Merged revisions 8681,8683,8714,8717,8723,8725-8732,8734-8746,8748-8798,8800-8812,8821-8826,8828-8832,8861-8862,8879,8893-8898,8900-8902,8909-8910,8916-8919,8925-8927,8929,8932,8935,8963,8971-8972,8974,8976-8977,8979-8990,8997-9003,9010-9011,9015-9017,9019-9024,9028-9040,9042-9043,9048-9066,9068-9069,9081,9194-9196,9198-9200,9202-9230 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
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r8681 | bugman | 2009-01-27 18:35:10 +0100 (Tue, 27 Jan 2009) | 6 lines
Removed the dependence of the relax_errors and relax_warnings modules on relax.
This fixes some rare circular import failures with the --debug flag and makes the modules much
cleaner and more independent.
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r8683 | bugman | 2009-01-27 18:48:32 +0100 (Tue, 27 Jan 2009) | 6 lines
Improvements to the relax_errors module.
The module function save_state() can now function if this module is used by something other than
relax. The saved state is also BZip compressed if the bz2 module exists.
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r8714 | bugman | 2009-02-02 10:58:41 +0100 (Mon, 02 Feb 2009) | 3 lines
Added some printouts stating which file the relax saved state is placed in when in Debug mode.
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r8717 | bugman | 2009-02-02 11:30:54 +0100 (Mon, 02 Feb 2009) | 11 lines
Fixed an annoying bug in the RelaxError debugging mode.
The problem here is that the relax state was being saved in the __init__() methods if in debug mode.
The result was that in try statements which catch and allow for RelaxErrors, the relax state was
being saved even though the error message and exception was suppressed. The fix was to shift the
state saving code into the __str__() method.
A side effect of this change is a simplification of all the RelaxError classes as the debug code is
no longer duplicated in each class.
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r8723 | bugman | 2009-02-03 18:05:58 +0100 (Tue, 03 Feb 2009) | 6 lines
Wrote 2 new system tests for the new structural data design.
In test_read_pdb_internal6(), 2 different structures are loaded as 2 molecules. In
test_read_pdb_internal7(), 2 identical structures are loaded as 2 molecules.
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r8725 | bugman | 2009-02-04 10:33:25 +0100 (Wed, 04 Feb 2009) | 3 lines
Duplicated 5 systems tests of the internal PDB reader for the Scientific python PDB reader.
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r8726 | bugman | 2009-02-04 10:37:40 +0100 (Wed, 04 Feb 2009) | 5 lines
Bug fix for the load_pdb() method.
When set_model_num is None, this is now handled properly.
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r8727 | bugman | 2009-02-04 10:51:40 +0100 (Wed, 04 Feb 2009) | 6 lines
Fixes for the test_read_pdb_mol_2_model_scientific() system test.
The Scientific python PDB reader somehow decided to split the single structures in
'lactose_MCMM4_S1_*.pdb' into 2.
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r8728 | bugman | 2009-02-04 15:55:49 +0100 (Wed, 04 Feb 2009) | 5 lines
Fixes for the load_pdb() method.
Previously loaded structures were not being taken into account.
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r8729 | bugman | 2009-02-04 16:16:25 +0100 (Wed, 04 Feb 2009) | 5 lines
More fixes for load_pdb().
Collapsing 2 models into 1 was failing.
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r8730 | bugman | 2009-02-04 17:22:01 +0100 (Wed, 04 Feb 2009) | 5 lines
Another fix for the load_pdb() method.
The mol_offset value should be calculated at all times!
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r8731 | bugman | 2009-02-04 17:22:38 +0100 (Wed, 04 Feb 2009) | 3 lines
Added error checking to load_pdb() for when the number of molecules exceeds the set_mol_name list.
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r8732 | bugman | 2009-02-04 17:24:47 +0100 (Wed, 04 Feb 2009) | 3 lines
The read_mol arg now does something in load_pdb()!!!
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r8734 | bugman | 2009-02-04 17:32:36 +0100 (Wed, 04 Feb 2009) | 6 lines
Fix for the test_read_pdb_complex_scientific() system test.
Retarded Scientific python splitting a perfectly good molecule into 2 when it can't recognise a
residue type!
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r8735 | bugman | 2009-02-05 10:00:21 +0100 (Thu, 05 Feb 2009) | 6 lines
Modified test_read_pdb_internal1() to catch a molecule name identification bug.
The test_read_pdb_scientific1() was similarly modified, but there is no bug in the Scientific python
code.
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r8736 | bugman | 2009-02-05 10:18:17 +0100 (Thu, 05 Feb 2009) | 5 lines
Bug fix for the atom_loop() method.
The molecule name was not being checked!
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r8737 | bugman | 2009-02-05 10:22:02 +0100 (Thu, 05 Feb 2009) | 3 lines
Added a check for the molecule name.
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r8738 | bugman | 2009-02-05 10:22:35 +0100 (Thu, 05 Feb 2009) | 3 lines
Modified a print out to make it clearer.
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r8739 | bugman | 2009-02-05 11:30:37 +0100 (Thu, 05 Feb 2009) | 3 lines
Modified the get_pipe() function to check if a data pipe exists.
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r8740 | bugman | 2009-02-05 11:43:43 +0100 (Thu, 05 Feb 2009) | 3 lines
Modified 2 system tests for the loading of N-Ca vectors.
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r8741 | bugman | 2009-02-05 14:41:36 +0100 (Thu, 05 Feb 2009) | 22 lines
Massive speed up of the bond_vectors() method.
The algorithm used was very, very poorly designed. Now when setting the profile flag to 1 gives the
following. Before in one test:
11168736 function calls (10986641 primitive calls) in 76.750 CPU seconds
ncalls tottime percall cumtime percall filename:lineno(function)
758954 12.160 0.000 51.060 0.000 /home/edau/relax/relax-1.3/generic_fns/relax_re.py:31(search)
141 0.890 0.006 67.620 0.480 /home/edau/relax/relax-1.3/generic_fns/structure/internal.py:444(bond_vectors)
All other function call info lines have been removed. After the changes:
2586419 function calls (2579305 primitive calls) in 21.370 CPU seconds
ncalls tottime percall cumtime percall filename:lineno(function)
62803 1.180 0.000 5.020 0.000 /home/edau/relax/relax-1.3/generic_fns/relax_re.py:31(search)
141 0.060 0.000 12.020 0.085 /home/edau/relax/relax-1.3/generic_fns/structure/internal.py:444(bond_vectors)
The difference is that the selection object is no longer used, as it is completely unnecessary.
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r8742 | bugman | 2009-02-05 14:42:51 +0100 (Thu, 05 Feb 2009) | 3 lines
Modified the base API bond_vectors() method.
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r8743 | bugman | 2009-02-05 14:46:28 +0100 (Thu, 05 Feb 2009) | 3 lines
Added the atoms 'NZ' and 'OH' as nitrogens and oxygens of amino acids respectively.
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r8744 | bugman | 2009-02-05 14:54:50 +0100 (Thu, 05 Feb 2009) | 8 lines
Fixes for the bond_vectors() method.
The atom_id string is now generated as it is no longer passed in. This is a temporary fix and this
function is very inefficient, just as the internal object bond_vectors() method was (which was fixed
in r8741).
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r8745 | bugman | 2009-02-05 15:00:36 +0100 (Thu, 05 Feb 2009) | 5 lines
Fix for the test_read_pdb_scientific1() system test.
The current data pipe was not aliased.
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r8746 | bugman | 2009-02-05 15:03:40 +0100 (Thu, 05 Feb 2009) | 3 lines
Removed some debugging print statements.
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r8748 | bugman | 2009-02-05 18:40:49 +0100 (Thu, 05 Feb 2009) | 3 lines
The __linear_constraints() method now handles the N-state models without probabilities.
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r8749 | bugman | 2009-02-05 18:48:59 +0100 (Thu, 05 Feb 2009) | 5 lines
Fix for the __linear_constraints() method.
The last probability N is not in the scaling matrix! Therefore don't scale.
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r8750 | bugman | 2009-02-06 11:57:46 +0100 (Fri, 06 Feb 2009) | 6 lines
Added a PDB file containing the N, H, and calcium atoms of Bax's 1J7P structure.
This will be used in the creation and testing of optimisation of alignment tensors from RDCs and
PCSs.
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r8751 | bugman | 2009-02-06 13:32:41 +0100 (Fri, 06 Feb 2009) | 3 lines
Created a directory for CaM RDC and PCS test data.
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r8752 | bugman | 2009-02-06 17:34:03 +0100 (Fri, 06 Feb 2009) | 5 lines
Created a script to generate RDC and PCS data for a synthetic alignment tensor.
PCS data still needs to be generated!
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r8753 | bugman | 2009-02-06 17:35:10 +0100 (Fri, 06 Feb 2009) | 3 lines
Generated and added the synthetic RDC data.
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r8754 | bugman | 2009-02-06 18:16:34 +0100 (Fri, 06 Feb 2009) | 3 lines
A few modifications for the PCS.
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r8755 | bugman | 2009-02-09 11:14:15 +0100 (Mon, 09 Feb 2009) | 3 lines
The PCS constant is now being calculated.
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r8756 | bugman | 2009-02-09 11:20:01 +0100 (Mon, 09 Feb 2009) | 3 lines
The PCS is now calculated for each spin.
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r8757 | bugman | 2009-02-09 11:30:41 +0100 (Mon, 09 Feb 2009) | 3 lines
Fixes for the PCS calculation.
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r8758 | bugman | 2009-02-09 11:35:20 +0100 (Mon, 09 Feb 2009) | 3 lines
Added the synthetic PCS values (note these are currently incorrect).
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r8759 | bugman | 2009-02-09 14:24:51 +0100 (Mon, 09 Feb 2009) | 3 lines
Fixes for the calculation of the PCS.
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r8760 | bugman | 2009-02-09 15:21:49 +0100 (Mon, 09 Feb 2009) | 3 lines
Decreased the alignment by a factor of 5.
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r8761 | bugman | 2009-02-09 16:05:12 +0100 (Mon, 09 Feb 2009) | 7 lines
Reverted r8760, as the tensor was originally roughly correct in size.
The command used was:
svn merge -r8760:8759 .
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r8762 | bugman | 2009-02-09 16:07:30 +0100 (Mon, 09 Feb 2009) | 3 lines
Shifted all print statements to the end.
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r8763 | bugman | 2009-02-10 11:09:02 +0100 (Tue, 10 Feb 2009) | 3 lines
Duplicated generate_data.py to create a script for generating a list of residues bleached by PRE.
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r8764 | bugman | 2009-02-10 11:31:47 +0100 (Tue, 10 Feb 2009) | 3 lines
Modified the PRE bleaching script to actually do what it's supposed to do.
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r8765 | bugman | 2009-02-10 13:51:40 +0100 (Tue, 10 Feb 2009) | 3 lines
Changed the PRE cut-off to 15 Angstrom.
