Author: bugman
Date: Tue Mar 10 09:37:20 2015
New Revision: 27790
URL: http://svn.gna.org/viewcvs/relax?rev=27790&view=rev
Log:
Merged revisions
27707-27714,27717-27719,27722-27751,27753-27756,27758-27761,27763-27767,27769,27771-27774,27776-27780,27782-27787
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
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r27707 | bugman | 2015-02-20 16:16:02 +0100 (Fri, 20 Feb 2015) | 6 lines
Python 3 fix for the new internal structural object MolContainer._sort()
method.
The list() builtin function is required to convert the output of the
range() function into a true
list in Python 3, so that the list.sort() method can be accessed.
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r27708 | bugman | 2015-02-20 16:46:14 +0100 (Fri, 20 Feb 2015) | 7 lines
Python 3 fix for the Test_msa.test_central_star unit test.
This is from the _lib._sequence_alignment.test_msa unit test module. The
logic of range() + range()
does not work in Python 3, so the range function calls are now wrapped in
list() function calls to
convert to the correct data structure type.
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r27709 | bugman | 2015-02-20 16:51:33 +0100 (Fri, 20 Feb 2015) | 6 lines
Python 3 fix for the internal structural object MolContainer._sort_key()
method.
This method is used as the key for the sort() function. However in Python
3, the key cannot be
None. So now if the residue number is None, the value of 0 is returned
instead.
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r27710 | bugman | 2015-02-20 16:54:24 +0100 (Fri, 20 Feb 2015) | 6 lines
Python 3 fix for the
pipe_control.structure.main.assemble_structural_coordinates() function.
This affects most of the structure user functions. This was another case
of requiring the list()
built in function to create a list object from an iterator.
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r27711 | bugman | 2015-02-20 16:56:44 +0100 (Fri, 20 Feb 2015) | 5 lines
Another Python 3 list() fix for the structure user functions.
This time the problem was in the
pipe_control.structure.main.sequence_alignment() function.
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r27712 | bugman | 2015-02-23 10:06:59 +0100 (Mon, 23 Feb 2015) | 9 lines
Large speed up of the structure.web_of_motion user function.
With the introduction of the _sort() internal structural object method and
it being called by the
add_atom(), the structure.web_of_motion user function was now painfully
slow. As sorting the
structural data is unnecessary for the backend of this user function, the
add_atom() boolean
argument 'sort' has been added to turn the sorting on and off, and the
structure.web_of_motion
backend now sets this to False.
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r27713 | bugman | 2015-02-23 11:49:05 +0100 (Mon, 23 Feb 2015) | 6 lines
Fix for the internal structural object unit test
Test_object.test_add_atom_sort.
This test of the _lib._structure._internal.test_object unit test module now
requires the sort
argument set to True when calling the add_atom() method.
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r27714 | bugman | 2015-02-23 11:50:54 +0100 (Mon, 23 Feb 2015) | 3 lines
Fix for a RelaxError message from the internal structural object when
validating models.
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r27717 | bugman | 2015-02-24 12:08:43 +0100 (Tue, 24 Feb 2015) | 3 lines
Improvement for a RelaxError message when assembling structural data but no
coordinates can be found.
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r27718 | bugman | 2015-02-25 13:46:35 +0100 (Wed, 25 Feb 2015) | 6 lines
Created a series of unit tests for implementing a new internal structural
object feature.
These tests check a new 'inv' argument for the selection() structural
object method for allowing all
atoms not matching the atom ID string to be selected.
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r27719 | bugman | 2015-02-25 13:58:45 +0100 (Wed, 25 Feb 2015) | 6 lines
Implemented the new 'inv' argument for the selection() structural object
method.
This allows for all atoms not matching the atom ID string to be selected.
The unit tests for this
argument now all pass, validating the implementation.
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r27722 | bugman | 2015-03-02 11:58:42 +0100 (Mon, 02 Mar 2015) | 6 lines
Improvement for the structure.mean user function.
This can now be used to store an averaged structure in an empty data pipe.
Previously structural
data needed to be present in the current data pipe for the user function to
work.
