Author: michaelbieri
Date: Mon May 10 05:14:24 2010
New Revision: 11177
URL: http://svn.gna.org/viewcvs/relax?rev=11177&view=rev
Log:
Merged revisions 11144-11175 via svnmerge from
svn+ssh://michaelbieri@xxxxxxxxxxx/svn/relax/1.3
........
r11144 | bugman | 2010-04-28 00:04:51 +1000 (Wed, 28 Apr 2010) | 6 lines
Created some test RDC and PCS data to test the handling of missing data.
This includes entire data sets missing, spins missing from one type of
data, and individual spins
missing.
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r11145 | bugman | 2010-04-28 00:08:02 +1000 (Wed, 28 Apr 2010) | 5 lines
Wrote a script for testing the missing RDC and PCS data.
This uses the N-state model with N=1, so direct testing of the single state
to 4 tensors.
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r11146 | bugman | 2010-04-28 00:17:54 +1000 (Wed, 28 Apr 2010) | 5 lines
Created the test_missing_data N-state model system test.
This should pull out a few hard to find bugs.
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r11147 | bugman | 2010-04-28 00:20:11 +1000 (Wed, 28 Apr 2010) | 5 lines
Loosened a value check in the test_pcs_fit_zero_pos N-state model system
test.
This was sometimes failing, but the value was correct enough.
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r11148 | bugman | 2010-04-28 00:22:01 +1000 (Wed, 28 Apr 2010) | 5 lines
Created a truncated version of the LE.pdb file for the RDC and PCS system
tests.
This contains just the atoms for PCS and RDCs, and will significantly speed
up the tests.
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r11149 | bugman | 2010-04-28 01:05:09 +1000 (Wed, 28 Apr 2010) | 5 lines
Modified the dna_pcs_fit.py N-state model system test script to use the
truncated PDB file.
This speeds the system test up by orders of magnitude.
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r11150 | bugman | 2010-04-28 01:30:47 +1000 (Wed, 28 Apr 2010) | 3 lines
Fixes for the structure.load_spins() user function docstring for RNA/DNA
work.
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r11151 | bugman | 2010-04-28 01:35:45 +1000 (Wed, 28 Apr 2010) | 3 lines
Removed a debugging print statement.
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r11152 | bugman | 2010-04-28 01:45:01 +1000 (Wed, 28 Apr 2010) | 6 lines
Bug fix for the __det_pdb_element() method.
RNA PDB files with missing element information is now handled properly.
The stripping of the "'"
was being ignored.
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r11153 | bugman | 2010-04-28 01:55:04 +1000 (Wed, 28 Apr 2010) | 7 lines
Big bug fixes for the _minimise_setup_pcs() and _minimise_setup_rdcs()
methods.
This allows the missing data PCS and RDC optimisation system test to pass.
Many problems were
solved to allow all types of data with anything missing (one spin in one
alignment, one spin in all
RDC or all PCS lists, or entire RDC or PCS lists for one alignment).
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r11154 | bugman | 2010-04-28 01:58:00 +1000 (Wed, 28 Apr 2010) | 7 lines
The n_state_model.select_model() user function can now change the model.
Previously a RelaxError was thrown, but now a warning is given that the
model is changing. This
allows the 'population' N-state model to be optimised by first optimising
the 'fixed' model and then
switching to 'population'.
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r11155 | bugman | 2010-04-28 01:59:14 +1000 (Wed, 28 Apr 2010) | 3 lines
Fixed the Q-factor calculating functions to handle missing RDC or PCS lists.
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r11156 | bugman | 2010-04-28 02:03:40 +1000 (Wed, 28 Apr 2010) | 5 lines
Forked the test_lactose_n_state() system test for both the 'population' and
'fixed' models.
The 2 new system tests are test_lactose_n_state_fixed() and
test_lactose_n_state_population().
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r11157 | bugman | 2010-04-28 02:15:55 +1000 (Wed, 28 Apr 2010) | 6 lines
Implemented dfunc_tensor_opt() and d2func_tensor_opt() allowing all
optimisation algorithms to be used.
The 'fixed' N-state model can now be optimised using Newton optimisation.
