Author: bugman
Date: Sat May 9 18:45:25 2009
New Revision: 9045
URL: http://svn.gna.org/viewcvs/relax?rev=9045&view=rev
Log:
Merged revisions 8640-9044 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
................
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.
................
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).
................
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.
................
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@xxxxxxxxxxxxx>).
................
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@xxxxxxxxxxxxx>).
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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@xxxxxxxxx>)
................
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
[... 993 lines stripped ...]
r9045 - in /branches/j_couplings: ./ data/ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ sample_scripts/ specific_f...