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r27723 | bugman | 2015-03-02 15:32:59 +0100 (Mon, 02 Mar 2015) | 9 lines
Bug fix for the results.write user function when loading relax state files.
The results.write user function can load not only the results file
consisting of a single data pipe,
but also relax state files if only a single pipe is present. However this
was causing the current
data pipe and other pipe-independent data (sequence alignments and the GUI)
to be overwritten, just
as when loading a state file. Now only the data from the data pipe will be
loaded and the pipe
independent data in the state file will be ignored.
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r27724 | bugman | 2015-03-02 15:34:59 +0100 (Mon, 02 Mar 2015) | 6 lines
Fix for the rdc.write user function.
The check for the missing rdc_data_types variable in the interatomic
containers is now more
comprehensive and checks for the presence of the alignment ID.
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r27725 | bugman | 2015-03-02 16:55:08 +0100 (Mon, 02 Mar 2015) | 6 lines
Created a system test to show a limitation of the rdc.copy user function.
Currently, it cannot work when spin systems in two data pipes are
different. The system test will
be used to implement the support.
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r27726 | bugman | 2015-03-02 17:16:44 +0100 (Mon, 02 Mar 2015) | 6 lines
Simplification of the new Rdc.test_rdc_copy_different_spins system test.
This no longer tests the deletion of interatomic data containers by the
spin.delete user function,
something which is not implemented.
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r27727 | bugman | 2015-03-02 17:16:56 +0100 (Mon, 02 Mar 2015) | 3 lines
Copyright update.
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r27728 | bugman | 2015-03-02 17:21:04 +0100 (Mon, 02 Mar 2015) | 3 lines
Added a printout to the sequence.attach_protons user function listing all
the newly created spins.
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r27729 | bugman | 2015-03-02 17:21:19 +0100 (Mon, 02 Mar 2015) | 3 lines
Copyright update.
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r27730 | bugman | 2015-03-02 17:24:08 +0100 (Mon, 02 Mar 2015) | 5 lines
Some more fixes for the Rdc.test_rdc_copy_different_spins system test.
The residue.delete and not spin.delete user function is required to delete
the sequence data.
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r27731 | bugman | 2015-03-02 17:27:21 +0100 (Mon, 02 Mar 2015) | 5 lines
Another small fix for the new Rdc.test_rdc_copy_different_spins system test.
The rdc.copy user function requires the pipe_to argument to be supplied in
this case.
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r27732 | bugman | 2015-03-02 18:09:12 +0100 (Mon, 02 Mar 2015) | 8 lines
Expansion of the Rdc.test_rdc_copy_different_spins system test.
The interatomic data containers are now defined via the interatom.define
user function, which
requires the spin.element user function to set up the element information.
A printout has also been
added to demonstrate a failure in the
pipe_control.interatomic.interatomic_loop() function in
handling the correct data pipe.
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r27733 | bugman | 2015-03-02 18:13:09 +0100 (Mon, 02 Mar 2015) | 8 lines
Big bug fix for the pipe_control.interatomic.interatomic_loop() function.
This was identified in the Rdc.test_rdc_copy_different_spins system test.
The problem was that the
pipe argument was being ignored when looking up the spin containers. Hence
if the pipe being worked
on was not the current data pipe, and the spin sequences were not
identical, the function would
fail. This mainly affects the rdc.copy user function.
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r27734 | bugman | 2015-03-02 18:19:26 +0100 (Mon, 02 Mar 2015) | 6 lines
Some more modifications for the Rdc.test_rdc_copy_different_spins system
test.
One of the interatomic data containers does not have RDC data, as it is not
present in the original
data pipe, hence this is checked for. And the printouts have more
formatting.
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r27735 | bugman | 2015-03-02 18:22:18 +0100 (Mon, 02 Mar 2015) | 7 lines
Expanded the functionality of the rdc.copy user function.
The user function will now operate on two data pipes with different spin
sequences. If the
interatomic data container is missing from the target data pipe, a warning
is given. And if the
interatomic data container is not present in the source data pipe, nothing
will be copied.
