines
The weights are passed into average_rdc_5D() as a keyword to make them optional.
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r6924 | bugman | 2008-07-09 19:44:35 +0200 (Wed, 09 Jul 2008) | 3 lines
Converted average_rdc_5D() to expect a numpy array for the 5D tensor.
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r6925 | bugman | 2008-07-09 19:45:05 +0200 (Wed, 09 Jul 2008) | 3 lines
The 5D tensor is passed directly into average_rdc_5D() from func_population().
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r6926 | bugman | 2008-07-09 19:52:22 +0200 (Wed, 09 Jul 2008) | 3 lines
Added weights to the average_rdc_5D() function.
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r6927 | bugman | 2008-07-09 19:53:41 +0200 (Wed, 09 Jul 2008) | 3 lines
Added weights to the average_rdc_tensor() function.
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r6928 | bugman | 2008-07-09 19:54:24 +0200 (Wed, 09 Jul 2008) | 3 lines
Docstring fixes.
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r6929 | bugman | 2008-07-10 09:43:16 +0200 (Thu, 10 Jul 2008) | 3 lines
Redesigned the disassemble_param_vector() method for the multiple N-state model types.
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r6930 | bugman | 2008-07-10 10:06:29 +0200 (Thu, 10 Jul 2008) | 3 lines
Updated the param_num() method to take the various models into account.
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r6931 | bugman | 2008-07-10 10:54:29 +0200 (Thu, 10 Jul 2008) | 3 lines
Fix for the counting of header lines. The residue or spin number need not be supplied.
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r6932 | bugman | 2008-07-10 13:26:51 +0200 (Thu, 10 Jul 2008) | 3 lines
Wrote the __assemble_scaling_matrix() method for creating a scaling matrix for the N-state model.
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r6933 | bugman | 2008-07-10 13:30:26 +0200 (Thu, 10 Jul 2008) | 3 lines
Made diagonal scaling optional.
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r6934 | bugman | 2008-07-10 13:42:41 +0200 (Thu, 10 Jul 2008) | 3 lines
Made some more use of the scaling matrix.
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r6935 | bugman | 2008-07-10 13:43:36 +0200 (Thu, 10 Jul 2008) | 3 lines
Unscaled the parameter vector after optimisation.
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r6936 | bugman | 2008-07-10 13:44:25 +0200 (Thu, 10 Jul 2008) | 3 lines
Missing import fix.
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r6937 | bugman | 2008-07-10 13:51:21 +0200 (Thu, 10 Jul 2008) | 3 lines
The minimisation code now uses the scaling matrix.
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r6938 | bugman | 2008-07-10 14:46:35 +0200 (Thu, 10 Jul 2008) | 3 lines
Inverted the population scaling factor in __assemble_scaling_matrix().
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r6941 | bugman | 2008-07-23 11:27:38 +0200 (Wed, 23 Jul 2008) | 3 lines
Started to add the framework for the addition of gradients and Hessians.
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r6942 | bugman | 2008-07-23 11:47:41 +0200 (Wed, 23 Jul 2008) | 3 lines
Split the rdc module in half, shifting the alignment tensor components into their own module.
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r6943 | bugman | 2008-07-23 11:48:36 +0200 (Wed, 23 Jul 2008) | 3 lines
Import fixes.
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r6944 | bugman | 2008-07-23 13:33:22 +0200 (Wed, 23 Jul 2008) | 3 lines
Wrote functions for all the alignment tensor gradients.
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r6945 | bugman | 2008-07-23 13:36:31 +0200 (Wed, 23 Jul 2008) | 3 lines
Fixes for the alignment tensor gradient function code.
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r6952 | bugman | 2008-07-24 14:49:13 +0200 (Thu, 24 Jul 2008) | 3 lines
A lot of modifications to the population N-state model optimisation code.
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r6957 | bugman | 2008-07-24 15:22:13 +0200 (Thu, 24 Jul 2008) | 3 lines
Spelling fix for the word 'indices'.
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r6958 | bugman | 2008-07-24 16:54:46 +0200 (Thu, 24 Jul 2008) | 3 lines
Fixed the setting up of optimisation of the population N-state model.