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r8766 | bugman | 2009-02-10 13:52:10 +0100 (Tue, 10 Feb 2009) | 3 lines
Added the list of PRE broadened residues.
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r8767 | bugman | 2009-02-10 14:30:18 +0100 (Tue, 10 Feb 2009) | 3 lines
Modified the script to output all spin info into 'unresolved'.
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r8768 | bugman | 2009-02-10 14:33:11 +0100 (Tue, 10 Feb 2009) | 3 lines
The spins from 'unresolved' are now removed from the RDC and PCS lists.
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r8769 | bugman | 2009-02-10 14:34:40 +0100 (Tue, 10 Feb 2009) | 3 lines
Decreased the synthetic alignment by half to bring the max PCS into the 3 ppm range.
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r8770 | bugman | 2009-02-10 17:27:04 +0100 (Tue, 10 Feb 2009) | 7 lines
Modified the full_analysis.py script to name spins if the sequence data contains no spin name info.
This is in response to the post by Pierre-Yves Savard <Pierre-Yves dot Savard att bcm dot ulaval dot
ca> at https://mail.gna.org/public/relax-users/2009-02/msg00001.html (Message-id:
<4991A4A6.5070309@...>).
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r8771 | bugman | 2009-02-11 14:14:59 +0100 (Wed, 11 Feb 2009) | 3 lines
Added a script for testing out the use of RDCs and PCSs to find the alignment tensor.
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r8772 | bugman | 2009-02-11 14:52:59 +0100 (Wed, 11 Feb 2009) | 3 lines
Activated the RDC and PCS tensor fitting system test.
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r8773 | bugman | 2009-02-11 15:18:54 +0100 (Wed, 11 Feb 2009) | 3 lines
Added a print outs for the reading of RDCs and PCSs.
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r8774 | bugman | 2009-02-11 15:21:24 +0100 (Wed, 11 Feb 2009) | 3 lines
Modified the data reading print outs.
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r8775 | bugman | 2009-02-11 15:26:25 +0100 (Wed, 11 Feb 2009) | 3 lines
The file data is now always checked.
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r8776 | bugman | 2009-02-11 15:29:41 +0100 (Wed, 11 Feb 2009) | 3 lines
Added checks for the presence of any extractable data from the file.
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r8777 | bugman | 2009-02-11 15:31:13 +0100 (Wed, 11 Feb 2009) | 3 lines
Fix for the system test script. The RDC and PCS data was not being read correctly.
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r8778 | bugman | 2009-02-11 15:38:28 +0100 (Wed, 11 Feb 2009) | 3 lines
Print out fixes.
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r8779 | bugman | 2009-02-11 15:47:15 +0100 (Wed, 11 Feb 2009) | 5 lines
Bug fix, changed all the default args to None.
If columns are normally missing, the column args should be None!
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r8780 | bugman | 2009-02-11 15:51:03 +0100 (Wed, 11 Feb 2009) | 3 lines
Bug fixes for the print outs.
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r8781 | bugman | 2009-02-11 16:54:43 +0100 (Wed, 11 Feb 2009) | 3 lines
Caught the missing paramagnetic centre.
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r8782 | bugman | 2009-02-11 17:03:39 +0100 (Wed, 11 Feb 2009) | 3 lines
The paramagnetic centre is now set.
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r8783 | bugman | 2009-02-11 17:07:33 +0100 (Wed, 11 Feb 2009) | 3 lines
Added a few more tests for data that needs to be input.
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r8784 | bugman | 2009-02-11 17:38:01 +0100 (Wed, 11 Feb 2009) | 3 lines
The N-state model with equal and fixed probabilities for each N state can now be optimised.
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r8785 | bugman | 2009-02-11 17:39:01 +0100 (Wed, 11 Feb 2009) | 3 lines
Added a grid search to the system test.
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r8786 | bugman | 2009-02-11 21:54:08 +0100 (Wed, 11 Feb 2009) | 7 lines
Bug fix for the setting of the spin name.
This was found by Pierre-Yves Savard <Pierre-Yves dot Savard att bcm dot ulaval dot ca> in the post
https://mail.gna.org/public/relax-users/2009-02/msg00008.html (Message-id:
<49932AF0.5040503@...>).
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r8787 | bugman | 2009-02-12 09:52:45 +0100 (Thu, 12 Feb 2009) | 3 lines
Modified the grid_search() method to handle alignment tensor parameters (which aren't in cdp.params).
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r8788 | bugman | 2009-02-12 09:57:11 +0100 (Thu, 12 Feb 2009) | 3 lines
Constraints are turned off for the 'fixed' model!
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r8789 | bugman | 2009-02-12 10:06:45 +0100 (Thu, 12 Feb 2009) | 3 lines
Set the grid search lower bound for alignment tensor elements from 0 to -1e-3.
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r8790 | bugman | 2009-02-12 10:13:40 +0100 (Thu, 12 Feb 2009) | 5 lines
Bug fix for the __disassemble_param_vector() method.
The probabilities do not exist in the 'fixed' model!
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r8791 | bugman | 2009-02-12 10:19:48 +0100 (Thu, 12 Feb 2009) | 3 lines
A few changes to the system test.
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r8792 | bugman | 2009-02-12 10:51:37 +0100 (Thu, 12 Feb 2009) | 3 lines
The alignment tensor elements are now explicitly set.
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r8793 | bugman | 2009-02-12 11:17:34 +0100 (Thu, 12 Feb 2009) | 3 lines
Bug fixes for the N-state model when N = 1.
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r8794 | bugman | 2009-02-12 14:39:23 +0100 (Thu, 12 Feb 2009) | 6 lines
Bug fix for the N-state model optimisation.
In __minimise_setup_rdcs(), the XH bond vector structure was being incorrectly set up if the spin
container xh_vect object is a single 3D vector.
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r8795 | bugman | 2009-02-12 19:59:24 +0100 (Thu, 12 Feb 2009) | 6 lines
Bug fix for the PCS alignment tensor fitting.
The __minimise_setup_pcs() method was failing to determine the paramagnetic, nuclear spin distance
correctly.
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r8796 | bugman | 2009-02-12 20:08:38 +0100 (Thu, 12 Feb 2009) | 3 lines
Modified the system test script to allow different combinations of RDC and/or PCS loading.
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r8797 | bugman | 2009-02-13 18:05:33 +0100 (Fri, 13 Feb 2009) | 3 lines
Fixes for the system test script.
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r8798 | bugman | 2009-02-13 18:06:25 +0100 (Fri, 13 Feb 2009) | 5 lines
Expansion of the alignment tensor fitting system tests to create 3 different tests.
The optimised values are now checked as well.
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r8800 | bugman | 2009-02-15 12:50:39 +0100 (Sun, 15 Feb 2009) | 5 lines
Debugged the __minimise_bc_data() method.
The calculated Q-factors for the RDC and PCS were completely incorrect!
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r8801 | bugman | 2009-02-15 12:51:13 +0100 (Sun, 15 Feb 2009) | 3 lines
Removed some debugging print outs.
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r8802 | bugman | 2009-02-15 14:44:38 +0100 (Sun, 15 Feb 2009) | 3 lines
Added the Ca atom of GLU 3.
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r8803 | bugman | 2009-02-15 14:45:10 +0100 (Sun, 15 Feb 2009) | 3 lines
Some fixes for the test_read_pdb_internal1() and test_read_pdb_scientific1() system tests.
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r8804 | bugman | 2009-02-15 14:54:29 +0100 (Sun, 15 Feb 2009) | 3 lines
When finding attached atoms, the radius of atoms assumed to be bonded has been increased to 2 Angstrom.
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r8805 | bugman | 2009-02-15 19:05:15 +0100 (Sun, 15 Feb 2009) | 5 lines
Modified how the generic peak intensity file is detected.
The change is that if no other formats are detected, relax falls back to the generic format.
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r8806 | bugman | 2009-02-16 11:34:05 +0100 (Mon, 16 Feb 2009) | 3 lines
The RDC data is now formatted for Pales, to check the synthetic test model and relax.
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r8807 | bugman | 2009-02-16 11:45:40 +0100 (Mon, 16 Feb 2009) | 3 lines
Modified the print out to remove the broken Eigenvalue sum and add the Saupe order matrix.
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r8808 | bugman | 2009-02-16 14:22:13 +0100 (Mon, 16 Feb 2009) | 3 lines
Added a debugging print out.
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r8809 | bugman | 2009-02-17 10:08:28 +0100 (Tue, 17 Feb 2009) | 5 lines
Modified the NH bond length to be 1.041 Angstrom.
This is from Ottiger, M. and Bax A., J. Am. Chem. Soc. (1998), 120, 12334-12341.
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r8810 | bugman | 2009-02-17 10:56:07 +0100 (Tue, 17 Feb 2009) | 5 lines
Modified the NH bond length to be 1.041 Angstrom in the system test script.
This is from Ottiger, M. and Bax A., J. Am. Chem. Soc. (1998), 120, 12334-12341.
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r8811 | bugman | 2009-02-17 11:03:19 +0100 (Tue, 17 Feb 2009) | 3 lines
Added comments saying what the gyromagnetic ratio constants used in Pales are.
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r8812 | bugman | 2009-02-17 11:22:03 +0100 (Tue, 17 Feb 2009) | 3 lines
Added the Pales output file.
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r8821 | semor | 2009-02-17 22:47:11 +0100 (Tue, 17 Feb 2009) | 7 lines
Corrected a out-of-date dosctring.
This was discussed in a thread at:
https://mail.gna.org/public/relax-devel/2009-02/msg00003.html
(Message-id: <498C75A0.4000408@...>)
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r8822 | bugman | 2009-02-18 11:40:33 +0100 (Wed, 18 Feb 2009) | 5 lines
Added the bond length values for RDC usage.
These are from Ottiger, M. and Bax A., J. Am. Chem. Soc. (1998), 120, 12334-12341.
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r8823 | bugman | 2009-02-18 11:56:49 +0100 (Wed, 18 Feb 2009) | 3 lines
Added a script to randomise the RDC and PCS data, and the randomised data.
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r8824 | bugman | 2009-02-18 14:12:54 +0100 (Wed, 18 Feb 2009) | 5 lines
Created a Pales input file for the randomised RDCs.
This randomised the data again!
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r8825 | bugman | 2009-02-18 14:16:29 +0100 (Wed, 18 Feb 2009) | 3 lines
Added the Pales output for the randomised RDCs.
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r8826 | bugman | 2009-02-18 14:29:49 +0100 (Wed, 18 Feb 2009) | 3 lines
Added 3 system tests checking the optimisation of the randomised RDC and PCS data.
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r8828 | bugman | 2009-02-18 14:49:26 +0100 (Wed, 18 Feb 2009) | 3 lines
The alignment tensor components are now also printed out for debugging.
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r8829 | bugman | 2009-02-18 15:02:33 +0100 (Wed, 18 Feb 2009) | 6 lines
Modified the randomised RDC and PCS tensor optimisation system test checks.
