Author: bugman
Date: Tue Oct 16 10:25:21 2012
New Revision: 17831
URL: http://svn.gna.org/viewcvs/relax?rev=17831&view=rev
Log:
Merged revisions 17552-17580 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r17552 | bugman | 2012-09-25 13:42:50 +0200 (Tue, 25 Sep 2012) | 7 lines
Fix for bug #20198 (https://gna.org/bugs/?20198) - the relaxation data
back-calculation error.
The problem was that the call to the model-free overfit_deselect() method
was deselecting any spins
lacking relaxation data! This should not happen, as no spins need to have
relaxation data for this
calculation.
........
r17553 | bugman | 2012-09-25 14:03:50 +0200 (Tue, 25 Sep 2012) | 5 lines
Added the data_check Boolean argument to all of the specific analysis
overfit_deselect() methods.
This allows the unit tests to pass.
........
r17554 | bugman | 2012-09-25 14:05:41 +0200 (Tue, 25 Sep 2012) | 7 lines
Added a tryptophan NE1 data set to the sphere model-free model test data.
This is in preparation to catch bug #20197 (https://gna.org/bugs/?20197).
The scripts have also been updated for the newer relax designs.
........
r17555 | bugman | 2012-09-25 14:38:21 +0200 (Tue, 25 Sep 2012) | 6 lines
Improved the model-free overfitting deselection printouts prior to
optimisation.
Only a single message per spin is now given when the spin is deselected,
minimising the amount of
output.
........
r17556 | bugman | 2012-09-25 14:53:03 +0200 (Tue, 25 Sep 2012) | 3 lines
More improvements to the model-free over-fitting deselection printouts.
........
r17557 | bugman | 2012-09-25 14:58:22 +0200 (Tue, 25 Sep 2012) | 5 lines
Printouts for the over-fitting deselection of spins are suppressed for the
back-calculation of relaxation data.
This affects the model-free Monte Carlo simulations, simplifying the output.
........
r17558 | bugman | 2012-09-25 15:01:37 +0200 (Tue, 25 Sep 2012) | 3 lines
All overfit_deselect() methods now accept and use the verbose argument.
........
r17559 | bugman | 2012-09-25 15:06:25 +0200 (Tue, 25 Sep 2012) | 3 lines
The overfit_deselect() printouts are now regularised and match the
model-free printouts.
........
r17560 | bugman | 2012-09-25 15:18:23 +0200 (Tue, 25 Sep 2012) | 6 lines
Small change to the sphere model model-free test suite data.
The trptophan indole data is now merged into the last residue (a glycine)
to catch bug #20197
(https://gna.org/bugs/?20197).
........
r17561 | bugman | 2012-09-25 15:21:43 +0200 (Tue, 25 Sep 2012) | 5 lines
Modified the Mf.test_dauvergne_protocol system test to catch bug #20197
(https://gna.org/bugs/?20197).
The sphere test data NE1 and HE1 data is now being used in this system
test, triggering the bug.
........
r17562 | bugman | 2012-09-25 16:37:03 +0200 (Tue, 25 Sep 2012) | 3 lines
Relaxation data is no longer loaded by relax_data.read if the values and
errors are both None.
........
r17563 | bugman | 2012-09-25 16:41:25 +0200 (Tue, 25 Sep 2012) | 3 lines
Fix for the N_state_model.test_monte_carlo_sims due to the changed
sphere.pdb test suite file.
........
r17564 | bugman | 2012-09-25 16:42:04 +0200 (Tue, 25 Sep 2012) | 3 lines
Fix to the Dasha system test needed for the changes to the relax_data.read
user function.
........
r17565 | bugman | 2012-09-25 17:02:49 +0200 (Tue, 25 Sep 2012) | 3 lines
Fix for the Relax_data.test_read unit tests for the relax_data.read user
function changes.
........
r17566 | bugman | 2012-09-25 17:07:18 +0200 (Tue, 25 Sep 2012) | 3 lines
Fix for the Relax_data.test_delete system test for the changes to the
relax_data.read user function.
........
r17567 | bugman | 2012-09-25 18:46:03 +0200 (Tue, 25 Sep 2012) | 6 lines
Fix for bug #20197 (https://gna.org/bugs/?20197) - the PyMOL and Molmol
macro failure.