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r6959 | bugman | 2008-07-24 16:55:09 +0200 (Thu, 24 Jul 2008) | 3 lines
Fixed the call to to_tensor().
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r6960 | bugman | 2008-07-24 17:00:43 +0200 (Thu, 24 Jul 2008) | 3 lines
Fixes for the func_population() target function.
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r6961 | bugman | 2008-07-24 17:02:21 +0200 (Thu, 24 Jul 2008) | 3 lines
Fixes for the setup of the N-state model optimisation code.
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r6962 | bugman | 2008-07-24 17:03:06 +0200 (Thu, 24 Jul 2008) | 3 lines
Missing import.
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r6963 | bugman | 2008-07-24 17:07:34 +0200 (Thu, 24 Jul 2008) | 3 lines
Fixed a call to the non-existant chi2_element() function (should be to chi2()).
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r6964 | bugman | 2008-07-24 17:07:59 +0200 (Thu, 24 Jul 2008) | 3 lines
Fixed some index names.
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r6965 | bugman | 2008-07-24 17:31:20 +0200 (Thu, 24 Jul 2008) | 3 lines
Large expansion of the dfunc_population() docstring.
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r6966 | bugman | 2008-07-25 10:04:15 +0200 (Fri, 25 Jul 2008) | 3 lines
More rewriting of the population N-state model optimisation code.
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r6967 | bugman | 2008-07-25 11:19:15 +0200 (Fri, 25 Jul 2008) | 5 lines
Wrote the average_rdc_tensor_dDij_dAmn() function.
This calculates the ensemble averaged RDC gradient element for the Amn partial derivative.
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r6968 | bugman | 2008-07-25 11:21:34 +0200 (Fri, 25 Jul 2008) | 3 lines
Fixed the N-state model code to use the renamed averaged RDC functions.
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r6969 | bugman | 2008-07-25 11:27:44 +0200 (Fri, 25 Jul 2008) | 3 lines
Added a missing import.
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r6970 | bugman | 2008-07-25 11:47:49 +0200 (Fri, 25 Jul 2008) | 9 lines
Wrote the dipolar_constant() function for calculating the dipolar constant.
The constant is defined as:
mu0 gI.gS.h_bar
d = - --- -----------
4pi r**3
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r6971 | bugman | 2008-07-25 11:49:58 +0200 (Fri, 25 Jul 2008) | 3 lines
Pre-calculated the dipolar constants prior to optimisation.
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r6972 | bugman | 2008-07-25 11:51:42 +0200 (Fri, 25 Jul 2008) | 3 lines
Updated a comment describing why the dipolar constant is multiplied by 3/(2pi).
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r6973 | bugman | 2008-07-25 12:03:53 +0200 (Fri, 25 Jul 2008) | 3 lines
Updated the is_spin_param() method to make a few parameters spin specific.
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r6974 | bugman | 2008-07-25 13:19:18 +0200 (Fri, 25 Jul 2008) | 3 lines
Added a dummy data_init() method to the Common_functions base class.
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r6975 | bugman | 2008-07-25 13:22:27 +0200 (Fri, 25 Jul 2008) | 3 lines
Typo bug fix.
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r6976 | bugman | 2008-07-25 13:24:57 +0200 (Fri, 25 Jul 2008) | 3 lines
Bug fix for the ave_rdc_tensor_dDij_dAmn() function. A numpy array cannot be appended to!
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r6977 | bugman | 2008-07-25 13:53:38 +0200 (Fri, 25 Jul 2008) | 3 lines
Docstring improvements for the ave_rdc_tensor() function.
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r6978 | bugman | 2008-07-25 14:06:08 +0200 (Fri, 25 Jul 2008) | 3 lines
Wrote the function rdc_tensor() to calculate the standard RDC.
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r6979 | bugman | 2008-07-25 14:12:21 +0200 (Fri, 25 Jul 2008) | 3 lines
Created the pc partial derivative part of the RDC gradient.
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r6980 | bugman | 2008-07-25 14:13:27 +0200 (Fri, 25 Jul 2008) | 3 lines
Removed a stray comment.