The values are now matched against those from relax! Not really reliable, but they are close to
Pales by 10% for the pure RDC fit, all except the Q-factor!
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r8830 | bugman | 2009-02-18 15:03:44 +0100 (Wed, 18 Feb 2009) | 3 lines
The Q-factors for the RDC and PCS were switched.
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r8831 | bugman | 2009-02-19 10:38:59 +0100 (Thu, 19 Feb 2009) | 3 lines
Converted all the remaining value user function to the new relax design.
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r8832 | bugman | 2009-02-19 10:41:03 +0100 (Thu, 19 Feb 2009) | 3 lines
A few fixes for the new relax design.
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r8861 | bugman | 2009-02-22 23:00:08 +0100 (Sun, 22 Feb 2009) | 3 lines
Fixed some circular import issues.
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r8862 | bugman | 2009-02-22 23:03:48 +0100 (Sun, 22 Feb 2009) | 3 lines
Converted the rest of the generic_fns.relax_data module to the 1.3 line relax design.
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r8879 | bugman | 2009-02-27 14:31:58 +0100 (Fri, 27 Feb 2009) | 5 lines
Allowed molecule.name() to name unnamed molecules.
I.e. the mol_id arg can be None.
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r8893 | bugman | 2009-02-27 18:58:24 +0100 (Fri, 27 Feb 2009) | 3 lines
The diagonalised alignment tensor is now being created (and is being done correctly).
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r8894 | bugman | 2009-03-02 17:26:48 +0100 (Mon, 02 Mar 2009) | 5 lines
Fix for the calc_tensor_diag() function.
The algorithm for finding Ayy was broken.
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r8895 | bugman | 2009-03-02 17:34:06 +0100 (Mon, 02 Mar 2009) | 5 lines
Fix for the test_name_argfail_mol_id() unit test.
The mol_id can be None, i.e. for naming unnamed molecules.
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r8896 | bugman | 2009-03-02 17:35:33 +0100 (Mon, 02 Mar 2009) | 3 lines
Fixed the check for None in molecule.name().
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r8897 | bugman | 2009-03-02 17:42:04 +0100 (Mon, 02 Mar 2009) | 5 lines
Allowed the spin_num arg of spin.create() to be None.
This is useful for polymers where the name is important rather than number.
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r8898 | bugman | 2009-03-04 10:32:28 +0100 (Wed, 04 Mar 2009) | 3 lines
Fix for the test_create_argfail_spin_num() unit test.
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r8900 | bugman | 2009-03-04 15:33:51 +0100 (Wed, 04 Mar 2009) | 6 lines
Changed the way the Q-factor is calculated.
The Q-factor is now calculated as Clore's R-factor divided by N. This now matches the Pales default
mode.
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r8901 | bugman | 2009-03-04 15:37:49 +0100 (Wed, 04 Mar 2009) | 3 lines
Both Q-factors are now being calculated.
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r8902 | bugman | 2009-03-04 17:17:28 +0100 (Wed, 04 Mar 2009) | 3 lines
Changed the Q-factors tested in the system tests.
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r8909 | bugman | 2009-03-06 10:59:32 +0100 (Fri, 06 Mar 2009) | 3 lines
Added another unit test to reveal a bug in the spin.copy() user function.
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r8910 | bugman | 2009-03-06 11:05:09 +0100 (Fri, 06 Mar 2009) | 5 lines
Bug fix for the spin.copy() user function.
Non-empty spin containers are no longer overwritten if the name and num are set to None.
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r8916 | bugman | 2009-03-06 14:29:19 +0100 (Fri, 06 Mar 2009) | 5 lines
The force flag has been introduced to the mol/res/spin naming and numbering functions.
The default is now not to overwrite.
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r8917 | bugman | 2009-03-06 14:37:58 +0100 (Fri, 06 Mar 2009) | 3 lines
Fixes for all the unit tests of the mol/res/spin naming and numbering.
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r8918 | bugman | 2009-03-06 14:46:30 +0100 (Fri, 06 Mar 2009) | 3 lines
All mol/res/spin naming and number user functions now accept the force arg.
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r8919 | bugman | 2009-03-06 15:05:14 +0100 (Fri, 06 Mar 2009) | 3 lines
Fixes for 2 unit vectors system tests.
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r8925 | bugman | 2009-03-06 19:21:27 +0100 (Fri, 06 Mar 2009) | 5 lines
The read() function has been split into to for code recycling in the bmrb branch.
The new pack_data() function has been spun off to fill the data pipe and spin containers.
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r8926 | bugman | 2009-03-06 19:25:21 +0100 (Fri, 06 Mar 2009) | 5 lines
Bug fix for the read() function.
The construction of the data for sending to pack_data() was failing.
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r8927 | bugman | 2009-03-06 19:25:49 +0100 (Fri, 06 Mar 2009) | 3 lines
Spacing fix.
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r8929 | bugman | 2009-03-08 22:36:03 +0100 (Sun, 08 Mar 2009) | 3 lines
None args are now allowed in pack_data(), and the arg lengths are checked.
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r8932 | bugman | 2009-03-08 23:35:24 +0100 (Sun, 08 Mar 2009) | 7 lines
Redesigned the spin.create() and residue.create() user functions.
The res_id and mol_id args are no longer supplied. Instead the residue name and number and molecule
name is used. If the molecule or residue does not exist when these user functions are called, then
they will be automatically created.
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r8935 | bugman | 2009-03-08 23:43:20 +0100 (Sun, 08 Mar 2009) | 5 lines
Fix for the pack_data() function.
The spin wasn't being fetched after its creation.
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r8963 | semor | 2009-03-10 20:52:43 +0100 (Tue, 10 Mar 2009) | 7 lines
Fix for bug 13163 : latex_mf_table.py sample script broken.
Discussion on this topic is in a thread at:
https://mail.gna.org/public/relax-devel/2009-03/msg00007.html
(Message-id: <49B6A6B1.4080305@...>)
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r8971 | bugman | 2009-03-12 10:37:49 +0100 (Thu, 12 Mar 2009) | 3 lines
Modified the full_analysis.py script to perform 500 MC sims and turned on automatic looping.
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r8972 | bugman | 2009-03-12 11:25:53 +0100 (Thu, 12 Mar 2009) | 5 lines
Added a line with the relax URL (http://nmr-relax.com) in the script docstring.
This is in case someone has the script and not relax.
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r8974 | semor | 2009-03-12 18:17:30 +0100 (Thu, 12 Mar 2009) | 7 lines
Fix for bug 13162: Rex values in XML results file not in s-1.
The units are now correctly given in the XML results fiel as discussed in a thread at:
https://mail.gna.org/public/relax-devel/2009-03/msg00010.html
(Message-id: <20090310-141629.sv7147.79009@...>)
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r8976 | semor | 2009-03-12 18:56:28 +0100 (Thu, 12 Mar 2009) | 10 lines
Reverted r8974.
This follows a remark by Ed at:
https://mail.gna.org/public/relax-devel/2009-03/msg00033.html
(Message-id: <7f080ed10903121024h7a0a3808m3c268ca1f276ee4a@...>)
The command used was:
svn merge -r8974:8973 .
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r8977 | semor | 2009-03-12 19:01:24 +0100 (Thu, 12 Mar 2009) | 7 lines
Now correctly fixed bug 13162: Rex values in XML results file not in s-1.
This follows a remark by Ed at:
https://mail.gna.org/public/relax-devel/2009-03/msg00033.html
(Message-id: <7f080ed10903121024h7a0a3808m3c268ca1f276ee4a@...>)
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r8979 | semor | 2009-03-16 19:52:15 +0100 (Mon, 16 Mar 2009) | 9 lines
Fix for bug 13032: Bug in structure.create diff tensor pdb
The Dz unit in dependency_generator() were erroneous, inputing 'alpha' and 'beta' instead of 'beta' and 'gamma'.
This had the effect of creating a weird shaped ellipsoid diffusion tensor representation when 'alpha' and 'beta' were set to unequal values.
This is now fixed, yielding properly shaped diffusion tensor representations for any angles 'alpha', beta' and 'gamma'.
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r8980 | semor | 2009-03-16 19:59:34 +0100 (Mon, 16 Mar 2009) | 11 lines
Changed units of model-free parameters in the test suite results file according to r8977.
ns -> seconds
ps -> seconds
Angstrom -> meters
x MHz -> sigma_ex = Rex / omega**2
ppm -> unitless
The bzipped file was changed directly with vim. The system tests now pass without error,
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r8981 | bugman | 2009-03-18 15:48:09 +0100 (Wed, 18 Mar 2009) | 5 lines
Bug fix!
Debugged intensity_sparky() to handle a Sparky assignment such as '004N-H'.
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r8982 | bugman | 2009-03-20 09:49:03 +0100 (Fri, 20 Mar 2009) | 5 lines
Added the Bruker ncproc parameter to handle Topspin's integer scaling of FID intensities.
The data is now internally scaled by 2**ncproc.
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r8983 | bugman | 2009-03-20 11:28:13 +0100 (Fri, 20 Mar 2009) | 3 lines
RMSD of baseplane noise is now scaled by NC_proc.
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r8984 | bugman | 2009-03-20 15:22:14 +0100 (Fri, 20 Mar 2009) | 3 lines
Fixed a bad apostrophe character causing the script to fail.
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r8985 | bugman | 2009-03-20 15:28:37 +0100 (Fri, 20 Mar 2009) | 3 lines
Comment fix - missing data and error column args.
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r8986 | bugman | 2009-03-20 15:39:45 +0100 (Fri, 20 Mar 2009) | 3 lines
Removed a check disallowing multiple NOE data sets at the same spectrometer frequency.
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r8987 | bugman | 2009-03-20 16:55:06 +0100 (Fri, 20 Mar 2009) | 5 lines
Bug fix for the results reading from_xml() method.
The molecule name was being evaluated?!?
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r8988 | bugman | 2009-03-20 17:35:00 +0100 (Fri, 20 Mar 2009) | 3 lines
Allowed vectors() to generate vectors even if the spin numbers are different (for different PDBs).
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r8989 | bugman | 2009-03-20 17:35:55 +0100 (Fri, 20 Mar 2009) | 3 lines
Also removed the molecule name (for different PDBs).
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r8990 | bugman | 2009-03-20 17:44:37 +0100 (Fri, 20 Mar 2009) | 5 lines
Made the call to cdp.structure.bond_vectors() more fault tolerant.
The molecule name, residue name, and spin number are removed to allow for different structures!
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r8997 | bugman | 2009-03-25 21:49:55 +0100 (Wed, 25 Mar 2009) | 5 lines
Modified the model elimination print out to show the data pipe name.
This was picked up while trying to debug bug #13259 (https://gna.org/bugs/index.php?13259).
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r8998 | bugman | 2009-03-25 22:26:06 +0100 (Wed, 25 Mar 2009) | 3 lines
Clean up of the model_loop() checking.
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r8999 | bugman | 2009-03-25 22:42:30 +0100 (Wed, 25 Mar 2009) | 6 lines
Removed the check for spin selection so that determine_model_type() works with nothing selected.