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r27736 | bugman | 2015-03-03 13:43:44 +0100 (Tue, 03 Mar 2015) | 3 lines
Modified the rdc.copy user function to printout all copied RDC values and
errors.
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r27737 | bugman | 2015-03-03 13:51:18 +0100 (Tue, 03 Mar 2015) | 6 lines
Created the Rdc.test_rdc_copy_back_calc system test.
This will be used to implement the back_calc Boolean argument for the
rdc.copy user function to
allow not only measured, but also back-calculated RDC values to be copied.
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r27738 | bugman | 2015-03-03 13:53:48 +0100 (Tue, 03 Mar 2015) | 3 lines
Modified the rdc.copy printout of RDCs to occur for each alignment ID.
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r27739 | bugman | 2015-03-03 14:01:13 +0100 (Tue, 03 Mar 2015) | 6 lines
Implemented the back_calc argument for the rdc.copy user function.
This allows the back-calculated RDCs to be additionally copied together
with the real value and
error.
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r27740 | bugman | 2015-03-03 14:06:31 +0100 (Tue, 03 Mar 2015) | 3 lines
Small formatting change for the rdc.copy user function printouts.
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r27741 | bugman | 2015-03-03 14:17:41 +0100 (Tue, 03 Mar 2015) | 6 lines
Created the Pcs.test_pcs_copy_different_spins system test.
This will be used to show a limitation of the pcs.copy user function in
that it cannot copy data
between two data pipes with different molecule, residue, and spin sequences.
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r27742 | bugman | 2015-03-03 14:34:41 +0100 (Tue, 03 Mar 2015) | 7 lines
Fix for the pcs.read user function.
The problem was caught by the new Pcs.test_pcs_copy_different_spins system
test. If the spin system
does not exist in the current data pipe, but data for it is present in the
PCS file, the pcs.read
user function would terminate in a TypeError.
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r27743 | bugman | 2015-03-03 14:38:33 +0100 (Tue, 03 Mar 2015) | 5 lines
Added a printout of the alignment ID for the pcs.copy user function.
This is to match the rdc.copy user function.
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r27744 | bugman | 2015-03-03 14:43:18 +0100 (Tue, 03 Mar 2015) | 7 lines
Created the Pcs.test_pcs_copy_back_calc system test.
This will be used to implement the back_calc Boolean argument for the
pcs.copy user function to
allow not only measured, but also back-calculated PCS values to be copied.
It matches the
equivalent Rdc.test_rdc_copy_back_calc system test.
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r27745 | bugman | 2015-03-03 14:46:20 +0100 (Tue, 03 Mar 2015) | 6 lines
Implemented the back_calc argument for the pcs.copy user function.
This allows the back-calculated PCSs to be additionally copied together
with the real value and
error. The implementation simply copies that of the rdc.copy user function.
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r27746 | bugman | 2015-03-03 15:04:47 +0100 (Tue, 03 Mar 2015) | 5 lines
Added full per-alignment data printouts to the pcs.copy user function to
match rdc.copy.
The feedback is important to know what was actually copied.
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r27747 | bugman | 2015-03-03 15:09:00 +0100 (Tue, 03 Mar 2015) | 3 lines
Modified the pcs.copy user function to handle different spin sequence
between data pipes.
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r27748 | bugman | 2015-03-03 15:13:03 +0100 (Tue, 03 Mar 2015) | 3 lines
Fixes for the Pcs.test_pcs_copy_different_spins and
Pcs.test_pcs_copy_back_calc system tests.
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r27749 | bugman | 2015-03-03 15:47:17 +0100 (Tue, 03 Mar 2015) | 5 lines
Fix for the pcs.copy user function for a recently introduced problem
(r27747).
The data pipe for the spin_loop() function must be supplied.
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r27750 | bugman | 2015-03-03 15:48:35 +0100 (Tue, 03 Mar 2015) | 3 lines
The pcs.copy user function now skips deselected spins.
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r27751 | bugman | 2015-03-03 15:59:41 +0100 (Tue, 03 Mar 2015) | 3 lines
Modified the N_state_model.test_data_copying system test to skip deselected
spins.