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r6981 | bugman | 2008-07-25 14:37:41 +0200 (Fri, 25 Jul 2008) | 3 lines
The chi-squared gradient is now calculated.
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r6982 | bugman | 2008-07-25 14:38:40 +0200 (Fri, 25 Jul 2008) | 3 lines
Sent the dipolar constant into the ave_rdc_tensor() function.
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r6983 | bugman | 2008-07-25 14:48:34 +0200 (Fri, 25 Jul 2008) | 3 lines
The dipolar constant is now accepted by the RDC functions.
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r6984 | bugman | 2008-07-25 14:49:29 +0200 (Fri, 25 Jul 2008) | 3 lines
Removed the unused setup_population_eqi() method.
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r6985 | bugman | 2008-07-25 14:57:42 +0200 (Fri, 25 Jul 2008) | 3 lines
No need to multiply by 1.0 to return a copy at the end - the gradient is reset at the start.
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r6986 | bugman | 2008-07-28 14:34:21 +0200 (Mon, 28 Jul 2008) | 5 lines
Changes to the linear_constraints() method.
The method is now private and accepts new arguments for the different types of N-state model.
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r6987 | bugman | 2008-07-28 14:37:24 +0200 (Mon, 28 Jul 2008) | 3 lines
Fixed the creation of the A and b constraint matrices.
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r6988 | bugman | 2008-07-28 14:59:26 +0200 (Mon, 28 Jul 2008) | 3 lines
Made the assemble_param_vector() and disassemble_param_vector() methods private.
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r6989 | bugman | 2008-07-28 15:17:00 +0200 (Mon, 28 Jul 2008) | 3 lines
Passed the data_type variable into the __disassemble_param_vector() method.
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r6990 | bugman | 2008-07-28 15:25:01 +0200 (Mon, 28 Jul 2008) | 3 lines
The data_type arg is now accepted by __disassemble_param_vector().
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r6991 | bugman | 2008-07-28 15:29:53 +0200 (Mon, 28 Jul 2008) | 6 lines
Bug fix for the __disassemble_param_vector() method.
The parameter vector with alignment tensor parameters is now properly split into the alignment
tensor components and probabilities.
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r6992 | bugman | 2008-07-28 19:18:06 +0200 (Mon, 28 Jul 2008) | 3 lines
Inverted the population parameter scaling factor to 100.
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r7021 | bugman | 2008-07-29 18:56:31 +0200 (Tue, 29 Jul 2008) | 3 lines
Fix in grid_search() for the checking of the set up of the N-state model.
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r7029 | bugman | 2008-07-30 10:02:45 +0200 (Wed, 30 Jul 2008) | 3 lines
Added the ability to handle missing RDCs.
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r7076 | bugman | 2008-08-07 15:11:42 +0200 (Thu, 07 Aug 2008) | 3 lines
Docstring fix for the rdc_tensor() function.
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r7077 | bugman | 2008-08-07 15:28:28 +0200 (Thu, 07 Aug 2008) | 3 lines
Created a module for the calculation of the pseudocontact shift (and its gradient and Hessian).
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r7080 | bugman | 2008-08-07 16:26:06 +0200 (Thu, 07 Aug 2008) | 5 lines
Pseudocontact shifts are supported by the N_state_opt.__init__() method.
The target functions still need to be updated.
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r7081 | bugman | 2008-08-07 16:39:06 +0200 (Thu, 07 Aug 2008) | 3 lines
Spelling fix in the docstrings.
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r7082 | bugman | 2008-08-07 16:40:36 +0200 (Thu, 07 Aug 2008) | 3 lines
Modified the func_population() target function to handle both RDCs and PCSs.
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r7083 | bugman | 2008-08-07 16:53:06 +0200 (Thu, 07 Aug 2008) | 3 lines
Modified the dfunc_population() gradient function to handle both RDCs and PCSs.
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r7084 | bugman | 2008-08-07 16:56:29 +0200 (Thu, 07 Aug 2008) | 3 lines
Set up the rdc and pcs flags in the __init__() method.
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r7085 | bugman | 2008-08-07 16:57:37 +0200 (Thu, 07 Aug 2008) | 3 lines
Import fix.
