Author: semor
Date: Fri Feb 13 21:02:45 2009
New Revision: 8799
URL: http://svn.gna.org/viewcvs/relax?rev=8799&view=rev
Log:
Merged revisions 8748-8798 via svnmerge from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.3
........
r8748 | bugman | 2009-02-05 12:40:49 -0500 (Thu, 05 Feb 2009) | 3 lines
The __linear_constraints() method now handles the N-state models without
probabilities.
........
r8749 | bugman | 2009-02-05 12:48:59 -0500 (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.
........
r8750 | bugman | 2009-02-06 05:57:46 -0500 (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.
........
r8751 | bugman | 2009-02-06 07:32:41 -0500 (Fri, 06 Feb 2009) | 3 lines
Created a directory for CaM RDC and PCS test data.
........
r8752 | bugman | 2009-02-06 11:34:03 -0500 (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!
........
r8753 | bugman | 2009-02-06 11:35:10 -0500 (Fri, 06 Feb 2009) | 3 lines
Generated and added the synthetic RDC data.
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r8754 | bugman | 2009-02-06 12:16:34 -0500 (Fri, 06 Feb 2009) | 3 lines
A few modifications for the PCS.
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r8755 | bugman | 2009-02-09 05:14:15 -0500 (Mon, 09 Feb 2009) | 3 lines
The PCS constant is now being calculated.
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r8756 | bugman | 2009-02-09 05:20:01 -0500 (Mon, 09 Feb 2009) | 3 lines
The PCS is now calculated for each spin.
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r8757 | bugman | 2009-02-09 05:30:41 -0500 (Mon, 09 Feb 2009) | 3 lines
Fixes for the PCS calculation.
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r8758 | bugman | 2009-02-09 05:35:20 -0500 (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 08:24:51 -0500 (Mon, 09 Feb 2009) | 3 lines
Fixes for the calculation of the PCS.
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r8760 | bugman | 2009-02-09 09:21:49 -0500 (Mon, 09 Feb 2009) | 3 lines
Decreased the alignment by a factor of 5.
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r8761 | bugman | 2009-02-09 10:05:12 -0500 (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 10:07:30 -0500 (Mon, 09 Feb 2009) | 3 lines
Shifted all print statements to the end.
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r8763 | bugman | 2009-02-10 05:09:02 -0500 (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 05:31:47 -0500 (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 07:51:40 -0500 (Tue, 10 Feb 2009) | 3 lines
Changed the PRE cut-off to 15 Angstrom.
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r8766 | bugman | 2009-02-10 07:52:10 -0500 (Tue, 10 Feb 2009) | 3 lines
Added the list of PRE broadened residues.
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r8767 | bugman | 2009-02-10 08:30:18 -0500 (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 08:33:11 -0500 (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 08:34:40 -0500 (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 11:27:04 -0500 (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@xxxxxxxxxxxxx>).
........
r8771 | bugman | 2009-02-11 08:14:59 -0500 (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 08:52:59 -0500 (Wed, 11 Feb 2009) | 3 lines
Activated the RDC and PCS tensor fitting system test.
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r8773 | bugman | 2009-02-11 09:18:54 -0500 (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 09:21:24 -0500 (Wed, 11 Feb 2009) | 3 lines
Modified the data reading print outs.
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r8775 | bugman | 2009-02-11 09:26:25 -0500 (Wed, 11 Feb 2009) | 3 lines
The file data is now always checked.
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r8776 | bugman | 2009-02-11 09:29:41 -0500 (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 09:31:13 -0500 (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 09:38:28 -0500 (Wed, 11 Feb 2009) | 3 lines
Print out fixes.
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r8779 | bugman | 2009-02-11 09:47:15 -0500 (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 09:51:03 -0500 (Wed, 11 Feb 2009) | 3 lines
Bug fixes for the print outs.
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r8781 | bugman | 2009-02-11 10:54:43 -0500 (Wed, 11 Feb 2009) | 3 lines
Caught the missing paramagnetic centre.