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r27753 | bugman | 2015-03-03 16:30:49 +0100 (Tue, 03 Mar 2015) | 3 lines
Added more checks to the three Pcs.test_pcs_copy* system tests.
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r27754 | bugman | 2015-03-03 16:33:21 +0100 (Tue, 03 Mar 2015) | 3 lines
Added more checks to the three Rdc.test_rdc_copy* system tests.
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r27755 | bugman | 2015-03-03 16:46:48 +0100 (Tue, 03 Mar 2015) | 7 lines
Created the Rdc.test_calc_q_factors_no_tensor system test.
This is to demonstrate a failure in the rdc.calc_q_factors user function
when no alignment tensor is
present. In addition, the test is also triggering an earlier problem of
spin isotope information
being missing. However the isotope is not required if the tensor is absent.
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r27756 | bugman | 2015-03-03 16:49:03 +0100 (Tue, 03 Mar 2015) | 7 lines
Fixes for the rdc.calc_q_factors user function for when no alignment tensor
is present.
This was caught by the Rdc.test_calc_q_factors_no_tensor system test. Now
if no tensor is present,
a warning is given and the 2Da^2(4 + 3R)/5 normalised Q factor is skipped.
Also, if present but no
spin isotope information is present, then RelaxSpinTypeError errors are
raised.
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r27758 | bugman | 2015-03-03 17:10:38 +0100 (Tue, 03 Mar 2015) | 6 lines
The Rdc.test_rdc_copy_* system tests now check for the 'rdc_data_types'
data structure.
This is in the Rdc.test_rdc_copy_different_spins and
Rdc.test_rdc_copy_back_calc system tests and
shows that the rdc.copy user function fails to duplicate this information.
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r27759 | bugman | 2015-03-03 17:11:47 +0100 (Tue, 03 Mar 2015) | 3 lines
Removed a debugging printout.
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r27760 | bugman | 2015-03-03 17:15:33 +0100 (Tue, 03 Mar 2015) | 6 lines
The Rdc.test_rdc_copy_* system tests now check for the 'absolute_rdc' data
structure.
This is in the Rdc.test_rdc_copy_different_spins and
Rdc.test_rdc_copy_back_calc system tests and
shows that the rdc.copy user function fails to duplicate this information
as well.
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r27761 | bugman | 2015-03-03 17:18:14 +0100 (Tue, 03 Mar 2015) | 3 lines
Expanded the rdc.copy user function to copy the RDC data type and absolute
RDC flag information.
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r27763 | bugman | 2015-03-03 17:34:39 +0100 (Tue, 03 Mar 2015) | 5 lines
Created the Rdc.test_corr_plot system test to check the rdc.corr_plot user
function.
This shows that this poorly tested function works correctly.
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r27764 | bugman | 2015-03-03 17:40:22 +0100 (Tue, 03 Mar 2015) | 5 lines
Created the Pcs.test_corr_plot system test to check the pcs.corr_plot user
function.
This user function is poorly tested, and this test triggers a series of
bugs.
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r27765 | bugman | 2015-03-03 17:42:30 +0100 (Tue, 03 Mar 2015) | 6 lines
Added the 'title' and 'subtitle' arguments to the pcs.corr_plot user
function.
This problem was detected by the new Pcs.test_corr_plot system test. The
pcs.corr_plot user
function now matches the rdc.corr_plot user function in terms of arguments.
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r27766 | bugman | 2015-03-03 17:46:21 +0100 (Tue, 03 Mar 2015) | 3 lines
Fix for the pcs.corr_plot user function when the spin containers have no
element information.
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r27767 | bugman | 2015-03-03 17:50:02 +0100 (Tue, 03 Mar 2015) | 5 lines
Completed the Pcs.test_corr_plot system test.
The file contents are now known and have been carefully checking in Grace.
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r27769 | bugman | 2015-03-04 13:33:45 +0100 (Wed, 04 Mar 2015) | 12 lines
Clarification of the RDC and PCS Q factors.