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r7086 | bugman | 2008-08-07 16:58:35 +0200 (Thu, 07 Aug 2008) | 3 lines
Renamed ave_pcs_tensor_ddelta_ij_dAmn() to ave_pcs_tensor_ddeltaij_dAmn() for consistency.
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r7087 | bugman | 2008-08-07 18:04:30 +0200 (Thu, 07 Aug 2008) | 3 lines
Spelling fix in the docstrings.
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r7088 | bugman | 2008-08-07 19:21:09 +0200 (Thu, 07 Aug 2008) | 3 lines
Created the interfaces for the PCS user functions.
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r7089 | bugman | 2008-08-07 19:30:26 +0200 (Thu, 07 Aug 2008) | 3 lines
Renamed the 'RDC identification string' to the 'alignment identification string'.
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r7090 | bugman | 2008-08-07 19:37:08 +0200 (Thu, 07 Aug 2008) | 3 lines
Activated the PCS user functions.
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r7091 | bugman | 2008-08-07 19:51:49 +0200 (Thu, 07 Aug 2008) | 3 lines
Created the generic_fns.pcs module, although nothing will work yet.
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r7092 | bugman | 2008-08-07 19:53:10 +0200 (Thu, 07 Aug 2008) | 3 lines
Removed a useless function.
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r7093 | bugman | 2008-08-07 19:53:50 +0200 (Thu, 07 Aug 2008) | 3 lines
Removed some more useless functions.
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r7106 | bugman | 2008-08-08 10:03:54 +0200 (Fri, 08 Aug 2008) | 3 lines
Changed a lot of references from cdp.rdc_ids to cdp.align_tensors.
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r7107 | bugman | 2008-08-08 10:08:27 +0200 (Fri, 08 Aug 2008) | 3 lines
Converted the read() function to handle PCS rather than RDC data.
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r7108 | bugman | 2008-08-08 10:11:49 +0200 (Fri, 08 Aug 2008) | 3 lines
Created 2 new RelaxErrors for PCSs.
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r7109 | bugman | 2008-08-08 10:20:41 +0200 (Fri, 08 Aug 2008) | 3 lines
Renamed __determine_data_type() to __base_data_type().
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r7110 | bugman | 2008-08-08 10:27:35 +0200 (Fri, 08 Aug 2008) | 3 lines
Redesigned __base_data_types() to determine all base data types, and return them as a list.
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r7111 | bugman | 2008-08-08 10:33:31 +0200 (Fri, 08 Aug 2008) | 3 lines
Modified the __update_model() to handle both RDCs and PCSs.
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r7112 | bugman | 2008-08-08 10:36:22 +0200 (Fri, 08 Aug 2008) | 3 lines
Fixed __base_data_types() to properly identify tensors as the base data source.
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r7113 | bugman | 2008-08-08 10:46:34 +0200 (Fri, 08 Aug 2008) | 3 lines
Fixed all the calls to __base_data_types() and subsequent use of the returned list.
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r7114 | bugman | 2008-08-08 10:47:39 +0200 (Fri, 08 Aug 2008) | 3 lines
Added a module docstring.
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r7115 | bugman | 2008-08-08 11:17:22 +0200 (Fri, 08 Aug 2008) | 5 lines
Changed the way optimisation of the N-state model is set up.
This will allow multiple base data types to be used simultaneously.
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r7116 | bugman | 2008-08-08 11:22:06 +0200 (Fri, 08 Aug 2008) | 3 lines
A call is now made to assemble the PCS data necessary for optimisation.
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r7117 | bugman | 2008-08-08 11:24:54 +0200 (Fri, 08 Aug 2008) | 5 lines
Fix for the __update_model() method.
This was only working if both RDC and PCS data are supplied.
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r7118 | bugman | 2008-08-08 11:26:18 +0200 (Fri, 08 Aug 2008) | 3 lines
Shifted the __update_model() method for fixing the alphabetical ordering of methods.
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r7119 | bugman | 2008-08-08 11:27:48 +0200 (Fri, 08 Aug 2008) | 3 lines
Converted minimise_setup_rdcs() and minimise_setup_tensors() into private methods.