This is a partial response to bug #13259 (https://gna.org/bugs/index.php?13259) reported by
Pierre-Yves Savard (pierre-yves dot savard att bcm dot ulaval dot ca).
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r9000 | bugman | 2009-03-26 00:21:17 +0100 (Thu, 26 Mar 2009) | 3 lines
Fixes for the MC sim methods for deselected spins.
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r9001 | bugman | 2009-03-26 00:42:14 +0100 (Thu, 26 Mar 2009) | 5 lines
Modified the structure.vectors() user function to fail if no vectors are found.
This saves a lot of sanity when debugging a user script which fails.
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r9002 | bugman | 2009-03-26 15:10:14 +0100 (Thu, 26 Mar 2009) | 7 lines
Bug fix for bug #13259 (https://gna.org/bugs/index.php?13259).
This bug was reported by Pierre-Yves Savard (pierre-yves dot savard att bcm dot ulaval dot ca).
The bug may not be completely gone yet.
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r9003 | bugman | 2009-03-26 16:40:57 +0100 (Thu, 26 Mar 2009) | 6 lines
Fix for the regression of bug #12607 (https://gna.org/bugs/?12607).
The determine_model_type() method now handles the strange case where no spins are selected
(gracefully).
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r9010 | bugman | 2009-04-15 14:33:53 +0200 (Wed, 15 Apr 2009) | 5 lines
Expanded the test_read_pdb_internal3() and test_read_pdb_scientific3() system tests.
Now the reading of atomic positions from different models is tested.
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r9011 | bugman | 2009-04-15 15:28:15 +0200 (Wed, 15 Apr 2009) | 6 lines
Removed a test in load_spins() causing a bug.
This test is totally unnecessary as the structures are not created if they already exist. This was
causing only the position from the first model to be extracted, if ave_pos was False.
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r9015 | bugman | 2009-04-27 15:26:25 +0200 (Mon, 27 Apr 2009) | 5 lines
Bug fix.
The PyMOL code was failing because of the new design of the structural data object.
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r9016 | bugman | 2009-04-28 13:47:51 +0200 (Tue, 28 Apr 2009) | 3 lines
Added a catch for bug #13442 (https://gna.org/bugs/index.php?13442) to the test suite.
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r9017 | bugman | 2009-04-28 14:02:02 +0200 (Tue, 28 Apr 2009) | 6 lines
Fix for bug #13442 (https://gna.org/bugs/index.php?13442).
The problem was that global minimisation objects were being accessed when the do not exist. These
are now skipped.
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r9019 | bugman | 2009-04-28 14:05:30 +0200 (Tue, 28 Apr 2009) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-8161" from
svn+ssh://bugman@.../svn/relax/branches/ave_noe
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r9020 | bugman | 2009-04-28 14:28:05 +0200 (Tue, 28 Apr 2009) | 321 lines
Merged revisions 8162-8179,8181-8182,8643-8655,8657-8668,8671-8672,8674,8677,8679-8680,8689-8695,8700-8701,8710-8713,8716,9005-9009,9013 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/ave_noe
........
r8162 | bugman | 2008-12-08 16:41:32 +0100 (Mon, 08 Dec 2008) | 5 lines
Fix for the noe.read_constraints() user function.
The noe object is called noe_obj.
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r8163 | bugman | 2008-12-08 16:46:53 +0100 (Mon, 08 Dec 2008) | 7 lines
The noe.read_constraints() user function now calls generic_fns.noesy.read_constraints().
The noe user functions need not all point to the specific NOE object! Maybe later the steady-state
NOE can be separated from the NOESY, but for now it isn't too illogical for both to be in the same
user function class.
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r8164 | bugman | 2008-12-08 16:48:34 +0100 (Mon, 08 Dec 2008) | 3 lines
Created an empty module for NOESY data.
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r8165 | bugman | 2008-12-09 10:30:36 +0100 (Tue, 09 Dec 2008) | 3 lines
Wrote a stub function generic_fns.noesy.read_constraints().
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r8166 | bugman | 2008-12-09 10:37:16 +0100 (Tue, 09 Dec 2008) | 3 lines
Added a directory to the test-suite for holding NOE restraint data.
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r8167 | bugman | 2008-12-09 10:39:00 +0100 (Tue, 09 Dec 2008) | 5 lines
Added an RNA H-bond Xplor restraint file.
This comes from http://bass.chem.yale.edu/labdocs/packages/xplor.html.
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r8168 | bugman | 2008-12-09 10:45:58 +0100 (Tue, 09 Dec 2008) | 5 lines
Added the system test framework for NOE restraint reading tests.
This includes one test for the reading of RNA H-bond restraints from an Xplor formatted input file.
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r8169 | bugman | 2008-12-09 10:47:29 +0100 (Tue, 09 Dec 2008) | 3 lines
Renamed 'constraints' to 'restraints' for the NOEs.
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r8170 | bugman | 2008-12-09 11:04:24 +0100 (Tue, 09 Dec 2008) | 3 lines
The RNA sequence of the noe_rna_hbond.dat file is now generated through a new class method.
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r8171 | bugman | 2008-12-09 11:06:01 +0100 (Tue, 09 Dec 2008) | 3 lines
Renamed all the noe.read_constraints() references in the unit tests to noe.read_restraints().
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r8172 | bugman | 2008-12-09 13:31:47 +0100 (Tue, 09 Dec 2008) | 5 lines
Completed the test_read_xplor_rna() system test.
Checks for the restraint list have now been added.
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r8173 | bugman | 2008-12-09 13:32:57 +0100 (Tue, 09 Dec 2008) | 3 lines
Activated the Noe_restraints system test framework.
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r8174 | bugman | 2008-12-09 13:33:19 +0100 (Tue, 09 Dec 2008) | 3 lines
Bug fix in the rna_seq() method.
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r8175 | bugman | 2008-12-09 13:36:17 +0100 (Tue, 09 Dec 2008) | 3 lines
Another bug fix for the rna_seq() sequence generation method.
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r8176 | bugman | 2008-12-09 13:49:38 +0100 (Tue, 09 Dec 2008) | 3 lines
Final fixes for the rna_seq() sequence generation method.
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r8177 | bugman | 2008-12-09 13:50:30 +0100 (Tue, 09 Dec 2008) | 3 lines
Fix for the call to noe.read_restraints() in test_read_xplor_rna().
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r8178 | bugman | 2008-12-09 13:57:32 +0100 (Tue, 09 Dec 2008) | 3 lines
Removed the non-existent frq arg and a docstring clarification about the relax formatted file.
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r8179 | bugman | 2008-12-09 14:02:53 +0100 (Tue, 09 Dec 2008) | 3 lines
Missing import!
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r8181 | bugman | 2008-12-10 14:30:44 +0100 (Wed, 10 Dec 2008) | 3 lines
Added a missing import.
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r8182 | bugman | 2008-12-10 15:18:38 +0100 (Wed, 10 Dec 2008) | 3 lines
Added some more code to the read_restraints() function.
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r8643 | bugman | 2009-01-26 11:52:11 +0100 (Mon, 26 Jan 2009) | 3 lines
Wrote the __file_format() function for determining the NOE restraint file format.
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r8644 | bugman | 2009-01-26 13:30:06 +0100 (Mon, 26 Jan 2009) | 3 lines
The non-implemented function generic_fns.xplor.parse_noe_restraints() is now being called.
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r8645 | bugman | 2009-01-26 13:44:06 +0100 (Mon, 26 Jan 2009) | 3 lines
Reverted to calling file.readlines() rather than file.read().
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r8646 | bugman | 2009-01-26 15:01:10 +0100 (Mon, 26 Jan 2009) | 6 lines
Created the Xplor module for handling Xplor formatted files.
The function parse_noe_restraints() has been added to parse the NOE restraints. The function
strip_comments() has been written to remove Xplor comments from the input data.
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r8647 | bugman | 2009-01-26 15:24:53 +0100 (Mon, 26 Jan 2009) | 3 lines
Created __convert_to_id() to convert from Xplor atom string to relax atom id.
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r8648 | bugman | 2009-01-26 15:31:05 +0100 (Mon, 26 Jan 2009) | 3 lines
Added checks to make sure spin containers corresponding to the Xplor atom strings exist.
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r8649 | bugman | 2009-01-26 16:26:45 +0100 (Mon, 26 Jan 2009) | 3 lines
Typo fix. 'H4' should have been 'N4'!
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r8650 | bugman | 2009-01-26 16:32:49 +0100 (Mon, 26 Jan 2009) | 3 lines
The NOE restraints are now stored in the current data pipe.
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r8651 | bugman | 2009-01-26 16:39:22 +0100 (Mon, 26 Jan 2009) | 3 lines
Fixes for the test_read_xplor_rna() system test.
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r8652 | bugman | 2009-01-26 16:40:32 +0100 (Mon, 26 Jan 2009) | 5 lines
Modified the NOE restraint list so that some restraints are spread across 2 lines.
This should test the Xplor parsing code better.
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r8653 | bugman | 2009-01-26 16:42:12 +0100 (Mon, 26 Jan 2009) | 5 lines
Bug fix for the parse_noe_restraints() function.
Xplor restraints spread across 2 lines are now properly handled.
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r8654 | bugman | 2009-01-26 16:43:23 +0100 (Mon, 26 Jan 2009) | 3 lines
Added a few comments to test the Xplor parsing even more.
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r8655 | bugman | 2009-01-26 18:44:13 +0100 (Mon, 26 Jan 2009) | 3 lines
Shifted the checks of the atom id strings from the Xplor parser to the NOE restraint reading fn.
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r8657 | bugman | 2009-01-27 09:35:53 +0100 (Tue, 27 Jan 2009) | 3 lines
Missing RelaxError import.
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r8658 | bugman | 2009-01-27 09:44:38 +0100 (Tue, 27 Jan 2009) | 3 lines
Added some test NOEs, in a generic formatted file, for phthalic acid and testing the NOE reading.
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r8659 | bugman | 2009-01-27 10:01:41 +0100 (Tue, 27 Jan 2009) | 3 lines
Created a system test for the reading of a generically formatted NOE restraint file.
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r8660 | bugman | 2009-01-27 10:15:15 +0100 (Tue, 27 Jan 2009) | 3 lines
Removed an unused import.
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r8661 | bugman | 2009-01-27 10:16:04 +0100 (Tue, 27 Jan 2009) | 3 lines
The generically formatted NOE restraint file is now being parsed.
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r8662 | bugman | 2009-01-27 11:10:45 +0100 (Tue, 27 Jan 2009) | 3 lines
Modified the phthalic acid NOE restraint reading test to include pseudo-atoms.
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r8663 | bugman | 2009-01-27 13:45:15 +0100 (Tue, 27 Jan 2009) | 3 lines
Removed the '@' from the pseudo-atom spin names.
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r8664 | bugman | 2009-01-27 13:47:35 +0100 (Tue, 27 Jan 2009) | 3 lines
Wrote a unit test for the creation of pseudo-atom spin containers.
