Author: bugman
Date: Tue Mar 3 16:02:51 2015
New Revision: 27752
URL: http://svn.gna.org/viewcvs/relax?rev=27752&view=rev
Log:
Merged revisions 27722-27751 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/data_store/__init__.py
branches/frame_order_cleanup/pipe_control/interatomic.py
branches/frame_order_cleanup/pipe_control/pcs.py
branches/frame_order_cleanup/pipe_control/rdc.py
branches/frame_order_cleanup/pipe_control/sequence.py
branches/frame_order_cleanup/pipe_control/structure/main.py
branches/frame_order_cleanup/test_suite/system_tests/n_state_model.py
branches/frame_order_cleanup/test_suite/system_tests/pcs.py
branches/frame_order_cleanup/test_suite/system_tests/rdc.py
branches/frame_order_cleanup/user_functions/pcs.py
branches/frame_order_cleanup/user_functions/rdc.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_cleanup/data_store/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/data_store/__init__.py?rev=27752&r1=27751&r2=27752&view=diff
Modified: branches/frame_order_cleanup/pipe_control/interatomic.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/interatomic.py?rev=27752&r1=27751&r2=27752&view=diff
Modified: branches/frame_order_cleanup/pipe_control/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/pcs.py?rev=27752&r1=27751&r2=27752&view=diff
Modified: branches/frame_order_cleanup/pipe_control/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/rdc.py?rev=27752&r1=27751&r2=27752&view=diff
Modified: branches/frame_order_cleanup/pipe_control/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/sequence.py?rev=27752&r1=27751&r2=27752&view=diff
Modified: branches/frame_order_cleanup/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/structure/main.py?rev=27752&r1=27751&r2=27752&view=diff
Modified:
branches/frame_order_cleanup/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/n_state_model.py?rev=27752&r1=27751&r2=27752&view=diff
Modified: branches/frame_order_cleanup/test_suite/system_tests/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/pcs.py?rev=27752&r1=27751&r2=27752&view=diff
Modified: branches/frame_order_cleanup/test_suite/system_tests/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/rdc.py?rev=27752&r1=27751&r2=27752&view=diff
Modified: branches/frame_order_cleanup/user_functions/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/pcs.py?rev=27752&r1=27751&r2=27752&view=diff
Modified: branches/frame_order_cleanup/user_functions/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/rdc.py?rev=27752&r1=27751&r2=27752&view=diff
r27752 - in /branches/frame_order_cleanup: ./ data_store/ pipe_control/ pipe_control/structure/ test_suite/system_tests/ use...