Author: bugman
Date: Fri Jan 20 14:42:30 2012
New Revision: 15206
URL: http://svn.gna.org/viewcvs/relax?rev=15206&view=rev
Log:
Merged revisions 15168-15203 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/spec_api
........
r15168 | bugman | 2012-01-18 15:17:34 +0100 (Wed, 18 Jan 2012) | 9 lines
Created a special specific API object called SPIN_PARAMS.
This will be used to handle all operations to do with model parameters.
This is initialised in the
base class, and can be set up in the specific __init__() methods. The
object Param_list has methods
for parameter initialisation (where all info is specified such as Grace
string, units, default
value, etc) and for determining if a parameter exists. More methods will
be added in the future to
expand the usability of this object and to simplify the specific API
methods.
........
r15169 | bugman | 2012-01-18 15:36:59 +0100 (Wed, 18 Jan 2012) | 3 lines
Created the Param_list.get_grace_string() method for returning the Grace
string.
........
r15170 | bugman | 2012-01-18 15:38:17 +0100 (Wed, 18 Jan 2012) | 6 lines
Some of the specific API common methods now use the new SPIN_PARAM
structure.
Some are now spin specific, and a few new spin specific methods have been
added for the specific
code to alias.
........
r15171 | bugman | 2012-01-18 15:40:06 +0100 (Wed, 18 Jan 2012) | 5 lines
Fix for the frame order analysis as one of the common API methods has been
renamed.
_return_data_name() is now _return_data_name_spin().
........
r15172 | bugman | 2012-01-18 15:40:42 +0100 (Wed, 18 Jan 2012) | 3 lines
The reduced spectral density analysis code now uses the SPIN_PARAMS API
object.
........
r15173 | bugman | 2012-01-18 16:00:27 +0100 (Wed, 18 Jan 2012) | 3 lines
Updated the consistency testing code to use the new SPIN_PARAMS specific
API structure.
........
r15174 | bugman | 2012-01-18 16:43:54 +0100 (Wed, 18 Jan 2012) | 3 lines
Created the Param_list.get_units() method for returning the units
corresponding to the parameter.
........
r15175 | bugman | 2012-01-18 16:44:42 +0100 (Wed, 18 Jan 2012) | 3 lines
The internal objects of the Param_list object are now private.
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r15176 | bugman | 2012-01-18 16:46:00 +0100 (Wed, 18 Jan 2012) | 5 lines
Created the structural API GLOBAL_PARAMS structure.
This is also based on the Param_list object and is initialised in the base
class for all analyses.
........
r15177 | bugman | 2012-01-18 17:02:34 +0100 (Wed, 18 Jan 2012) | 8 lines
Created a few additional specific API common methods.
These include:
_return_data_name()
_return_data_name_global()
_return_units_global()
........
r15178 | bugman | 2012-01-18 17:09:59 +0100 (Wed, 18 Jan 2012) | 3 lines
Started to migrate the frame order analysis to use the SPIN_PARAMS and
GLOBAL_PARAMS specific API objects.
........
r15179 | bugman | 2012-01-18 17:13:00 +0100 (Wed, 18 Jan 2012) | 5 lines
Removed the spin_id set to None check in the _set_param_values_global()
specific API common method.
This check was not functioning correctly.
........
r15180 | bugman | 2012-01-18 18:15:26 +0100 (Wed, 18 Jan 2012) | 6 lines
Removed the spin and spin_id args from the specific API return_units()
method.
This was needed for the model-free Rex parameter where the first field
strength was part of the
units. This has been replaced by the first global frequency value.
........
r15181 | bugman | 2012-01-19 09:24:04 +0100 (Thu, 19 Jan 2012) | 3 lines
Removed the spin arg from the return_data_desc() specific function API
method.
........
r15182 | bugman | 2012-01-19 09:25:04 +0100 (Thu, 19 Jan 2012) | 3 lines
Created the Param_list.get_desc() method for returning the parameter
description.
........
r15183 | bugman | 2012-01-19 09:30:22 +0100 (Thu, 19 Jan 2012) | 3 lines
Created the specific function API common method _return_data_desc_spin().
........
r15184 | bugman | 2012-01-19 09:46:45 +0100 (Thu, 19 Jan 2012) | 3 lines
The Param_list.get_desc() method now returns None rather than a RelaxError
if the param is missing.
........
r15185 | bugman | 2012-01-19 09:48:14 +0100 (Thu, 19 Jan 2012) | 3 lines
Added the 'select' and 'fixed' objects to the base SPIN_PARAM list.