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r8665 | bugman | 2009-01-27 13:55:57 +0100 (Tue, 27 Jan 2009) | 3 lines
Wrote 5 arg unit tests for the spin.create_pseudo() user function.
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r8666 | bugman | 2009-01-27 14:00:37 +0100 (Tue, 27 Jan 2009) | 3 lines
Wrote the interface for the spin.create_pseudo() user function.
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r8667 | bugman | 2009-01-27 14:03:18 +0100 (Tue, 27 Jan 2009) | 3 lines
Fixes for the arg unit tests of spin.create_pseudo().
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r8668 | bugman | 2009-01-27 14:06:13 +0100 (Tue, 27 Jan 2009) | 3 lines
Imported the non-existant create_pseudo_spin() function.
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r8671 | bugman | 2009-01-27 16:14:22 +0100 (Tue, 27 Jan 2009) | 3 lines
Wrote the create_pseudo_spin() and __linear_ave() functions for pseudo-atom support.
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r8672 | bugman | 2009-01-27 16:17:07 +0100 (Tue, 27 Jan 2009) | 5 lines
Fix for the phthalic acid NOE restraint reading system test.
Pseudo-atom creation was not correctly called.
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r8674 | bugman | 2009-01-27 16:27:54 +0100 (Tue, 27 Jan 2009) | 3 lines
Fixes for the create_pseudo_spin() and __linear_ave() functions.
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r8677 | bugman | 2009-01-27 16:41:23 +0100 (Tue, 27 Jan 2009) | 3 lines
Fixes for the 2 test_create_pseudo_spin() unit tests.
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r8679 | bugman | 2009-01-27 16:49:58 +0100 (Tue, 27 Jan 2009) | 3 lines
Fixes for the test_create_pseudo_spin() unit test. The atomic positions are now set.
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r8680 | bugman | 2009-01-27 16:51:47 +0100 (Tue, 27 Jan 2009) | 3 lines
The __linear_ave() now handles the coordinates as numpy arrays.
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r8689 | bugman | 2009-01-28 11:24:04 +0100 (Wed, 28 Jan 2009) | 3 lines
Added some more checks for the test_create_pseudo_spin() unit test.
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r8690 | bugman | 2009-01-28 11:30:24 +0100 (Wed, 28 Jan 2009) | 3 lines
Wrote a second unit test for the creation of a pseudo-spin.
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r8691 | bugman | 2009-01-28 11:38:57 +0100 (Wed, 28 Jan 2009) | 3 lines
Modified the checks for the pseudo-spin creation unit tests.
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r8692 | bugman | 2009-01-28 11:40:14 +0100 (Wed, 28 Jan 2009) | 5 lines
The pseudo-spin name and number is now stored in the member spin containers.
This gives a mapping between from the spin to the pseudo-spin.
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r8693 | bugman | 2009-01-28 11:40:50 +0100 (Wed, 28 Jan 2009) | 3 lines
Fixes for test_create_pseudo_spin() and test_create_pseudo_spin2().
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r8694 | bugman | 2009-01-28 11:41:27 +0100 (Wed, 28 Jan 2009) | 3 lines
One more fix for test_create_pseudo_spin().
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r8695 | bugman | 2009-01-28 11:42:32 +0100 (Wed, 28 Jan 2009) | 3 lines
The members list is now stored in the pseudo-spin to map this to the respective spin containers.
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r8700 | bugman | 2009-01-29 09:42:21 +0100 (Thu, 29 Jan 2009) | 3 lines
Added a call to calc() to test the quadratic potential calculation.
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r8701 | bugman | 2009-01-29 16:40:07 +0100 (Thu, 29 Jan 2009) | 5 lines
Created a module for calculating different optimisation/energy potentials.
The function quad_pot() has been written to provide a flat-bottom potential.
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r8710 | bugman | 2009-02-02 10:44:48 +0100 (Mon, 02 Feb 2009) | 3 lines
Added tests for the existence of the current data pipe.
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r8711 | bugman | 2009-02-02 10:49:06 +0100 (Mon, 02 Feb 2009) | 3 lines
Modified the RelaxNoModelError print out to be more informative, especially for the N-state model.
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r8712 | bugman | 2009-02-02 10:51:17 +0100 (Mon, 02 Feb 2009) | 3 lines
Added the start of the calculate() method.
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r8713 | bugman | 2009-02-02 10:51:45 +0100 (Mon, 02 Feb 2009) | 3 lines
The N-state model is now selected in the NOESY system test.
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r8716 | bugman | 2009-02-02 11:05:21 +0100 (Mon, 02 Feb 2009) | 3 lines
Modified __base_data_types() to include NOE restraints.
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r9005 | bugman | 2009-04-09 19:33:13 +0200 (Thu, 09 Apr 2009) | 3 lines
Fixed the calls to generic_fns.mol_res_spin.spin.create() function.
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r9006 | bugman | 2009-04-09 19:46:04 +0200 (Thu, 09 Apr 2009) | 5 lines
Fix for the rna_seq() method.
The create_residue() and create_molecule() functions were being incorrectly called.
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r9007 | bugman | 2009-04-10 20:43:00 +0200 (Fri, 10 Apr 2009) | 5 lines
Added the calc_ave_dist() method.
This doesn't work yet and has been cut and paste from an external relax script.
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r9008 | bugman | 2009-04-15 11:46:03 +0200 (Wed, 15 Apr 2009) | 3 lines
Completed the calculate() and calc_ave_dist() methods for the dynamically averaged NOE analysis.
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r9009 | bugman | 2009-04-15 14:04:02 +0200 (Wed, 15 Apr 2009) | 3 lines
Bug fix in the calc_ave_dist() method for multiple models.
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r9013 | bugman | 2009-04-15 17:06:54 +0200 (Wed, 15 Apr 2009) | 5 lines
Bug fix for the calc_ave_dist() method.
The negative of the exponential was being used!
........
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r9021 | bugman | 2009-04-28 15:02:54 +0200 (Tue, 28 Apr 2009) | 3 lines
Fixed the testing of the Monte Carlo simulations.
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r9022 | bugman | 2009-04-28 15:03:39 +0200 (Tue, 28 Apr 2009) | 5 lines
Bug fix.
The minimisation statistics are no longer reset by the Monte Carlo simulation setup.
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r9023 | bugman | 2009-04-28 17:50:25 +0200 (Tue, 28 Apr 2009) | 6 lines
The centre() function can now handle pseudoatoms.
Positional information is taken from the mol, res, spin data structure rather than the structural
object, hence pseudoatoms can be supported.
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r9024 | bugman | 2009-04-28 17:52:06 +0200 (Tue, 28 Apr 2009) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/ave_noe
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r9028 | bugman | 2009-04-28 18:06:17 +0200 (Tue, 28 Apr 2009) | 3 lines
Fix for the __assemble_scaling_matrix() method for the 'fixed' N-state model.
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r9029 | bugman | 2009-04-28 19:34:45 +0200 (Tue, 28 Apr 2009) | 5 lines
Fix for the 'fixed' N-state model.
When constraints are automatically turned off for this, the minimisation algorithm should as change.
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r9030 | bugman | 2009-04-28 19:45:17 +0200 (Tue, 28 Apr 2009) | 6 lines
Fixed a bug introduced at r9029.
The removal of the 'Method of Multipliers' algorithm with automatic constraint removal didn't take
the grid search into account.
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r9031 | bugman | 2009-04-29 10:41:43 +0200 (Wed, 29 Apr 2009) | 6 lines
Fixed a bug introduced at r9023.
The spin position was being assumed to be a list of numpy arrays, but in some cases it was simply a
numpy array.
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r9032 | bugman | 2009-04-29 10:57:31 +0200 (Wed, 29 Apr 2009) | 3 lines
The lanthanide atoms are now loaded into the relax data store for the lactose N-state model test.
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r9033 | bugman | 2009-04-29 11:01:49 +0200 (Wed, 29 Apr 2009) | 5 lines
Some more fixes for the centre() function.
This should now be fully debugged!
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r9034 | bugman | 2009-04-29 11:10:20 +0200 (Wed, 29 Apr 2009) | 3 lines
Added the ave_pos flag to the pcs.centre() user function.
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r9035 | bugman | 2009-04-29 11:23:36 +0200 (Wed, 29 Apr 2009) | 3 lines
Added support for multiple paramagnetic centre extraction to the centre() function.
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r9036 | bugman | 2009-05-06 10:50:56 +0200 (Wed, 06 May 2009) | 3 lines
Added an Xplor NOE restraint file fragment with a methyl group.
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r9037 | bugman | 2009-05-06 10:55:04 +0200 (Wed, 06 May 2009) | 3 lines
Added a system test for the reading of the Xplor pseudoatom data.
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r9038 | bugman | 2009-05-06 13:52:18 +0200 (Wed, 06 May 2009) | 3 lines
Fixes for the NOE restraint system tests.
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r9039 | bugman | 2009-05-06 16:50:13 +0200 (Wed, 06 May 2009) | 3 lines
Added pseudoatom support to the parse_noe_restraints() function.
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r9040 | bugman | 2009-05-06 17:03:00 +0200 (Wed, 06 May 2009) | 6 lines
Rewrote how the Xplor NOE restraints are read.
Two new functions, first_parse() and second_parse() have been written to first extract all assign
statements and then handle pseudoatoms.
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r9042 | bugman | 2009-05-09 18:10:07 +0200 (Sat, 09 May 2009) | 5 lines
Bug fix for the test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149() system test.
This is solely for Python 2.6.
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r9043 | bugman | 2009-05-09 18:22:35 +0200 (Sat, 09 May 2009) | 5 lines
Python 2.6 bug fix for the RelaxWarnings format() function.
The warn.formatwarning() function this replaces has a new keyword arg.
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r9048 | bugman | 2009-05-12 10:47:02 +0200 (Tue, 12 May 2009) | 3 lines
Updated the pipes.hybridise() user function interface to the 1.3 line design.
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r9049 | bugman | 2009-05-12 11:09:24 +0200 (Tue, 12 May 2009) | 3 lines
Added 3 new RelaxErrors for sequence matching.
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r9050 | bugman | 2009-05-12 11:21:59 +0200 (Tue, 12 May 2009) | 3 lines
Added the pipe keyword to all the sequence counting functions.
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r9051 | bugman | 2009-05-12 11:22:41 +0200 (Tue, 12 May 2009) | 3 lines
Renamed the hybridise() pipes keyword to pipe_list.
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r9052 | bugman | 2009-05-12 11:25:38 +0200 (Tue, 12 May 2009) | 3 lines
Created the compare_sequence() for checking if 2 sequences are the same.
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r9053 | bugman | 2009-05-12 11:28:49 +0200 (Tue, 12 May 2009) | 3 lines
Converted the hybridise() method to the 1.3 line design.
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r9054 | bugman | 2009-05-12 11:31:08 +0200 (Tue, 12 May 2009) | 3 lines
Added the hybrid data pipe to the list of allowable data pipes.