On my machine, the
performance vs. Nelder-Mead simplex for ~20 states is a drop from ~1 hour
to less than one minute!
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r11158 | bugman | 2010-04-28 02:39:26 +1000 (Wed, 28 Apr 2010) | 6 lines
Created a system test for the 'population' N-state model with missing data.
This should thoroughly test out this model! First the 'fixed' model is
optimised, and then the
'population' model optimised from that starting point. This is to keep the
test fast.
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r11159 | bugman | 2010-04-28 02:51:21 +1000 (Wed, 28 Apr 2010) | 3 lines
Modified the RDC and PCS read() function to not add align_id to the cdp
structures if no data is present.
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r11160 | bugman | 2010-04-28 02:57:55 +1000 (Wed, 28 Apr 2010) | 5 lines
Removed the calls to rdc.display() and pcs.display().
These were rightfully failing for the empty data lists, so should not be
tested.
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r11161 | bugman | 2010-04-28 04:11:41 +1000 (Wed, 28 Apr 2010) | 3 lines
Added the pymol_macro method to the specific object API.
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r11162 | bugman | 2010-04-28 19:26:03 +1000 (Wed, 28 Apr 2010) | 5 lines
The weights of each state are now set to equal probability prior to the
'population' opt.
This is in the 'population' N-state model system test script.
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r11163 | bugman | 2010-04-29 00:35:26 +1000 (Thu, 29 Apr 2010) | 6 lines
Huge bug fix for the 'population' N-state model.
The probabilities of each state was being set to that of the last state.
This is fatal for this
model. Earlier code did not have this problem, but it is unknown when this
bug was introduced.
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r11164 | bugman | 2010-04-29 01:04:06 +1000 (Thu, 29 Apr 2010) | 5 lines
Fix for the _update_model() method for handling missing RDC and PCS data.
The alignment tensor initialisation order was being mixed up!
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r11165 | bugman | 2010-04-29 01:50:40 +1000 (Thu, 29 Apr 2010) | 6 lines
Another fix for _update_model().
This was introduced in the last change. The alignment tensors are only
updated if alignment data
is loaded.
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r11166 | bugman | 2010-04-29 02:53:08 +1000 (Thu, 29 Apr 2010) | 5 lines
Another fix for the huge bug identified in r11163.
This is for the PCS part - this was also using equal weights for all states
set to pN!
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r11167 | bugman | 2010-04-29 03:48:53 +1000 (Thu, 29 Apr 2010) | 5 lines
Bug fix for the 'population' N-state model optimisation.
Constraints must be used at all times for this to work!!!
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r11168 | bugman | 2010-04-29 22:52:20 +1000 (Thu, 29 Apr 2010) | 7 lines
Bug fix for the N-state model 'fixed' and 'population' models.
If too many tensors are initialised in comparison to PCS and RDC
alignments, then the parameter
vector or parameter number was not being correctly assembled. The
cdp.align_ids is now being used
to validate all setups.
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r11169 | bugman | 2010-04-29 23:38:02 +1000 (Thu, 29 Apr 2010) | 3 lines
Updated and corrected all the Hessian method docstrings.
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r11170 | bugman | 2010-04-30 03:00:51 +1000 (Fri, 30 Apr 2010) | 5 lines
Created the d2func_population() Hessian target function for the N-state
model.
This may either be buggy or too sparse to run Newton optimisation well!
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r11171 | bugman | 2010-04-30 03:06:52 +1000 (Fri, 30 Apr 2010) | 3 lines
Updates to the 'population' N-state model system test script.
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r11172 | bugman | 2010-05-03 08:52:26 +1000 (Mon, 03 May 2010) | 7 lines
Bug fix for when structural models are loaded out of order.
Now the API generator method model_loop() is being used by the scientific
python and internal
structural objects. The bond vectors and atomic positions are now loaded
into the spin containers
in correct numerical model order.
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r11173 | bugman | 2010-05-03 08:54:06 +1000 (Mon, 03 May 2010) | 5 lines
Added 3 system tests for the correct loading of XH bond vectors into the
spin containers.
This catches the previously fixed model looping bug.