The macro creation now only operates on spins called 'N' and assumes these
are the backbone
nitrogens. The sidechain tryptophan indole NH data will need to be
detected and added later.
........
r17568 | bugman | 2012-09-27 10:03:08 +0200 (Thu, 27 Sep 2012) | 3 lines
Lots of editing of the model-free GUI section of the user manual.
........
r17569 | bugman | 2012-09-27 10:04:04 +0200 (Thu, 27 Sep 2012) | 3 lines
Fix for the comment on the 'Export' button in the BMRB export window.
........
r17570 | bugman | 2012-09-27 10:04:22 +0200 (Thu, 27 Sep 2012) | 3 lines
Removed some debugging printouts.
........
r17571 | bugman | 2012-09-27 10:05:14 +0200 (Thu, 27 Sep 2012) | 3 lines
Added star versions of the standard spin IDs to the spin ID GUI element
(e.g. '@N*', '@H*').
........
r17572 | bugman | 2012-09-27 10:07:03 +0200 (Thu, 27 Sep 2012) | 6 lines
The CSA setting in the model-free auto GUI analysis now defaults to the
'@N*' spin ID.
Previously no spin ID was being used so that the protons where also having
their CSA values set to
that of the nitrogens. Now the execution checking code skips the proton
CSA check.
........
r17573 | bugman | 2012-09-27 10:08:12 +0200 (Thu, 27 Sep 2012) | 3 lines
Fixes for the checks in the Mf.test_mf_auto_analysis() GUI test for the
recent test suite data changes.
........
r17574 | bugman | 2012-09-27 16:14:47 +0200 (Thu, 27 Sep 2012) | 6 lines
Removed the 'force flag' text from the RelaxWarning messages output by the
bruker.read user function.
The force flag arguments of the generic_fns.mol_res_spin.name_spin() and
generic_fns.mol_res_spin.set_spin_isotope() functions can now be set to
None to suppress the text.
........
r17575 | bugman | 2012-09-27 16:29:40 +0200 (Thu, 27 Sep 2012) | 7 lines
Fix for bug #20201 (https://gna.org/bugs/?20201).
The bruker.read user function can now handle the situation where multiple
spins per residue are
already loaded prior to the user function call. The isotope value from the
DC file is now
translated to the element name and this is used as part of the spin ID
string.
........
r17576 | bugman | 2012-09-27 19:19:13 +0200 (Thu, 27 Sep 2012) | 3 lines
Some changes in preparation for Python 3.
........
r17577 | bugman | 2012-09-28 10:02:02 +0200 (Fri, 28 Sep 2012) | 3 lines
Fix for a fatal bug introduced in the last revision (r17576).
........
r17578 | bugman | 2012-09-28 10:49:08 +0200 (Fri, 28 Sep 2012) | 5 lines
Removed all of the xrange() calls from the system tests as these are not
necessary.
This is in preparation for Python 3.
........
r17579 | bugman | 2012-09-28 10:55:55 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparation - changed the import of SystemTestCase to use the
absolute module path.
........
r17580 | bugman | 2012-09-28 10:57:54 +0200 (Fri, 28 Sep 2012) | 3 lines
Python 3 preparation - the test_suite.system_tests package now uses the
absolute module path for imports.
........