This affects the rdc.calc_q_factors and pcs.calc_q_factors user functions,
as well as all other
operations involving the calculation of Q factors. The printouts have been
modified to clarify if
the normalisation is via the tensor size (2Da^2(4 + 3R)/5) or via the sum
of data squared, and the
separation of the two is now clearer. This allows for better RDC vs. PCS
comparisons.
In addition, the data pipe variable names have been updated to reflect the
normalisation, so it is
instantly known when looking at the XML contents of results or save files
which was used. The
backwards compatibility hooks have been modified to support the data pipe
variable name changes.
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r27771 | bugman | 2015-03-04 14:28:46 +0100 (Wed, 04 Mar 2015) | 6 lines
Created the Align_tensor.test_copy_pipes system test.
This is to show a problem in the align_tensor.copy user function when
copying all tensors between
data pipes.
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r27772 | bugman | 2015-03-04 14:30:30 +0100 (Wed, 04 Mar 2015) | 5 lines
The align_tensor.copy user function 'tensor_from' argument can now be None.
This is to enable the copying of all alignment tensors from one data pipe
to another.
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r27773 | bugman | 2015-03-04 14:34:07 +0100 (Wed, 04 Mar 2015) | 5 lines
Modified the pipe_control.align_tensor.align_data_exists() function to
handle no tensor IDs.
If no tensor ID is supplied, this will then return True if any alignment
data exists.
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r27774 | bugman | 2015-03-04 14:47:21 +0100 (Wed, 04 Mar 2015) | 6 lines
Improvement for the align_tensor.copy user function.
The user function has been modified to allow all alignment tensors to be
copied between two data
pipes. This allows the Align_tensor.test_copy_pipes system test to pass.
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r27776 | bugman | 2015-03-04 15:10:39 +0100 (Wed, 04 Mar 2015) | 5 lines
Fixes for the align_tensor.copy user function argument unit tests.
The tensor_from and tensor_to arguments can now be None.
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r27777 | bugman | 2015-03-04 15:23:13 +0100 (Wed, 04 Mar 2015) | 6 lines
Created the Align_tensor.test_copy_pipes_sims system test.
This demonstrates a failure of the align_tensor.copy user function when
Monte Carlo simulated
tensors are present.
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r27778 | bugman | 2015-03-04 15:28:53 +0100 (Wed, 04 Mar 2015) | 3 lines
Copyright update.
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r27779 | bugman | 2015-03-04 15:32:53 +0100 (Wed, 04 Mar 2015) | 6 lines
Deleted the data_store.align_tensor.AlignTensorSimList.append() method.
This replacement list method was proving fatal when copy.deepcopy() is
called on the alignment
tensor object. The change allows the Align_tensor.test_copy_pipes_sims
system test to pass.
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r27780 | bugman | 2015-03-04 15:33:20 +0100 (Wed, 04 Mar 2015) | 3 lines
Copyright update.
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r27782 | bugman | 2015-03-05 11:02:08 +0100 (Thu, 05 Mar 2015) | 9 lines
Huge speed up for loading results and state files with Monte Carlo
simulation alignment tensors.
The reading of the alignment tensor component of XML formatted results and
state files has been
modified. Previously the
data_store.align_tensor.AlignTensorData._update_object() method for
updating the alignment tensor object (for values, errors, simulations) was
being called once for
each Monte Carlo simulation. Now is it called only once for all
simulations. In one test, the
reading of the save file with 500 simulations dropped from 253.7 to 10.0
seconds.
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r27783 | bugman | 2015-03-05 14:49:00 +0100 (Thu, 05 Mar 2015) | 6 lines
Added an extra check for the assembly of RDC data.
This is in the pipe_control.rdc.return_rdc_data() function and the check is
for any unit vectors set
to None, which is a fatal condition.
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r27784 | bugman | 2015-03-05 15:05:28 +0100 (Thu, 05 Mar 2015) | 3 lines
Improved the RelaxError message from the RDC assembly function when unit
vectors are None.
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r27790 - in /branches/nmrglue: ./ auto_analyses/ data_store/ lib/structure/internal/ pipe_control/ pipe_control/structure/ t...