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r7120 | bugman | 2008-08-08 11:59:09 +0200 (Fri, 08 Aug 2008) | 5 lines
Modified the N_state_opt class to accept PCS data.
The __init__() docstring has been significantly expanded as well.
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r7121 | bugman | 2008-08-08 16:19:24 +0200 (Fri, 08 Aug 2008) | 3 lines
Wrote the __minimise_setup_pcs() method.
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r7130 | bugman | 2008-08-11 11:41:08 +0200 (Mon, 11 Aug 2008) | 3 lines
Added the user function interface for setting the experimental temperature.
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r7131 | bugman | 2008-08-11 11:42:40 +0200 (Mon, 11 Aug 2008) | 3 lines
Activated the temperature user function interface.
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r7132 | bugman | 2008-08-11 11:49:53 +0200 (Mon, 11 Aug 2008) | 3 lines
Added a stub function generic_fns.temperature.set() to fix the missing import problem.
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r7133 | bugman | 2008-08-11 11:51:42 +0200 (Mon, 11 Aug 2008) | 3 lines
Fixed the setting up of the temperature user function.
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r7134 | bugman | 2008-08-11 11:53:42 +0200 (Mon, 11 Aug 2008) | 3 lines
Allowed the temperature to be entered as a integer as well as a float.
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r7135 | bugman | 2008-08-11 11:58:38 +0200 (Mon, 11 Aug 2008) | 3 lines
Completed the generic_fns.temperature.set() function.
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r7136 | bugman | 2008-08-11 13:41:30 +0200 (Mon, 11 Aug 2008) | 3 lines
Made the experimental id string compulsory.
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r7137 | bugman | 2008-08-11 13:47:44 +0200 (Mon, 11 Aug 2008) | 3 lines
Added the user function interface for setting the spectrometer frequency of an experiment.
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r7138 | bugman | 2008-08-11 13:49:13 +0200 (Mon, 11 Aug 2008) | 3 lines
Added the frq and temperature modules to the __all__ list.
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r7139 | bugman | 2008-08-11 13:59:01 +0200 (Mon, 11 Aug 2008) | 3 lines
Wrote the spectrometer frequency setting function generic_fns.frq.set().
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r7140 | bugman | 2008-08-11 14:00:37 +0200 (Mon, 11 Aug 2008) | 3 lines
Activated the frq.set() user function.
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r7141 | bugman | 2008-08-11 14:02:47 +0200 (Mon, 11 Aug 2008) | 3 lines
Fixes for the frq.set() user function.
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r7142 | bugman | 2008-08-11 14:08:10 +0200 (Mon, 11 Aug 2008) | 3 lines
Added the frq and temperature modules to the __all__ list.
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r7143 | bugman | 2008-08-11 14:21:41 +0200 (Mon, 11 Aug 2008) | 3 lines
Create the interface for the pcs.centre() user function.
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r7144 | bugman | 2008-08-11 14:53:55 +0200 (Mon, 11 Aug 2008) | 3 lines
Implemented the generic_fns.pcs.centre() function.
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r7145 | bugman | 2008-08-11 15:11:40 +0200 (Mon, 11 Aug 2008) | 3 lines
The structure identifier arg is now used by the atom_loop() method.
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r7146 | bugman | 2008-08-11 15:28:34 +0200 (Mon, 11 Aug 2008) | 3 lines
Fixed the atom_loop() call in __minimise_setup_pcs().
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r7148 | bugman | 2008-08-11 15:37:06 +0200 (Mon, 11 Aug 2008) | 3 lines
Wrote the pcs_constant() function to calculate the pseudocontact shift constant.
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r7149 | bugman | 2008-08-11 15:41:13 +0200 (Mon, 11 Aug 2008) | 3 lines
Added Boltzmann's constant to the physical_constants module.
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r7150 | bugman | 2008-08-11 16:01:02 +0200 (Mon, 11 Aug 2008) | 8 lines
Fixes for the PCS constant, as it is dependent on the indices i, j and c.
These are:
i, the experiment or alignment index,
j, the spin index,
c, the state index.