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/docs/latex/model-free.tex
branches/frame_order_testing/extern/scientific_python/Geometry/VectorModule.py
branches/frame_order_testing/extern/scientific_python/Geometry/__init__.py
branches/frame_order_testing/extern/scientific_python/IO/FortranFormat.py
branches/frame_order_testing/extern/scientific_python/IO/PDB.py
branches/frame_order_testing/generic_fns/bruker.py
branches/frame_order_testing/generic_fns/mol_res_spin.py
branches/frame_order_testing/generic_fns/relax_data.py
branches/frame_order_testing/gui/analyses/auto_model_free.py
branches/frame_order_testing/gui/export_bmrb.py
branches/frame_order_testing/gui/input_elements/spin_id.py
branches/frame_order_testing/specific_fns/api_base.py
branches/frame_order_testing/specific_fns/api_common.py
branches/frame_order_testing/specific_fns/consistency_tests.py
branches/frame_order_testing/specific_fns/jw_mapping.py
branches/frame_order_testing/specific_fns/model_free/macro_base.py
branches/frame_order_testing/specific_fns/model_free/main.py
branches/frame_order_testing/specific_fns/noe/main.py
branches/frame_order_testing/specific_fns/relax_fit.py
branches/frame_order_testing/test_suite/gui_tests/model_free.py
branches/frame_order_testing/test_suite/shared_data/model_free/sphere/create_ri.py
branches/frame_order_testing/test_suite/shared_data/model_free/sphere/create_sphere.py
branches/frame_order_testing/test_suite/shared_data/model_free/sphere/noe.500.out
branches/frame_order_testing/test_suite/shared_data/model_free/sphere/noe.900.out
branches/frame_order_testing/test_suite/shared_data/model_free/sphere/r1.500.out
branches/frame_order_testing/test_suite/shared_data/model_free/sphere/r1.900.out
branches/frame_order_testing/test_suite/shared_data/model_free/sphere/r2.500.out
branches/frame_order_testing/test_suite/shared_data/model_free/sphere/r2.900.out
branches/frame_order_testing/test_suite/shared_data/model_free/sphere/sphere.pdb
branches/frame_order_testing/test_suite/system_tests/__init__.py
branches/frame_order_testing/test_suite/system_tests/align_tensor.py
branches/frame_order_testing/test_suite/system_tests/angles.py
branches/frame_order_testing/test_suite/system_tests/bmrb.py
branches/frame_order_testing/test_suite/system_tests/bruker.py
branches/frame_order_testing/test_suite/system_tests/consistency_tests.py
branches/frame_order_testing/test_suite/system_tests/dasha.py
branches/frame_order_testing/test_suite/system_tests/diffusion_tensor.py
branches/frame_order_testing/test_suite/system_tests/frame_order.py
branches/frame_order_testing/test_suite/system_tests/generic.py
branches/frame_order_testing/test_suite/system_tests/grace.py
branches/frame_order_testing/test_suite/system_tests/interatomic.py
branches/frame_order_testing/test_suite/system_tests/jw_mapping.py
branches/frame_order_testing/test_suite/system_tests/load_spins.py
branches/frame_order_testing/test_suite/system_tests/model_elimination.py
branches/frame_order_testing/test_suite/system_tests/model_free.py
branches/frame_order_testing/test_suite/system_tests/model_selection.py
branches/frame_order_testing/test_suite/system_tests/mol_res_spin.py
branches/frame_order_testing/test_suite/system_tests/n_state_model.py
branches/frame_order_testing/test_suite/system_tests/noe.py
branches/frame_order_testing/test_suite/system_tests/noe_restraints.py
branches/frame_order_testing/test_suite/system_tests/palmer.py
branches/frame_order_testing/test_suite/system_tests/peak_lists.py
branches/frame_order_testing/test_suite/system_tests/pipes.py
branches/frame_order_testing/test_suite/system_tests/rdc.py
branches/frame_order_testing/test_suite/system_tests/relax_data.py
branches/frame_order_testing/test_suite/system_tests/relax_fit.py
branches/frame_order_testing/test_suite/system_tests/results.py
branches/frame_order_testing/test_suite/system_tests/scripts/1UBQ_relax_fit.py
branches/frame_order_testing/test_suite/system_tests/scripts/bug_17276_peak_lists.py
branches/frame_order_testing/test_suite/system_tests/scripts/consistency_tests_calc_test.py
branches/frame_order_testing/test_suite/system_tests/scripts/curve_fitting/bug_18789_no_grace_errors.py
branches/frame_order_testing/test_suite/system_tests/scripts/curve_fitting/bug_19887_curvefit_fail.py
branches/frame_order_testing/test_suite/system_tests/scripts/jw_mapping_calc_test.py
branches/frame_order_testing/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/5_state_xz.py
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/monte_carlo_testing.py
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/populations.py
branches/frame_order_testing/test_suite/system_tests/scripts/peak_lists/ccpn_analysis.py
branches/frame_order_testing/test_suite/system_tests/scripts/relax_fit.py
branches/frame_order_testing/test_suite/system_tests/sequence.py
branches/frame_order_testing/test_suite/system_tests/state.py
branches/frame_order_testing/test_suite/system_tests/structure.py
branches/frame_order_testing/test_suite/system_tests/unit_vectors.py
branches/frame_order_testing/test_suite/unit_tests/relax_data_testing_base.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_testing/docs/latex/model-free.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/docs/latex/model-free.tex?rev=17831&r1=17830&r2=17831&view=diff