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r8782 | bugman | 2009-02-11 11:03:39 -0500 (Wed, 11 Feb 2009) | 3 lines
The paramagnetic centre is now set.
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r8783 | bugman | 2009-02-11 11:07:33 -0500 (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 11:38:01 -0500 (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 11:39:01 -0500 (Wed, 11 Feb 2009) | 3 lines
Added a grid search to the system test.
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r8786 | bugman | 2009-02-11 15:54:08 -0500 (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@xxxxxxxxxxxxx>).
........
r8787 | bugman | 2009-02-12 03:52:45 -0500 (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 03:57:11 -0500 (Thu, 12 Feb 2009) | 3 lines
Constraints are turned off for the 'fixed' model!
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r8789 | bugman | 2009-02-12 04:06:45 -0500 (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 04:13:40 -0500 (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 04:19:48 -0500 (Thu, 12 Feb 2009) | 3 lines
A few changes to the system test.
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r8792 | bugman | 2009-02-12 04:51:37 -0500 (Thu, 12 Feb 2009) | 3 lines
The alignment tensor elements are now explicitly set.
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r8793 | bugman | 2009-02-12 05:17:34 -0500 (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 08:39:23 -0500 (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 13:59:24 -0500 (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 14:08:38 -0500 (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 12:05:33 -0500 (Fri, 13 Feb 2009) | 3 lines
Fixes for the system test script.
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r8798 | bugman | 2009-02-13 12:06:25 -0500 (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.
........
Added:
branches/relax_disp/test_suite/shared_data/align_data/CaM/
- copied from r8798, 1.3/test_suite/shared_data/align_data/CaM/
branches/relax_disp/test_suite/shared_data/structures/bax_C_1J7P_N_H_Ca.pdb
- copied unchanged from r8798,
1.3/test_suite/shared_data/structures/bax_C_1J7P_N_H_Ca.pdb
branches/relax_disp/test_suite/system_tests/scripts/align_fit.py
- copied unchanged from r8798,
1.3/test_suite/system_tests/scripts/align_fit.py
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/generic_fns/pcs.py
branches/relax_disp/generic_fns/rdc.py
branches/relax_disp/maths_fns/n_state_model.py
branches/relax_disp/maths_fns/pcs.py
branches/relax_disp/maths_fns/rdc.py
branches/relax_disp/prompt/pcs.py
branches/relax_disp/prompt/rdc.py
branches/relax_disp/sample_scripts/full_analysis.py
branches/relax_disp/specific_fns/n_state_model.py
branches/relax_disp/test_suite/system_tests/n_state_model.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/relax_disp/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/pcs.py?rev=8799&r1=8798&r2=8799&view=diff
Modified: branches/relax_disp/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/rdc.py?rev=8799&r1=8798&r2=8799&view=diff
Modified: branches/relax_disp/maths_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/maths_fns/n_state_model.py?rev=8799&r1=8798&r2=8799&view=diff
Modified: branches/relax_disp/maths_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/maths_fns/pcs.py?rev=8799&r1=8798&r2=8799&view=diff
Modified: branches/relax_disp/maths_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/maths_fns/rdc.py?rev=8799&r1=8798&r2=8799&view=diff
Modified: branches/relax_disp/prompt/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/prompt/pcs.py?rev=8799&r1=8798&r2=8799&view=diff
Modified: branches/relax_disp/prompt/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/prompt/rdc.py?rev=8799&r1=8798&r2=8799&view=diff
Modified: branches/relax_disp/sample_scripts/full_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/sample_scripts/full_analysis.py?rev=8799&r1=8798&r2=8799&view=diff
Modified: branches/relax_disp/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_fns/n_state_model.py?rev=8799&r1=8798&r2=8799&view=diff
Modified: branches/relax_disp/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/n_state_model.py?rev=8799&r1=8798&r2=8799&view=diff
r8799 - in /branches/relax_disp: ./ generic_fns/ maths_fns/ prompt/ sample_scripts/ specific_fns/ test_suite/shared_data/ali...