Author: semor
Date: Fri Jul 22 11:55:52 2011
New Revision: 13824
URL: http://svn.gna.org/viewcvs/relax?rev=13824&view=rev
Log:
Merged revisions
13153,13258,13357-13359,13411,13510-13512,13577,13631-13632,13641,13655,13660,13683,13686,13706,13742-13743,13748-13749,13780
via svnmerge from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.3
........
r13153 | bugman | 2011-06-21 19:18:15 +0200 (Tue, 21 Jun 2011) | 5 lines
Removed a test for the sequence in the user function
structure.create_diff_tensor_pdb() backend.
The sequence data is not needed for this.
........
r13258 | bugman | 2011-06-28 12:37:30 +0200 (Tue, 28 Jun 2011) | 6 lines
Bug fix for the NOE auto-analysis - the column numbers for the deselected
spins file are now assumed.
The residue number is assumed to be in the first column. This is a hack
until the spin selection
part is better designed.
........
r13357 | bugman | 2011-07-01 13:33:41 +0200 (Fri, 01 Jul 2011) | 3 lines
Added support for old save files in the Peak_intensity.sync_ds() method.
........
r13358 | bugman | 2011-07-01 13:35:09 +0200 (Fri, 01 Jul 2011) | 6 lines
Fix for the bug reported as sr #2764
(https://gna.org/support/index.php?2764).
The problem was that the sequence file is now in the variable sequence_file.
........
r13359 | bugman | 2011-07-01 13:36:36 +0200 (Fri, 01 Jul 2011) | 5 lines
Another fix for the bug of sr #2764 (https://gna.org/support/?2764).
The sequence file variable is in self.data!!!
........
r13411 | michaelbieri | 2011-07-04 01:15:43 +0200 (Mon, 04 Jul 2011) | 2
lines
Argument change_all for deselecting residues in the d'Auvergne protocol has
to be boolean.
........
r13510 | bugman | 2011-07-08 08:58:14 +0200 (Fri, 08 Jul 2011) | 3 lines
Bug fix for the sequence.read() user function - the force flag is now being
passed on.
........
r13511 | bugman | 2011-07-08 09:00:06 +0200 (Fri, 08 Jul 2011) | 5 lines
Another fix for the sequence.write() user function - the force flag is
passed to open_write_file().
This is from the relax_io.write_spin_data() function.
........
r13512 | bugman | 2011-07-08 09:01:05 +0200 (Fri, 08 Jul 2011) | 5 lines
Bug fix for the sequence.write() user function when the column separator is
not whitespace.
The column widths are no longer fixed is the separator is not whitespace.
........
r13577 | bugman | 2011-07-13 11:44:38 +0200 (Wed, 13 Jul 2011) | 5 lines
Many bug fixes for the functions of the generic_fns.mol_res_spin module.
These fixes are for when a data pipe other than the current data pipe is
used.
........
r13631 | bugman | 2011-07-14 18:38:10 +0200 (Thu, 14 Jul 2011) | 5 lines
Bug fix for the relax save states - the current data pipe is now saved and
restored.
The info about the cdp was being blacklisted, so was not stored in the
relax save file.
........
r13632 | bugman | 2011-07-14 20:09:47 +0200 (Thu, 14 Jul 2011) | 7 lines
Fix for the loading of saved state files prior to r13631 - the cdp is now
set to the last pipe.
The earlier saved state files did not store the current data pipe info, so
the current data pipe was
set by default to the last data pipe. This behaviour was broken with
r13631 but is now restored for
the old state files.
........
r13641 | bugman | 2011-07-15 12:25:21 +0200 (Fri, 15 Jul 2011) | 3 lines
Fix for the new relax save state with current pipe info - the cdp ojbect is
now set after loading.
........
r13655 | bugman | 2011-07-15 16:37:34 +0200 (Fri, 15 Jul 2011) | 3 lines
Bug fix for the atomic position check in the spin.create_pseudo user
function.
........
r13660 | bugman | 2011-07-15 19:50:44 +0200 (Fri, 15 Jul 2011) | 6 lines
Bug fix for pseudo-atom support when only a single structure is loaded.
Pseudo-atom support was only working correctly for when multiple models
were loaded and atomic
positions were not averaged.
........
r13683 | bugman | 2011-07-18 14:00:29 +0200 (Mon, 18 Jul 2011) | 6 lines
Bug fix for the spectrum.read_intensities int_method argument for volumes.
Volume integration should be called 'point sum', but the back end code was
checking against the
string 'volume'.
........
r13686 | bugman | 2011-07-18 14:24:00 +0200 (Mon, 18 Jul 2011) | 3 lines
Bug fix in one of the relaxation curve-fitting system tests - 'volume'
should have been 'point sum'.
........
r13706 | bugman | 2011-07-18 20:13:04 +0200 (Mon, 18 Jul 2011) | 6 lines
Fix for the PCS back-calculation function - divide by zero is now avoided.
The PCS back-calculation function was calculating the normalised bond
vector between the lanthanide
atom and itself. The normalisation in this case is now avoided.
........
r13742 | bugman | 2011-07-19 17:02:29 +0200 (Tue, 19 Jul 2011) | 6 lines
Changed the order of some of the replicated spectra in the
test_curve_fitting_height system test.
