Merged revisions 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 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
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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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