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r7151 | bugman | 2008-08-11 16:48:36 +0200 (Mon, 11 Aug 2008) | 3 lines
Redesigned the __minimise_setup_pcs() method.
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r7152 | bugman | 2008-08-11 18:45:14 +0200 (Mon, 11 Aug 2008) | 3 lines
Added the ave arg to the structure.load_spins() user function.
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r7153 | bugman | 2008-08-11 18:46:21 +0200 (Mon, 11 Aug 2008) | 3 lines
Renamed the ave arg of structure.load_spins() to ave_pos.
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r7154 | bugman | 2008-08-11 18:53:05 +0200 (Mon, 11 Aug 2008) | 3 lines
The load_spins() function is now either loading the average or all atom positions.
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r7155 | bugman | 2008-08-11 19:42:13 +0200 (Mon, 11 Aug 2008) | 5 lines
Fixes for the __minimise_setup_pcs() method.
Multi-dimensional arrays were not being properly created or referenced.
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r7156 | bugman | 2008-08-12 09:39:46 +0200 (Tue, 12 Aug 2008) | 3 lines
Fixed the call to __minimise_setup_pcs().
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r7157 | bugman | 2008-08-12 09:44:44 +0200 (Tue, 12 Aug 2008) | 3 lines
Fixed the initialisation of the variables pcs, pcs_vect, and pcs_dj.
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r7158 | bugman | 2008-08-12 09:52:32 +0200 (Tue, 12 Aug 2008) | 3 lines
Fixes for the N_state_opt.__init__() docstring.
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r7159 | bugman | 2008-08-12 09:53:08 +0200 (Tue, 12 Aug 2008) | 3 lines
Placed the PCS constants into self.
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r7160 | bugman | 2008-08-12 09:58:15 +0200 (Tue, 12 Aug 2008) | 3 lines
Converted the PCS constant data structure into a numpy array in __minimise_setup_pcs().
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r7161 | bugman | 2008-08-12 09:58:44 +0200 (Tue, 12 Aug 2008) | 3 lines
Fixed a typo bug.
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r7162 | bugman | 2008-08-12 10:00:03 +0200 (Tue, 12 Aug 2008) | 3 lines
Bug fix for the ave_pcs_tensor() function.
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r7163 | bugman | 2008-08-12 10:38:00 +0200 (Tue, 12 Aug 2008) | 5 lines
Modified the setup of the RDC data.
Spins missing RDC data but other data now have rows of None appended to the data structures.
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r7164 | bugman | 2008-08-12 10:43:24 +0200 (Tue, 12 Aug 2008) | 3 lines
Converted the RDC constant list into a numpy array.
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r7165 | bugman | 2008-08-12 10:49:16 +0200 (Tue, 12 Aug 2008) | 6 lines
Fixes for the set up of the RDC constant array.
None (or NaN after numpy converion) is placed into the list when other data exists but the RDC is
missing.
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r7166 | bugman | 2008-08-12 10:50:18 +0200 (Tue, 12 Aug 2008) | 3 lines
Fixes for the __init__() docstring.
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r7167 | bugman | 2008-08-12 10:58:28 +0200 (Tue, 12 Aug 2008) | 5 lines
Bug fix for the target function.
The RDC vector and PCS vectors are not the same!
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r7168 | bugman | 2008-08-12 11:45:44 +0200 (Tue, 12 Aug 2008) | 3 lines
Big debugging of the N-state model setup, target, and gradient functions.
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r7169 | bugman | 2008-08-12 11:49:07 +0200 (Tue, 12 Aug 2008) | 3 lines
Fixed some of the tests in the __init__() method.
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r7170 | bugman | 2008-08-12 12:10:38 +0200 (Tue, 12 Aug 2008) | 3 lines
Scaled the PCS value from ppm to no units.
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r7171 | bugman | 2008-08-12 12:11:27 +0200 (Tue, 12 Aug 2008) | 3 lines
Removed some commented out and no longer used code.
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r7172 | bugman | 2008-08-12 12:15:06 +0200 (Tue, 12 Aug 2008) | 3 lines
Shrunk the size of the default PCS errors, so the chi-squared value is comparable to the RDC.