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r9055 | bugman | 2009-05-12 11:34:40 +0200 (Tue, 12 May 2009) | 3 lines
Added a check for the pipe type to hybridise().
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r9056 | bugman | 2009-05-12 11:41:12 +0200 (Tue, 12 May 2009) | 3 lines
Converted the duplicate_data() method to the 1.3 line design.
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r9057 | bugman | 2009-05-12 14:42:06 +0200 (Tue, 12 May 2009) | 3 lines
Removed a test that disallowed model selection between different pipe types.
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r9058 | bugman | 2009-05-12 14:56:23 +0200 (Tue, 12 May 2009) | 5 lines
Converted all parts of the hybrid module to the 1.3 line design.
This includes the addition of many new, very simple methods and the translation of old code.
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r9059 | bugman | 2009-05-15 10:47:59 +0200 (Fri, 15 May 2009) | 3 lines
Created the R_axis_angle() function to generate the rotation matrix from the axis-angle notation.
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r9060 | bugman | 2009-05-15 11:58:55 +0200 (Fri, 15 May 2009) | 3 lines
Added the functions random_rot_axis() and random_R() to generate random rotations.
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r9061 | bugman | 2009-05-25 13:45:14 +0200 (Mon, 25 May 2009) | 6 lines
Changed the precision of the te check in the model-free system tests.
This is in response to Sebastian's post at
https://mail.gna.org/public/relax-devel/2009-05/msg00003.html.
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r9062 | bugman | 2009-05-28 15:37:08 +0200 (Thu, 28 May 2009) | 3 lines
Renamed random_R() to R_random_axis().
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r9063 | bugman | 2009-05-28 15:57:48 +0200 (Thu, 28 May 2009) | 3 lines
Wrote 2 new functions, R_random_hypersphere() and quaternion_to_R().
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r9064 | bugman | 2009-05-28 16:53:23 +0200 (Thu, 28 May 2009) | 3 lines
Bug fix for the quaternion_to_R() function.
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r9065 | bugman | 2009-05-29 10:47:09 +0200 (Fri, 29 May 2009) | 3 lines
Fix for the align_tensor.init() user function docstring.
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r9066 | bugman | 2009-06-02 13:54:11 +0200 (Tue, 02 Jun 2009) | 3 lines
Indentation fix.
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r9068 | bugman | 2009-06-08 16:21:38 +0200 (Mon, 08 Jun 2009) | 3 lines
Added a function for calculating the Kronecker product.
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r9069 | bugman | 2009-06-08 17:13:54 +0200 (Mon, 08 Jun 2009) | 3 lines
Added a copyright notice and spun out the T14 transpose into its own function.
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r9081 | bugman | 2009-06-18 15:01:00 +0200 (Thu, 18 Jun 2009) | 3 lines
Added numpy int and float data types to the list of tested user function args.
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r9194 | bugman | 2009-07-12 23:55:17 +0200 (Sun, 12 Jul 2009) | 3 lines
Commented out a data type temporarily until someone complains about int32 types.
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r9195 | bugman | 2009-07-13 00:03:51 +0200 (Mon, 13 Jul 2009) | 5 lines
Created lists of number types (python and numpy).
These are in the prompt.num_types module and are now used by value.set() for argument checking.
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r9196 | bugman | 2009-07-13 00:05:31 +0200 (Mon, 13 Jul 2009) | 6 lines
Reverted r9194, the temporary commenting out of a data type.
The command used was:
svn merge -r9194:9193 .
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r9198 | bugman | 2009-07-13 00:07:41 +0200 (Mon, 13 Jul 2009) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-9069" from
svn+ssh://bugman@.../svn/relax/branches/frame_order
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r9199 | bugman | 2009-07-13 00:11:11 +0200 (Mon, 13 Jul 2009) | 566 lines
Merged revisions 9070-9187,9190-9196,9198 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order
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r9070 | bugman | 2009-06-17 19:27:42 +0200 (Wed, 17 Jun 2009) | 3 lines
Created a branch for the new Frame Order theories.
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r9071 | bugman | 2009-06-17 19:34:39 +0200 (Wed, 17 Jun 2009) | 3 lines
Added Frame Order to the list of allowable data pipes.
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r9072 | bugman | 2009-06-17 19:36:36 +0200 (Wed, 17 Jun 2009) | 3 lines
Added a stub package for Frame Order related calculation code.
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r9073 | bugman | 2009-06-17 20:03:58 +0200 (Wed, 17 Jun 2009) | 3 lines
Added a function for printing out the 2nd degree Frame Order matrix.
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r9074 | bugman | 2009-06-17 20:05:50 +0200 (Wed, 17 Jun 2009) | 3 lines
Shifted the print_frame_order_2nd_degree() function to generic_fns.
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r9075 | bugman | 2009-06-17 20:10:17 +0200 (Wed, 17 Jun 2009) | 3 lines
Added a missing import.
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r9076 | bugman | 2009-06-17 20:30:26 +0200 (Wed, 17 Jun 2009) | 3 lines
Added functions for populating the Frame Order matrices for isotropic cones.
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r9077 | bugman | 2009-06-18 10:41:27 +0200 (Thu, 18 Jun 2009) | 5 lines
Renamed the frame_order package to frame_order_matrix_ops.
This is to make way for the target function code.
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r9078 | bugman | 2009-06-18 10:42:31 +0200 (Thu, 18 Jun 2009) | 6 lines
Added the Frame Order target function class.
It currently contains only one target function for an isotropic cone model directly optimised to the
Frame Order matrix elements.
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r9079 | bugman | 2009-06-18 10:47:30 +0200 (Thu, 18 Jun 2009) | 3 lines
A few fixes for the Frame_order class.
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r9080 | bugman | 2009-06-18 11:29:22 +0200 (Thu, 18 Jun 2009) | 3 lines
Aliased self.func_iso_cone_elements to self.func.
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r9082 | bugman | 2009-06-18 22:04:39 +0200 (Thu, 18 Jun 2009) | 3 lines
Renamed the user function n_state_model.set_type() to align_tensor.reduction().
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r9083 | bugman | 2009-06-18 22:15:18 +0200 (Thu, 18 Jun 2009) | 3 lines
Shifted the N-state model set_type() method to the align_tensor function reduction().
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r9084 | bugman | 2009-06-19 10:18:35 +0200 (Fri, 19 Jun 2009) | 3 lines
Added the Frame Order theories to the setup of the specific code.
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r9085 | bugman | 2009-06-19 10:30:00 +0200 (Fri, 19 Jun 2009) | 3 lines
Added the skeleton of the Frame Order specific code.
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r9086 | bugman | 2009-06-19 10:31:03 +0200 (Fri, 19 Jun 2009) | 3 lines
Added the Frame Order type to get_string().
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r9087 | bugman | 2009-06-19 10:43:37 +0200 (Fri, 19 Jun 2009) | 3 lines
Implemented most of the grid_search() method.
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r9088 | bugman | 2009-06-19 10:50:19 +0200 (Fri, 19 Jun 2009) | 5 lines
Created the Frame Order user function class.
The only user function yet available is frame_order.select_model().
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r9089 | bugman | 2009-06-19 10:51:59 +0200 (Fri, 19 Jun 2009) | 3 lines
Registered the Frame Order user function class into the interpreter.
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r9090 | bugman | 2009-06-19 10:55:28 +0200 (Fri, 19 Jun 2009) | 3 lines
Wrote the select_model() method.
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r9091 | bugman | 2009-06-19 10:58:47 +0200 (Fri, 19 Jun 2009) | 3 lines
Added the __update_model() method.
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r9092 | bugman | 2009-06-19 11:01:22 +0200 (Fri, 19 Jun 2009) | 3 lines
Some fixed for the grid_search() method.
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r9093 | bugman | 2009-06-19 11:29:00 +0200 (Fri, 19 Jun 2009) | 3 lines
Modifications to the __update_model() method.
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r9094 | bugman | 2009-06-19 11:44:57 +0200 (Fri, 19 Jun 2009) | 5 lines
Wrote the minimise() and __unpack_opt_results() methods.
The minimise() method is rudimentary and will not work.
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r9095 | bugman | 2009-06-19 11:50:26 +0200 (Fri, 19 Jun 2009) | 3 lines
Modified the __init__() method and spun of some code into __init_iso_cone_elements().
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r9096 | bugman | 2009-06-19 11:51:24 +0200 (Fri, 19 Jun 2009) | 3 lines
Docstring update.
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r9097 | bugman | 2009-06-19 11:52:00 +0200 (Fri, 19 Jun 2009) | 3 lines
Missing RelaxError import.
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r9098 | bugman | 2009-06-19 15:27:08 +0200 (Fri, 19 Jun 2009) | 3 lines
Fixes for the minimise() method.
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r9099 | bugman | 2009-06-19 15:57:11 +0200 (Fri, 19 Jun 2009) | 3 lines
Created the compile_2nd_matrix_iso_cone() function for building the 2nd degree Frame Order matrix.
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r9100 | bugman | 2009-06-19 16:03:20 +0200 (Fri, 19 Jun 2009) | 3 lines
Shifted more code into the compile_2nd_matrix_iso_cone() function.
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r9101 | bugman | 2009-06-19 16:05:14 +0200 (Fri, 19 Jun 2009) | 3 lines
Fixed the arguments of compile_2nd_matrix_iso_cone().
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r9102 | bugman | 2009-06-19 16:06:39 +0200 (Fri, 19 Jun 2009) | 3 lines
Missing numpy imports.
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r9103 | bugman | 2009-06-19 16:07:41 +0200 (Fri, 19 Jun 2009) | 5 lines
Preliminary support for optimisation against alignment tensors.
Added the func_iso_cone() and __init_iso_cone() methods.
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r9104 | bugman | 2009-06-19 16:09:33 +0200 (Fri, 19 Jun 2009) | 3 lines
Added a check for incorrectly supplied arguments.
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r9105 | bugman | 2009-06-19 16:35:47 +0200 (Fri, 19 Jun 2009) | 3 lines
Created the __minimise_setup_tensors() method to compile the data needed for optimisation.
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r9106 | bugman | 2009-06-19 16:39:03 +0200 (Fri, 19 Jun 2009) | 3 lines
Modified the reduction() function to store alignment tensor indices rather than names.
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r9107 | bugman | 2009-06-19 16:41:15 +0200 (Fri, 19 Jun 2009) | 3 lines
Fixed for the __minimise_setup_tensors() method.
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r9108 | bugman | 2009-06-19 16:42:19 +0200 (Fri, 19 Jun 2009) | 3 lines
Fix for the frame_order_models.Frame_order setup within minimise().
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r9109 | bugman | 2009-06-19 16:43:16 +0200 (Fri, 19 Jun 2009) | 3 lines
Removed an unused print statement.
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r9110 | bugman | 2009-06-19 16:50:03 +0200 (Fri, 19 Jun 2009) | 3 lines
Docstring fixes and variable renaming in __minimise_setup_tensors().
