Author: bugman
Date: Wed Jul 4 12:50:18 2012
New Revision: 17199
URL: http://svn.gna.org/viewcvs/relax?rev=17199&view=rev
Log:
Merged revisions 16851,16856-16857,17187-17193,17195-17196 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/absolute_rdc
........
r16851 | bugman | 2012-06-11 20:13:41 +0200 (Mon, 11 Jun 2012) | 5 lines
Added the 'absolute' keyword arg to the rdc.read user function definition.
This will be used to mark RDCs as being unsigned.
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r16856 | bugman | 2012-06-11 20:21:58 +0200 (Mon, 11 Jun 2012) | 3 lines
Created an initial system (and GUI) test for the absolute RDC concept.
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r16857 | bugman | 2012-06-11 20:23:02 +0200 (Mon, 11 Jun 2012) | 3 lines
Added the script for the system test of the last commit (r16856).
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r17187 | bugman | 2012-07-04 11:18:32 +0200 (Wed, 04 Jul 2012) | 5 lines
The rdc.read user function backend now accepts the 'absolute' argument.
This is used to signal that the RDCs are signless absolute values.
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r17188 | bugman | 2012-07-04 11:19:23 +0200 (Wed, 04 Jul 2012) | 3 lines
Created an absolute value version of the synthetic CaM RDC file for the
test suite.
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r17189 | bugman | 2012-07-04 11:34:20 +0200 (Wed, 04 Jul 2012) | 3 lines
Whitespace fix.
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r17190 | bugman | 2012-07-04 11:34:43 +0200 (Wed, 04 Jul 2012) | 3 lines
Converted the N-state model absolute_rdcs.py system test script to the
interatomic data design.
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r17191 | bugman | 2012-07-04 11:56:28 +0200 (Wed, 04 Jul 2012) | 3 lines
The rdc.read user function backend is now storing the absolute value flag
in interatom.absolute_rdc.
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r17192 | bugman | 2012-07-04 11:58:44 +0200 (Wed, 04 Jul 2012) | 6 lines
Added support for the absolute or signless RDCs to the N-state model.
This simply propagates the absolute flags into the maths_fns.rdc module
functions whereby the
absolute RDC values and gradients can be returned.
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r17193 | bugman | 2012-07-04 12:04:51 +0200 (Wed, 04 Jul 2012) | 9 lines
Fix for the absolute_rdcs.py system test script.
The signed and signless data are now loaded using the same alignment ID. A
single RDC has been
removed from the test_suite/shared_data/align_data/CaM/synth_rdc_abs RDC
file which is negative in
the corresponding synth_rdc file. The signed RDCs are first loaded
followed by the signless RDCs
which overwrite the original RDCs - all except for the single negative
value with the absolute flag
turned off. The single negative RDC allows the tensor negative and
positive lobes to be defined.
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r17195 | bugman | 2012-07-04 12:24:44 +0200 (Wed, 04 Jul 2012) | 5 lines
Bug fix for the N_state_model _target_fn_setup() method for the
absolute_rdc data structure.
This needs to be initialised to None for any analysis which doesn't include
RDC data.
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r17196 | bugman | 2012-07-04 12:27:21 +0200 (Wed, 04 Jul 2012) | 6 lines
Bug fix for the N-state model _minimise_setup_rdcs() method for when the
RDC data is incomplete.
The set up of the absolute RDC flag data structure can no handle the
absence of the flag for certain
interatomic data containers or alignments.
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Added:
trunk/test_suite/shared_data/align_data/CaM/synth_rdc_abs
- copied unchanged from r17196,
branches/absolute_rdc/test_suite/shared_data/align_data/CaM/synth_rdc_abs
trunk/test_suite/system_tests/scripts/n_state_model/absolute_rdcs.py
- copied, changed from r16857,
branches/absolute_rdc/test_suite/system_tests/scripts/n_state_model/absolute_rdcs.py
Modified:
trunk/ (props changed)
trunk/generic_fns/rdc.py
trunk/maths_fns/n_state_model.py
trunk/maths_fns/rdc.py
trunk/specific_fns/n_state_model.py
trunk/test_suite/system_tests/n_state_model.py
trunk/user_functions/rdc.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/rdc.py?rev=17199&r1=17198&r2=17199&view=diff
Modified: trunk/maths_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/maths_fns/n_state_model.py?rev=17199&r1=17198&r2=17199&view=diff
Modified: trunk/maths_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/maths_fns/rdc.py?rev=17199&r1=17198&r2=17199&view=diff
Modified: trunk/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_fns/n_state_model.py?rev=17199&r1=17198&r2=17199&view=diff
Modified: trunk/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/n_state_model.py?rev=17199&r1=17198&r2=17199&view=diff
Copied: trunk/test_suite/system_tests/scripts/n_state_model/absolute_rdcs.py
(from r16857,
branches/absolute_rdc/test_suite/system_tests/scripts/n_state_model/absolute_rdcs.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/n_state_model/absolute_rdcs.py?p2=trunk/test_suite/system_tests/scripts/n_state_model/absolute_rdcs.py&p1=branches/absolute_rdc/test_suite/system_tests/scripts/n_state_model/absolute_rdcs.py&r1=16857&r2=17199&rev=17199&view=diff
Modified: trunk/user_functions/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/rdc.py?rev=17199&r1=17198&r2=17199&view=diff
r17199 - in /trunk: ./ generic_fns/ maths_fns/ specific_fns/ test_suite/shared_data/align_data/CaM/ test_suite/system_tests/...