Modified:
branches/frame_order_testing/extern/scientific_python/Geometry/VectorModule.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/extern/scientific_python/Geometry/VectorModule.py?rev=17831&r1=17830&r2=17831&view=diff
Modified:
branches/frame_order_testing/extern/scientific_python/Geometry/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/extern/scientific_python/Geometry/__init__.py?rev=17831&r1=17830&r2=17831&view=diff
Modified:
branches/frame_order_testing/extern/scientific_python/IO/FortranFormat.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/extern/scientific_python/IO/FortranFormat.py?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/extern/scientific_python/IO/PDB.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/extern/scientific_python/IO/PDB.py?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/generic_fns/bruker.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/bruker.py?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/mol_res_spin.py?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/relax_data.py?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/gui/analyses/auto_model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/gui/analyses/auto_model_free.py?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/gui/export_bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/gui/export_bmrb.py?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/gui/input_elements/spin_id.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/gui/input_elements/spin_id.py?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/specific_fns/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/api_base.py?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/specific_fns/api_common.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/api_common.py?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/consistency_tests.py?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/jw_mapping.py?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/specific_fns/model_free/macro_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/model_free/macro_base.py?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/model_free/main.py?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/specific_fns/noe/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/noe/main.py?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/relax_fit.py?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/test_suite/gui_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/gui_tests/model_free.py?rev=17831&r1=17830&r2=17831&view=diff
Modified:
branches/frame_order_testing/test_suite/shared_data/model_free/sphere/create_ri.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/model_free/sphere/create_ri.py?rev=17831&r1=17830&r2=17831&view=diff
Modified:
branches/frame_order_testing/test_suite/shared_data/model_free/sphere/create_sphere.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/model_free/sphere/create_sphere.py?rev=17831&r1=17830&r2=17831&view=diff
Modified:
branches/frame_order_testing/test_suite/shared_data/model_free/sphere/noe.500.out
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/model_free/sphere/noe.500.out?rev=17831&r1=17830&r2=17831&view=diff
Modified:
branches/frame_order_testing/test_suite/shared_data/model_free/sphere/noe.900.out
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/model_free/sphere/noe.900.out?rev=17831&r1=17830&r2=17831&view=diff
Modified:
branches/frame_order_testing/test_suite/shared_data/model_free/sphere/r1.500.out
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/model_free/sphere/r1.500.out?rev=17831&r1=17830&r2=17831&view=diff
Modified:
branches/frame_order_testing/test_suite/shared_data/model_free/sphere/r1.900.out
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/model_free/sphere/r1.900.out?rev=17831&r1=17830&r2=17831&view=diff
Modified:
branches/frame_order_testing/test_suite/shared_data/model_free/sphere/r2.500.out
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/model_free/sphere/r2.500.out?rev=17831&r1=17830&r2=17831&view=diff
Modified:
branches/frame_order_testing/test_suite/shared_data/model_free/sphere/r2.900.out
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/model_free/sphere/r2.900.out?rev=17831&r1=17830&r2=17831&view=diff
Modified:
branches/frame_order_testing/test_suite/shared_data/model_free/sphere/sphere.pdb
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/model_free/sphere/sphere.pdb?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/test_suite/system_tests/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/__init__.py?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/test_suite/system_tests/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/align_tensor.py?rev=17831&r1=17830&r2=17831&view=diff
Modified: branches/frame_order_testing/test_suite/system_tests/angles.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/angles.py?rev=17831&r1=17830&r2=17831&view=diff
[... 135 lines stripped ...]
r17831 - in /branches/frame_order_testing: ./ docs/latex/ extern/scientific_python/Geometry/ extern/scientific_python/IO/ ge...