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r15186 | bugman | 2012-01-19 09:48:54 +0100 (Thu, 19 Jan 2012) | 3 lines
Converted the NOE specific analysis to use the new SPIN_PARAM list API
structure.
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r15187 | bugman | 2012-01-19 10:53:32 +0100 (Thu, 19 Jan 2012) | 3 lines
The relaxation curve-fitting specific analysis now uses the new SPIN_PARAMS
list API object.
........
r15188 | bugman | 2012-01-19 11:20:08 +0100 (Thu, 19 Jan 2012) | 5 lines
Added the ability to store and return conversion factors in the Param_list
specific API object.
This includes accepting functions so that factors requiring user loaded
data can be supported.
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r15189 | bugman | 2012-01-19 11:32:54 +0100 (Thu, 19 Jan 2012) | 3 lines
Fix for the Param_list.get_conv_factor() method - the function type was not
properly handled.
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r15190 | bugman | 2012-01-19 11:33:48 +0100 (Thu, 19 Jan 2012) | 5 lines
The Param_list.get_units() method can now handle function type objects.
This is needed for the model-free Rex parameter.
........
r15191 | bugman | 2012-01-19 11:35:16 +0100 (Thu, 19 Jan 2012) | 3 lines
Created the specific function API _return_conversion_factor_spin() method.
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r15192 | bugman | 2012-01-19 11:36:30 +0100 (Thu, 19 Jan 2012) | 5 lines
Removed spin args from return_conversion_factor() and added optimisation
parameters.
The global and spin specific optimisation parameters are now set up for all
specific analyses.
........
r15193 | bugman | 2012-01-19 11:37:50 +0100 (Thu, 19 Jan 2012) | 3 lines
Fix for the initialisation of the conversion factor storage in Param_list.
........
r15194 | bugman | 2012-01-19 12:21:06 +0100 (Thu, 19 Jan 2012) | 5 lines
Fix for the specific API _return_conversion_factor_spin() method.
The wrong variable was being used.
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r15195 | bugman | 2012-01-19 13:29:47 +0100 (Thu, 19 Jan 2012) | 5 lines
Fix for the function checking in the specific API Param_list objects.
Class methods were not being detected!
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r15196 | bugman | 2012-01-19 13:58:04 +0100 (Thu, 19 Jan 2012) | 3 lines
Updated the arg_check.is_func() function for handling class methods.
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r15197 | bugman | 2012-01-19 18:06:36 +0100 (Thu, 19 Jan 2012) | 5 lines
Fix for the specific API common method _return_value_general() for when
spectrum IDs are not present.
Not sure why this change is necessary! This could introduce future bugs,
or hide a new bug!
........
r15198 | bugman | 2012-01-20 11:31:09 +0100 (Fri, 20 Jan 2012) | 15 lines
Mass conversion to the new GLOBAL_PARAMS and SPIN_PARAMS specific API data
structures.
This involves mainly the conversion of the model-free analysis to these new
objects, and the
subsequent changes to how model-free parameters are handled. The
parameters are now all lowercase,
for example ['S2', 'te', 'Rex'] is now ['s2', 'te', 'rex']. The follow
parameters are now converted
throughout relax:
'bond_length' to 'r',
'CSA' to 'csa',
'heteronucleus' to 'heteronuc_type',
'proton' to 'proton_type'.
The regularisation of the specific analysis parameters via GLOBAL_PARAMS
and SPIN_PARAMS has
significantly simplified the current code and make it much easier to
introduce new analyses.
........
r15199 | bugman | 2012-01-20 11:45:13 +0100 (Fri, 20 Jan 2012) | 3 lines
Reintroduced the specific API default_value() method to most of the
analyses.
........
r15200 | bugman | 2012-01-20 11:48:39 +0100 (Fri, 20 Jan 2012) | 3 lines
Fix for the model-free specific API default_value() method.
........
r15201 | bugman | 2012-01-20 11:52:45 +0100 (Fri, 20 Jan 2012) | 5 lines
Fix for the specific API common _default_value_spin() method.
The value is now returned!
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r15202 | bugman | 2012-01-20 12:11:59 +0100 (Fri, 20 Jan 2012) | 3 lines
Added the api_objects module to the package __all__ list.
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r15203 | bugman | 2012-01-20 13:42:50 +0100 (Fri, 20 Jan 2012) | 5 lines
Fixes for all of the value.set user function back end unit tests.
The parameter names are now regularised.
........