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r9111 | bugman | 2009-06-19 16:51:53 +0200 (Fri, 19 Jun 2009) | 3 lines
Docstring updates.
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r9112 | bugman | 2009-06-19 16:52:04 +0200 (Fri, 19 Jun 2009) | 3 lines
Bug fix for the tensor optimisation.
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r9113 | bugman | 2009-06-19 17:12:57 +0200 (Fri, 19 Jun 2009) | 3 lines
Temporary fix for func_iso_cone().
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r9114 | bugman | 2009-06-19 17:15:33 +0200 (Fri, 19 Jun 2009) | 3 lines
Bug fixes for the __unpack_opt_results() method.
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r9115 | bugman | 2009-06-19 17:21:56 +0200 (Fri, 19 Jun 2009) | 3 lines
Parameter values are initialised to zero so that a grid search is not necessary.
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r9116 | bugman | 2009-06-19 17:31:41 +0200 (Fri, 19 Jun 2009) | 6 lines
Fix for the compilation of the Frame Order matrix.
The compile_2nd_matrix_iso_cone() function now returns the matrix as it is now in a different
memory location.
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r9117 | bugman | 2009-06-19 19:22:07 +0200 (Fri, 19 Jun 2009) | 5 lines
Added the function reduce_alignment_tensor().
This calculates how the Frame Order matrix reduces the alignment tensor.
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r9118 | bugman | 2009-06-19 19:22:29 +0200 (Fri, 19 Jun 2009) | 3 lines
Bug fix for reduce_alignment_tensor().
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r9119 | bugman | 2009-06-19 19:22:59 +0200 (Fri, 19 Jun 2009) | 3 lines
The reduced tensors are now back calculated.
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r9120 | bugman | 2009-06-19 19:23:23 +0200 (Fri, 19 Jun 2009) | 3 lines
Simplification of func_iso_cone().
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r9121 | bugman | 2009-06-19 19:23:48 +0200 (Fri, 19 Jun 2009) | 3 lines
Another bug fix for reduce_alignment_tensor().
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r9122 | bugman | 2009-06-19 19:24:19 +0200 (Fri, 19 Jun 2009) | 3 lines
Imported reduce_alignment_tensor().
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r9123 | bugman | 2009-06-19 19:25:09 +0200 (Fri, 19 Jun 2009) | 3 lines
Bug fix for func_iso_cone().
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r9124 | bugman | 2009-06-19 19:25:33 +0200 (Fri, 19 Jun 2009) | 3 lines
Another bug fix for reduce_alignment_tensor().
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r9125 | bugman | 2009-06-19 19:30:06 +0200 (Fri, 19 Jun 2009) | 3 lines
Bug fix for the initialisation of self.red_tensors_bc.
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r9126 | bugman | 2009-06-19 19:42:51 +0200 (Fri, 19 Jun 2009) | 3 lines
Made the default errors more reasonable.
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r9127 | bugman | 2009-06-22 19:52:00 +0200 (Mon, 22 Jun 2009) | 3 lines
Bug fix for the reduce_alignment_tensor() function.
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r9128 | bugman | 2009-06-23 11:14:13 +0200 (Tue, 23 Jun 2009) | 5 lines
Elimination of an Euler angle from the isotropic cone model.
Only the cone axis theta and phi angles are now optimised.
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r9129 | bugman | 2009-06-23 11:20:16 +0200 (Tue, 23 Jun 2009) | 3 lines
Set up the z-axis data structures.
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r9130 | bugman | 2009-06-23 11:31:59 +0200 (Tue, 23 Jun 2009) | 3 lines
Added the cone axis storage structure.
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r9131 | bugman | 2009-06-23 11:32:19 +0200 (Tue, 23 Jun 2009) | 3 lines
Updated the compile_2nd_matrix_iso_cone() function to use the cone axis angles rather than Euler.
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r9132 | bugman | 2009-06-23 11:37:05 +0200 (Tue, 23 Jun 2009) | 5 lines
Bug fix for compile_2nd_matrix_iso_cone().
The rotation matrix uses the polar angle, not the cone angle.
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r9133 | bugman | 2009-06-23 12:58:40 +0200 (Tue, 23 Jun 2009) | 5 lines
Bug fix for the compile_2nd_matrix_iso_cone() function.
The cross product of 2 normal vectors is not a normal vector!!!
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r9134 | bugman | 2009-06-23 13:42:26 +0200 (Tue, 23 Jun 2009) | 5 lines
Removed the sequence test in the Monte Carlo create_data() function.
No all data pipes in relax require sequence info.
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r9135 | bugman | 2009-06-23 14:23:53 +0200 (Tue, 23 Jun 2009) | 3 lines
Added a dummy eliminate() method.
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r9136 | bugman | 2009-06-23 16:22:12 +0200 (Tue, 23 Jun 2009) | 19 lines
Added the ability to perform Monte Carlo sims for the Frame Order theories.
For this, the following methods have been added:
__tensor_loop()
back_calc()
base_data_loop()
create_mc_data()
data_names()
model_loop()
return_error()
set_selected_sim()
sim_init_values()
sim_pack_data()
sim_return_param()
sim_return_selected()
Many other methods have also been modified.
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r9137 | bugman | 2009-06-23 16:45:44 +0200 (Tue, 23 Jun 2009) | 3 lines
Updated the init() and set() method to allow alignment tensor errors to be input.
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r9138 | bugman | 2009-06-23 17:41:52 +0200 (Tue, 23 Jun 2009) | 3 lines
More fixes for error setting in the set() function.
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r9139 | bugman | 2009-06-23 17:52:07 +0200 (Tue, 23 Jun 2009) | 5 lines
Bug fix for the init() method.
Now errors are being placed in the pre-existing tensor, rather than a new tensor being added.
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r9140 | bugman | 2009-06-23 18:19:49 +0200 (Tue, 23 Jun 2009) | 5 lines
Another bug fix for the init() method.
Errors are not properly handled for all input data types.
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r9141 | bugman | 2009-06-23 19:23:11 +0200 (Tue, 23 Jun 2009) | 5 lines
Removed ambiguity from the align_tensor.reduction() user function.
The from_tensor and to_tensor args have been renamed to full_tensor and red_tensor respectively.
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r9142 | bugman | 2009-06-25 12:00:41 +0200 (Thu, 25 Jun 2009) | 3 lines
Created the interface to the frame_order.cone_pdb() user function.
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r9143 | bugman | 2009-06-25 13:17:53 +0200 (Thu, 25 Jun 2009) | 3 lines
Created the interface for the frame_order.pivot() user function.
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r9144 | bugman | 2009-06-25 13:38:11 +0200 (Thu, 25 Jun 2009) | 5 lines
Bug fix for the R_2vect() function.
The rotation axis is not always of unit length!
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r9145 | bugman | 2009-06-25 13:42:50 +0200 (Thu, 25 Jun 2009) | 3 lines
Spun out the cone axis generation code into generate_vector().
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r9146 | bugman | 2009-06-25 13:45:54 +0200 (Thu, 25 Jun 2009) | 3 lines
Simplified compile_2nd_matrix_iso_cone() by using R_2vect().
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r9147 | bugman | 2009-06-25 14:02:23 +0200 (Thu, 25 Jun 2009) | 3 lines
Bug fix for the generate_vector_residues() for numpy MC sim structures.
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r9148 | bugman | 2009-06-25 14:03:36 +0200 (Thu, 25 Jun 2009) | 3 lines
Another bug fix for the generate_vector_residues() function for MC simulations.
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r9149 | bugman | 2009-06-25 14:22:32 +0200 (Thu, 25 Jun 2009) | 5 lines
Bug fix for generate_vector_residues() when the neg flag is False.
The atoms were incorrectly numbered.
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r9150 | bugman | 2009-06-25 14:24:51 +0200 (Thu, 25 Jun 2009) | 3 lines
Wrote the cone_pdb() and pivot() methods.
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r9151 | bugman | 2009-06-25 15:02:34 +0200 (Thu, 25 Jun 2009) | 5 lines
Renaming and fixes for stitch_cone_to_edge().
This was stitch_cap_to_cone().
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r9152 | bugman | 2009-06-25 15:24:01 +0200 (Thu, 25 Jun 2009) | 5 lines
Bug fixes for the write_pdb() method.
The Hetrogen section was failing with MC simulations.
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r9153 | bugman | 2009-06-25 15:24:41 +0200 (Thu, 25 Jun 2009) | 3 lines
Fixes for the cone_pdb() method.
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r9154 | bugman | 2009-06-25 15:58:39 +0200 (Thu, 25 Jun 2009) | 5 lines
Bug fixes for the generate_vector_dist() function.
The protons were not being correctly stitched together!
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r9155 | bugman | 2009-06-25 16:02:26 +0200 (Thu, 25 Jun 2009) | 3 lines
Added a test for a loaded structure to the pymol.cartoon() user function.
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r9156 | bugman | 2009-06-25 16:26:11 +0200 (Thu, 25 Jun 2009) | 5 lines
Bug fix for the pymol.cartoon() user function.
This was failing when multiple proteins were loaded.
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r9157 | bugman | 2009-06-25 16:34:17 +0200 (Thu, 25 Jun 2009) | 3 lines
Changed the scaling arg to a direct size arg.
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r9158 | bugman | 2009-06-25 16:36:00 +0200 (Thu, 25 Jun 2009) | 3 lines
cone_pdb() now handles the AXE residue.
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r9159 | bugman | 2009-06-25 16:37:03 +0200 (Thu, 25 Jun 2009) | 3 lines
Renamed the axis atom from 'Axe' to 'Axis'.
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r9160 | bugman | 2009-06-25 16:41:25 +0200 (Thu, 25 Jun 2009) | 3 lines
Made the cone_pdb() function less specific for the N-state model and added SIM as an axis to decorate.
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r9161 | bugman | 2009-06-25 16:46:40 +0200 (Thu, 25 Jun 2009) | 3 lines
The user can now set the number of increments used to generate the cone PDB.
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r9162 | bugman | 2009-06-29 10:24:03 +0200 (Mon, 29 Jun 2009) | 3 lines
Wrote the calculate() method for calculating the chi-squared value for the current parameters.
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r9163 | bugman | 2009-06-29 10:25:13 +0200 (Mon, 29 Jun 2009) | 6 lines
Expansion of frame order to both the forward and reverse rotations.
reduce_alignment_tensor() was renamed to reduce_alignment_tensor_reverse(), and the new function
reduce_alignment_tensor() added.
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r9164 | bugman | 2009-06-30 11:21:49 +0200 (Tue, 30 Jun 2009) | 3 lines
Added checks for the presence of the data structures necessary for frame_order.cone_pdb().
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r9165 | bugman | 2009-06-30 11:24:12 +0200 (Tue, 30 Jun 2009) | 3 lines
Bug fix for frame_order.cone_pdb() for when no MC sims exist.