This triggers a bug in the spectra.error_analysis user function which looks
like the replicated
spectra list is order dependent (when it shouldn't be).
........
r13743 | bugman | 2011-07-19 17:18:49 +0200 (Tue, 19 Jul 2011) | 7 lines
Bug fix for the spectrum user functions for when the ID order does not
match those loaded.
If the order of IDs sent to spectrum.replicated did not match the order
they were loaded by
spectrum.read_intensities, then the spectrum.error_analysis user function
would fail. The order is
no longer important.
........
r13748 | bugman | 2011-07-19 17:58:00 +0200 (Tue, 19 Jul 2011) | 5 lines
The relax_fit overfit_deselect() method now skips deselected spins.
This prevents unnecessary warnings about missing data for deselected spins.
........
r13749 | bugman | 2011-07-19 18:00:13 +0200 (Tue, 19 Jul 2011) | 3 lines
All of the overfit_deselect() methods now skip deselected spins, avoiding
confusing warnings.
........
r13780 | bugman | 2011-07-20 15:56:27 +0200 (Wed, 20 Jul 2011) | 6 lines
Bug fix - the pipe switching flag is now propagated all the way to the data
store add() method.
The flag was previously not sent to the method so that the creation of a
new data pipe always
resulted in a switch to that pipe. This bug is normally harmless.
........
Modified:
branches/inversion-recovery/ (props changed)
branches/inversion-recovery/auto_analyses/dauvergne_protocol.py
branches/inversion-recovery/auto_analyses/noe.py
branches/inversion-recovery/data/__init__.py
branches/inversion-recovery/generic_fns/mol_res_spin.py
branches/inversion-recovery/generic_fns/pcs.py
branches/inversion-recovery/generic_fns/pipes.py
branches/inversion-recovery/generic_fns/sequence.py
branches/inversion-recovery/generic_fns/spectrum.py
branches/inversion-recovery/generic_fns/structure/geometric.py
branches/inversion-recovery/generic_fns/structure/main.py
branches/inversion-recovery/gui/analyses/auto_rx_base.py
branches/inversion-recovery/gui/components/spectrum.py
branches/inversion-recovery/relax_io.py
branches/inversion-recovery/specific_fns/consistency_tests.py
branches/inversion-recovery/specific_fns/jw_mapping.py
branches/inversion-recovery/specific_fns/model_free/main.py
branches/inversion-recovery/specific_fns/relax_fit.py
branches/inversion-recovery/test_suite/system_tests/relax_fit.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/inversion-recovery/auto_analyses/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/auto_analyses/dauvergne_protocol.py?rev=13824&r1=13823&r2=13824&view=diff
Modified: branches/inversion-recovery/auto_analyses/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/auto_analyses/noe.py?rev=13824&r1=13823&r2=13824&view=diff
Modified: branches/inversion-recovery/data/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/data/__init__.py?rev=13824&r1=13823&r2=13824&view=diff
Modified: branches/inversion-recovery/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/generic_fns/mol_res_spin.py?rev=13824&r1=13823&r2=13824&view=diff
Modified: branches/inversion-recovery/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/generic_fns/pcs.py?rev=13824&r1=13823&r2=13824&view=diff
Modified: branches/inversion-recovery/generic_fns/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/generic_fns/pipes.py?rev=13824&r1=13823&r2=13824&view=diff
Modified: branches/inversion-recovery/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/generic_fns/sequence.py?rev=13824&r1=13823&r2=13824&view=diff
Modified: branches/inversion-recovery/generic_fns/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/generic_fns/spectrum.py?rev=13824&r1=13823&r2=13824&view=diff
Modified: branches/inversion-recovery/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/generic_fns/structure/geometric.py?rev=13824&r1=13823&r2=13824&view=diff
Modified: branches/inversion-recovery/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/generic_fns/structure/main.py?rev=13824&r1=13823&r2=13824&view=diff
Modified: branches/inversion-recovery/gui/analyses/auto_rx_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/gui/analyses/auto_rx_base.py?rev=13824&r1=13823&r2=13824&view=diff
Modified: branches/inversion-recovery/gui/components/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/gui/components/spectrum.py?rev=13824&r1=13823&r2=13824&view=diff
Modified: branches/inversion-recovery/relax_io.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/relax_io.py?rev=13824&r1=13823&r2=13824&view=diff
Modified: branches/inversion-recovery/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/specific_fns/consistency_tests.py?rev=13824&r1=13823&r2=13824&view=diff
Modified: branches/inversion-recovery/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/specific_fns/jw_mapping.py?rev=13824&r1=13823&r2=13824&view=diff
Modified: branches/inversion-recovery/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/specific_fns/model_free/main.py?rev=13824&r1=13823&r2=13824&view=diff
Modified: branches/inversion-recovery/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/specific_fns/relax_fit.py?rev=13824&r1=13823&r2=13824&view=diff
Modified: branches/inversion-recovery/test_suite/system_tests/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/test_suite/system_tests/relax_fit.py?rev=13824&r1=13823&r2=13824&view=diff
r13824 - in /branches/inversion-recovery: ./ auto_analyses/ data/ generic_fns/ generic_fns/structure/ gui/analyses/ gui/comp...