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r11174 | bugman | 2010-05-03 08:57:22 +1000 (Mon, 03 May 2010) | 7 lines
Bug fix for a very long standing bug!
This is the 'population' N-state model bug whereby the last probability,
which is not a parameter,
has a negative value. The constraint was not being scaled! So the
constraint was actually a
probability 0 <= pN <= 100!!!
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r11175 | bugman | 2010-05-03 09:05:30 +1000 (Mon, 03 May 2010) | 3 lines
Shorted the 'population' N-state model system test and randomise the model
loading order.
........
Added:
branches/bieri_gui/test_suite/shared_data/align_data/missing_data/
- copied from r11175,
1.3/test_suite/shared_data/align_data/missing_data/
branches/bieri_gui/test_suite/shared_data/align_data/population_model/
- copied from r11175,
1.3/test_suite/shared_data/align_data/population_model/
branches/bieri_gui/test_suite/shared_data/structures/dna/LE_trunc.pdb
- copied unchanged from r11175,
1.3/test_suite/shared_data/structures/dna/LE_trunc.pdb
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
- copied unchanged from r11175,
1.3/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/populations.py
- copied unchanged from r11175,
1.3/test_suite/system_tests/scripts/n_state_model/populations.py
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/vector_loading.py
- copied unchanged from r11175,
1.3/test_suite/system_tests/scripts/n_state_model/vector_loading.py
Modified:
branches/bieri_gui/ (props changed)
branches/bieri_gui/generic_fns/pcs.py
branches/bieri_gui/generic_fns/rdc.py
branches/bieri_gui/generic_fns/structure/api_base.py
branches/bieri_gui/generic_fns/structure/cones.py
branches/bieri_gui/generic_fns/structure/internal.py
branches/bieri_gui/generic_fns/structure/scientific.py
branches/bieri_gui/maths_fns/n_state_model.py
branches/bieri_gui/maths_fns/pcs.py
branches/bieri_gui/maths_fns/rdc.py
branches/bieri_gui/prompt/structure.py
branches/bieri_gui/specific_fns/n_state_model.py
branches/bieri_gui/specific_fns/setup.py
branches/bieri_gui/test_suite/system_tests/n_state_model.py
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/dna_pcs_fit.py
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/bieri_gui/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/pcs.py?rev=11177&r1=11176&r2=11177&view=diff
Modified: branches/bieri_gui/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/rdc.py?rev=11177&r1=11176&r2=11177&view=diff
Modified: branches/bieri_gui/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/structure/api_base.py?rev=11177&r1=11176&r2=11177&view=diff
Modified: branches/bieri_gui/generic_fns/structure/cones.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/structure/cones.py?rev=11177&r1=11176&r2=11177&view=diff
Modified: branches/bieri_gui/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/structure/internal.py?rev=11177&r1=11176&r2=11177&view=diff
Modified: branches/bieri_gui/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/structure/scientific.py?rev=11177&r1=11176&r2=11177&view=diff
Modified: branches/bieri_gui/maths_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/maths_fns/n_state_model.py?rev=11177&r1=11176&r2=11177&view=diff
Modified: branches/bieri_gui/maths_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/maths_fns/pcs.py?rev=11177&r1=11176&r2=11177&view=diff
Modified: branches/bieri_gui/maths_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/maths_fns/rdc.py?rev=11177&r1=11176&r2=11177&view=diff
Modified: branches/bieri_gui/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/prompt/structure.py?rev=11177&r1=11176&r2=11177&view=diff
Modified: branches/bieri_gui/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/specific_fns/n_state_model.py?rev=11177&r1=11176&r2=11177&view=diff
Modified: branches/bieri_gui/specific_fns/setup.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/specific_fns/setup.py?rev=11177&r1=11176&r2=11177&view=diff
Modified: branches/bieri_gui/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/n_state_model.py?rev=11177&r1=11176&r2=11177&view=diff
Modified:
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/dna_pcs_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/dna_pcs_fit.py?rev=11177&r1=11176&r2=11177&view=diff
Modified:
branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py?rev=11177&r1=11176&r2=11177&view=diff
r11177 - in /branches/bieri_gui: ./ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ specific_fns/ test_suite/shared_d...