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r9166 | bugman | 2009-06-30 11:43:31 +0200 (Tue, 30 Jun 2009) | 5 lines
Bug fix for the cone PDB generation.
If there were more than 1000 protons, the PDB file was corrupted by the proton name being too long.
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r9167 | bugman | 2009-07-01 13:05:09 +0200 (Wed, 01 Jul 2009) | 6 lines
Reverted r9128 to r9133, the elimination of a Euler angle (maybe only temporarily).
The command used was:
svn merge -r9134:9127 .
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r9168 | bugman | 2009-07-01 16:08:46 +0200 (Wed, 01 Jul 2009) | 3 lines
Renamed theta to theta cone (again due to the reversion).
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r9169 | bugman | 2009-07-02 02:28:25 +0200 (Thu, 02 Jul 2009) | 3 lines
Missing import.
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r9170 | bugman | 2009-07-02 02:33:45 +0200 (Thu, 02 Jul 2009) | 3 lines
The cone axis is back, and better support for the Euler angles.
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r9171 | bugman | 2009-07-02 02:36:53 +0200 (Thu, 02 Jul 2009) | 3 lines
Return of the cone axis, and rotation of the reduced tensor.
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r9172 | bugman | 2009-07-02 02:55:17 +0200 (Thu, 02 Jul 2009) | 6 lines
Partly reverted r9167 - the previous reversion.
The command used was:
svn merge -r9167:9166 generic_fns/monte_carlo.py
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r9173 | bugman | 2009-07-02 02:58:54 +0200 (Thu, 02 Jul 2009) | 8 lines
Partly reverted r9167 - the previous revision.
The command used was:
svn merge -r9167:9166 maths_fns/frame_order_matrix_ops.py
This returns the cone axis.
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r9174 | bugman | 2009-07-02 03:01:41 +0200 (Thu, 02 Jul 2009) | 6 lines
Partly reverted r9167 - the previous reversion.
The command used was:
svn merge -r9167:9166 maths_fns/frame_order_models.py
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r9175 | bugman | 2009-07-02 03:02:12 +0200 (Thu, 02 Jul 2009) | 3 lines
Missing import.
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r9176 | bugman | 2009-07-02 03:19:39 +0200 (Thu, 02 Jul 2009) | 3 lines
The Euler angles are now wrapped between 0 and 2pi.
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r9177 | bugman | 2009-07-02 14:03:17 +0200 (Thu, 02 Jul 2009) | 3 lines
Added the new function R_to_axis_angle().
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r9178 | bugman | 2009-07-02 15:25:08 +0200 (Thu, 02 Jul 2009) | 3 lines
Bug fix for the R_to_axis_angle() function. The axis needs to be normalised.
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r9179 | bugman | 2009-07-02 15:25:40 +0200 (Thu, 02 Jul 2009) | 3 lines
Both the positive and negative cones are now made.
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r9180 | bugman | 2009-07-02 16:50:51 +0200 (Thu, 02 Jul 2009) | 3 lines
Fixes for the negative cone.
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r9181 | bugman | 2009-07-02 17:18:50 +0200 (Thu, 02 Jul 2009) | 3 lines
Fix for the N-state model arg checks.
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r9182 | bugman | 2009-07-02 23:09:23 +0200 (Thu, 02 Jul 2009) | 3 lines
Bug fix for cone_pdb() for when no MC sims are run.
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r9183 | bugman | 2009-07-02 23:13:13 +0200 (Thu, 02 Jul 2009) | 3 lines
Created and now using the full_in_ref_frame data structure (copy of N-state model).
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r9184 | bugman | 2009-07-02 23:22:55 +0200 (Thu, 02 Jul 2009) | 3 lines
Added a check for the reference domain setup to __minimise_setup_tensors().
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r9185 | bugman | 2009-07-02 23:25:33 +0200 (Thu, 02 Jul 2009) | 3 lines
Renamed n_state_model.set_domain() to align_tensor.set_domain().
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r9186 | bugman | 2009-07-02 23:27:38 +0200 (Thu, 02 Jul 2009) | 3 lines
Shifted the set_domain() back-end from the N-state model to the alignment tensor.
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r9187 | bugman | 2009-07-03 00:11:43 +0200 (Fri, 03 Jul 2009) | 3 lines
Added the interface for the frame_order.n_state_model() user function.
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r9190 | bugman | 2009-07-12 23:31:31 +0200 (Sun, 12 Jul 2009) | 3 lines
Fixes for the unit tests of the user functions shifted from n_state_model to align_tensor.
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r9191 | bugman | 2009-07-12 23:38:43 +0200 (Sun, 12 Jul 2009) | 3 lines
Fixes for the 5-state model system test.
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r9192 | bugman | 2009-07-12 23:49:33 +0200 (Sun, 12 Jul 2009) | 3 lines
Modified the N-state model code to be more like the Frame Order matrix code.
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r9193 | bugman | 2009-07-12 23:52:54 +0200 (Sun, 12 Jul 2009) | 3 lines
Copyright statement update.
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r9200 | bugman | 2009-07-13 00:14:36 +0200 (Mon, 13 Jul 2009) | 3 lines
Removed merge properties.
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r9202 | bugman | 2009-07-13 10:08:16 +0200 (Mon, 13 Jul 2009) | 7 lines
Removed all usages of float128, as this type is not present on all machines.
This was reported by Sebastian Morin in the post:
https://mail.gna.org/public/relax-devel/2009-07/msg00000.html (Message-id:
<4A5A7338.4030500@...>).
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r9203 | bugman | 2009-07-13 15:16:27 +0200 (Mon, 13 Jul 2009) | 3 lines
Missing import.
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r9204 | bugman | 2009-07-13 15:17:34 +0200 (Mon, 13 Jul 2009) | 3 lines
Bug fixes for the get_specific_fn() function.
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r9205 | bugman | 2009-07-13 15:18:36 +0200 (Mon, 13 Jul 2009) | 3 lines
Bug fixes for the grace.write() user function.
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r9206 | bugman | 2009-07-13 15:19:41 +0200 (Mon, 13 Jul 2009) | 5 lines
Bug fix for the molmol macro setup.
This was not being correctly retrieved.
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r9207 | bugman | 2009-07-13 15:21:55 +0200 (Mon, 13 Jul 2009) | 3 lines
Changed the statistics ordering when running profiling.
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r9208 | bugman | 2009-07-13 15:22:33 +0200 (Mon, 13 Jul 2009) | 3 lines
align_tensor.init() can now accept any type of float or int (python or numpy).
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r9209 | bugman | 2009-07-13 16:28:58 +0200 (Mon, 13 Jul 2009) | 6 lines
Partial reversion of r9204.
The AttributeError should be checked for, not the NameError! NameError was only triggered by
another bug.
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r9210 | bugman | 2009-07-13 18:29:31 +0200 (Mon, 13 Jul 2009) | 5 lines
Bug fixes for return_conversion_factor() and return_units() functions.
The spin and spin_id args are now accepted.
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r9211 | bugman | 2009-07-13 18:30:04 +0200 (Mon, 13 Jul 2009) | 5 lines
Fix for the write_multi_header() function.
The spin_id variable now exists.
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r9212 | bugman | 2009-07-13 18:30:45 +0200 (Mon, 13 Jul 2009) | 3 lines
Bug fix: The return_conversion_factor() method now accepts the spin arg.
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r9213 | bugman | 2009-07-13 18:31:07 +0200 (Mon, 13 Jul 2009) | 3 lines
Bug fix: The return_units() method now accepts the spin_id keyword arg.
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r9214 | bugman | 2009-07-13 18:32:32 +0200 (Mon, 13 Jul 2009) | 3 lines
Bug fix for the return_units() method, the spin_id keyword arg is now accepted.
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r9215 | bugman | 2009-07-13 18:38:06 +0200 (Mon, 13 Jul 2009) | 5 lines
Fix for the return_units() method.
The spin and spin_id args are now accepted.
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r9216 | bugman | 2009-07-14 11:04:22 +0200 (Tue, 14 Jul 2009) | 3 lines
Added a check for the chi-squared value for the 5-state model system test.
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r9217 | bugman | 2009-07-14 11:26:12 +0200 (Tue, 14 Jul 2009) | 3 lines
Bug fix: The tensor reduction was specified back to front!
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r9218 | bugman | 2009-07-14 11:26:55 +0200 (Tue, 14 Jul 2009) | 3 lines
Fix for the func_2domain() method for the N-state model tensor reduction code.
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r9219 | bugman | 2009-07-14 11:27:30 +0200 (Tue, 14 Jul 2009) | 3 lines
Removed a debugging print out.
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r9220 | bugman | 2009-07-14 11:31:51 +0200 (Tue, 14 Jul 2009) | 3 lines
Fixes for all the N-state model optimisation unit tests.
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r9221 | bugman | 2009-07-14 11:49:22 +0200 (Tue, 14 Jul 2009) | 3 lines
Fix for the return_units() method. The spin and spin_id args are now accepted.
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r9222 | bugman | 2009-07-14 12:02:38 +0200 (Tue, 14 Jul 2009) | 5 lines
Fixes for Tyler's peptide system test.
The residue was 111 in the PDB but 211 in the results file, and the spin was unnamed.
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r9223 | bugman | 2009-07-14 13:24:30 +0200 (Tue, 14 Jul 2009) | 5 lines
Bug fix for the generate_vector_dist() function.
Now the diffusion tensor and cone geometric objects are correctly created!
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r9224 | bugman | 2009-07-14 13:31:53 +0200 (Tue, 14 Jul 2009) | 5 lines
Bug fix for the generate_vector_residues() function.
Now the negative vector actually is negative! It was previously the same as the positive vector.
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r9225 | bugman | 2009-07-14 14:10:30 +0200 (Tue, 14 Jul 2009) | 6 lines
Improvements for the reload_pdb() method.
Now the system path is searched for the PDB file. This allows the system tests to pass when not
running from the installation path.
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r9226 | bugman | 2009-07-14 14:11:19 +0200 (Tue, 14 Jul 2009) | 3 lines
Extended the OMP model-free system test to run MC sims for the diffusion tensor.
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r9227 | bugman | 2009-07-14 15:12:22 +0200 (Tue, 14 Jul 2009) | 5 lines
Bug fix for the setup of MC simulations of the diffusion tensor.
MC sims were not working when all parameters except for the diffusion tensor are fixed.
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r9228 | bugman | 2009-07-14 15:26:28 +0200 (Tue, 14 Jul 2009) | 5 lines
Bug fixes for the OMP model-free system test.
The diffusion tensor MC simulation test was not functional.
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r9229 | bugman | 2009-07-14 15:56:19 +0200 (Tue, 14 Jul 2009) | 5 lines
Fix for the checks in test_omp_analysis().
The wrong data pipe was being accessed.
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r9230 | bugman | 2009-07-14 15:57:59 +0200 (Tue, 14 Jul 2009) | 5 lines
The diffusion and alignment tensor *_sim and *_err attributes are now listed as modifiable.
This means that this data is placed into the results file, and read back out again!
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