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r7173 | bugman | 2008-08-12 12:20:19 +0200 (Tue, 12 Aug 2008) | 5 lines
Fix for the paramagnetic centre to nucleus distances.
The distances are now converted from Angstrom to meters.
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r7174 | bugman | 2008-08-12 12:33:19 +0200 (Tue, 12 Aug 2008) | 3 lines
Changed the PCS scaling factor.
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r7175 | bugman | 2008-08-12 14:34:12 +0200 (Tue, 12 Aug 2008) | 3 lines
Fixes for all the N-state model unit tests.
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r7176 | bugman | 2008-08-12 14:46:48 +0200 (Tue, 12 Aug 2008) | 3 lines
Added a test to see if the model has been selected.
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r7177 | bugman | 2008-08-12 14:47:32 +0200 (Tue, 12 Aug 2008) | 3 lines
Fixed the test___assemble_param_vector() unit test.
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r7178 | bugman | 2008-08-12 14:53:24 +0200 (Tue, 12 Aug 2008) | 3 lines
Added a test to __disassemble_param_vector() to set if the model has been selected.
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r7179 | bugman | 2008-08-12 14:54:19 +0200 (Tue, 12 Aug 2008) | 3 lines
Fixes for the test___disassemble_param_vector() unit test.
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r7180 | bugman | 2008-08-12 15:05:39 +0200 (Tue, 12 Aug 2008) | 3 lines
Set the 2-domain N-state model gradient and Hessian methods to None.
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r7181 | bugman | 2008-08-12 15:09:22 +0200 (Tue, 12 Aug 2008) | 3 lines
Allowed the align_tensor.display() arg to be None (to display all tensors).
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r7182 | bugman | 2008-08-12 15:15:52 +0200 (Tue, 12 Aug 2008) | 3 lines
Modified the display() function to allow all alignment tensors to be displayed.
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r7183 | bugman | 2008-08-12 15:33:09 +0200 (Tue, 12 Aug 2008) | 3 lines
Modified the N-state model methods to set the alignment tensor parameter rather Saupe order matrix.
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r7184 | bugman | 2008-08-12 15:34:37 +0200 (Tue, 12 Aug 2008) | 5 lines
Changed the list of modifiable alignment tensor objects.
Alignment tensor parameters rather than Saupe order matrix elements can now be changed.
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r7185 | bugman | 2008-08-12 17:04:13 +0200 (Tue, 12 Aug 2008) | 3 lines
Updated the set() function to set the alignment tensor parameters rather than Saupe order matrix.
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r7186 | bugman | 2008-08-12 17:16:06 +0200 (Tue, 12 Aug 2008) | 3 lines
Modified the unit tests of the alignment tensor objects to use Axx rather than Sxx, etc.
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r7187 | bugman | 2008-08-12 17:47:57 +0200 (Tue, 12 Aug 2008) | 6 lines
Modified the alignment tensor objects.
These are now storing everything as alignment tensor parameters rather than Saupe order matrix
components and hence all the updating functions have been modified to match.
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r7188 | bugman | 2008-08-12 17:48:27 +0200 (Tue, 12 Aug 2008) | 3 lines
Loosened some unit tests for the alignment tensor.
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r7189 | bugman | 2008-08-12 17:49:53 +0200 (Tue, 12 Aug 2008) | 3 lines
Fix for the test_display_argfail_tensor() unit test.
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r7191 | bugman | 2008-08-13 11:55:56 +0200 (Wed, 13 Aug 2008) | 3 lines
Added the ability to reload alignment tensors from the XML results file into the relax data store.
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r7192 | bugman | 2008-08-14 11:31:10 +0200 (Thu, 14 Aug 2008) | 10 lines
Bug fixes and expansion of the __linear_constraints() method.
The bug fix is that the b array was not being scaled! This is essential when diagonal scaling is
active.
The added feature is that the pN weight of state N, which is not a parameter of the model, is now
constrained to be between 0 and 1. This is because the value is equal to 1 minus the sum of all
other probabilities, hence linear constraints can be created.
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r7193 | bugman | 2008-08-14 14:39:24 +0200 (Thu, 14 Aug 2008) | 3 lines
Wrote the model_statistics() method.
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r7194 | bugman | 2008-08-14 14:49:45 +0200 (Thu, 14 Aug 2008) | 3 lines
Wrote the num_data_points() method for determining n.
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r7195 | bugman | 2008-08-14 16:47:29 +0200 (Thu, 14 Aug 2008) | 3 lines
Added the pipe arg to the pcs.centre() user function.
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r7196 | bugman | 2008-08-14 16:52:06 +0200 (Thu, 14 Aug 2008) | 3 lines
The data pipe arg is now accepted by the centre() function.
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r7197 | bugman | 2008-08-14 16:56:46 +0200 (Thu, 14 Aug 2008) | 3 lines
Shifted the calculation of the paramagnetic centre from __minimise_setup_pcs() to centre().
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r7198 | bugman | 2008-08-14 16:57:58 +0200 (Thu, 14 Aug 2008) | 3 lines
Added a missing import and fixed an incorrect reference to the data pipe container.
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r7199 | bugman | 2008-08-14 17:09:00 +0200 (Thu, 14 Aug 2008) | 3 lines
The calculated paramagnetic centre is now being placed into the current data pipe.
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r7200 | bugman | 2008-08-14 17:09:41 +0200 (Thu, 14 Aug 2008) | 3 lines
Added a print out to the centre() function.
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r7201 | bugman | 2008-08-15 10:09:17 +0200 (Fri, 15 Aug 2008) | 5 lines
Allowed the data column to be None in the rdc.read() user function.
This allows a file containing only errors to be read.
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r7202 | bugman | 2008-08-16 14:51:32 +0200 (Sat, 16 Aug 2008) | 3 lines
RDC errors can now be read separately and independently from the data values.
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r7203 | bugman | 2008-08-17 18:25:44 +0200 (Sun, 17 Aug 2008) | 3 lines
Allowed the PCS data column to be None, so that a file with only PCS errors can be read.
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r7204 | bugman | 2008-08-17 19:06:16 +0200 (Sun, 17 Aug 2008) | 5 lines
PCS errors in a file separate from the data can now be read.
This matches the changes for the RDC at r7202.
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r7205 | bugman | 2008-08-17 19:08:49 +0200 (Sun, 17 Aug 2008) | 6 lines
Reverted the last revision, r7204, as this included too much.
The command used was:
svn merge -r7204:7203 .
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r7206 | bugman | 2008-08-17 19:10:17 +0200 (Sun, 17 Aug 2008) | 5 lines
Try 2: PCS errors in a file separate from the data can now be read.
This matches the changes for the RDC at r7202, and is what r7204 should have been.
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r7207 | bugman | 2008-08-17 19:12:21 +0200 (Sun, 17 Aug 2008) | 5 lines
The RDC and PCS errors data structures are now created by the __minimise_setup_*() methods.
These are also passed into the minimisation code.
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r7208 | bugman | 2008-08-17 19:15:29 +0200 (Sun, 17 Aug 2008) | 3 lines
The RDC and PCS error data structures are now properly handled and setup in __init__().
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r7226 | bugman | 2008-08-23 02:37:51 +0200 (Sat, 23 Aug 2008) | 3 lines
Wrote the __minimise_bc_data() method to extract the back calculated data after minimisation.
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r7227 | bugman | 2008-08-23 03:31:59 +0200 (Sat, 23 Aug 2008) | 3 lines
Wrote a function to calculate the RDC Q-factor.
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r7230 | bugman | 2008-09-24 14:21:18 +0200 (Wed, 24 Sep 2008) | 3 lines
Some bug fixes and added the ability to calculate the Q-factor values.
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r7231 | bugman | 2008-09-24 14:22:11 +0200 (Wed, 24 Sep 2008) | 3 lines
Small bug fix causing insignificant duplication of ID strings.
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r7307 | bugman | 2008-09-25 18:19:41 +0200 (Thu, 25 Sep 2008) | 5 lines
Bug fix for the loading of results files when they contain not alignment tensor data.
The bug was in the PipeContainer.from_xml() method.
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