Added:
1.3/specific_fns/api_objects.py
- copied unchanged from r15203,
branches/spec_api/specific_fns/api_objects.py
Modified:
1.3/ (props changed)
1.3/arg_check.py
1.3/auto_analyses/dauvergne_protocol.py
1.3/auto_analyses/relax_fit.py
1.3/auto_analyses/stereochem_analysis.py
1.3/data/mol_res_spin.py
1.3/generic_fns/dasha.py
1.3/generic_fns/diffusion_tensor.py
1.3/generic_fns/grace.py
1.3/generic_fns/minimise.py
1.3/generic_fns/palmer.py
1.3/generic_fns/pdc.py
1.3/gui/user_functions/molmol.py
1.3/gui/user_functions/pymol.py
1.3/maths_fns/mf.py
1.3/opendx/base_map.py
1.3/prompt/dx.py
1.3/prompt/grace.py
1.3/prompt/model_free.py
1.3/prompt/molmol.py
1.3/prompt/pymol_control.py
1.3/prompt/value.py
1.3/sample_scripts/consistency_tests.py
1.3/sample_scripts/generate_ri.py
1.3/sample_scripts/jw_mapping.py
1.3/sample_scripts/model_free/cv.py
1.3/sample_scripts/model_free/dasha.py
1.3/sample_scripts/model_free/dauvergne_protocol.py
1.3/sample_scripts/model_free/diff_min.py
1.3/sample_scripts/model_free/map.py
1.3/sample_scripts/model_free/mf_multimodel.py
1.3/sample_scripts/model_free/molmol_plot.py
1.3/sample_scripts/model_free/palmer.py
1.3/sample_scripts/model_free/remap.py
1.3/sample_scripts/model_free/single_model.py
1.3/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py
1.3/sample_scripts/noe.py
1.3/sample_scripts/relax_fit.py
1.3/specific_fns/__init__.py
1.3/specific_fns/api_base.py
1.3/specific_fns/api_common.py
1.3/specific_fns/consistency_tests.py
1.3/specific_fns/frame_order.py
1.3/specific_fns/jw_mapping.py
1.3/specific_fns/model_free/__init__.py
1.3/specific_fns/model_free/bmrb.py
1.3/specific_fns/model_free/macro_base.py
1.3/specific_fns/model_free/main.py
1.3/specific_fns/model_free/mf_minimise.py
1.3/specific_fns/model_free/results.py
1.3/specific_fns/n_state_model.py
1.3/specific_fns/noe/__init__.py
1.3/specific_fns/noe/main.py
1.3/specific_fns/relax_fit.py
1.3/test_suite/gui_tests/model_free.py
1.3/test_suite/shared_data/frame_order/free_rotor/back_calc.py
1.3/test_suite/shared_data/frame_order/free_rotor/tensor_fit.py
1.3/test_suite/shared_data/frame_order/free_rotor2/back_calc.py
1.3/test_suite/shared_data/frame_order/free_rotor2/tensor_fit.py
1.3/test_suite/shared_data/frame_order/iso_cone_free_rotor/back_calc.py
1.3/test_suite/shared_data/frame_order/iso_cone_free_rotor/tensor_fit.py
1.3/test_suite/shared_data/frame_order/iso_cone_free_rotor2/back_calc.py
1.3/test_suite/shared_data/frame_order/iso_cone_free_rotor2/tensor_fit.py
1.3/test_suite/shared_data/frame_order/rigid/back_calc.py
1.3/test_suite/shared_data/frame_order/rigid/tensor_fit.py
1.3/test_suite/shared_data/frame_order/rotor/back_calc.py
1.3/test_suite/shared_data/frame_order/rotor/tensor_fit.py
1.3/test_suite/shared_data/frame_order/rotor2/back_calc.py
1.3/test_suite/shared_data/frame_order/rotor2/tensor_fit.py
1.3/test_suite/shared_data/frame_order/rotor_2_state/back_calc.py
1.3/test_suite/shared_data/frame_order/rotor_2_state/tensor_fit.py
1.3/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3.bz2
1.3/test_suite/shared_data/model_free/sphere/create_ri.py
1.3/test_suite/system_tests/consistency_tests.py
1.3/test_suite/system_tests/dasha.py
1.3/test_suite/system_tests/generic.py
1.3/test_suite/system_tests/jw_mapping.py
1.3/test_suite/system_tests/model_free.py
1.3/test_suite/system_tests/palmer.py
1.3/test_suite/system_tests/scripts/1UBQ_relax_fit.py
1.3/test_suite/system_tests/scripts/bug_17276_peak_lists.py
1.3/test_suite/system_tests/scripts/consistency_tests.py
1.3/test_suite/system_tests/scripts/dasha.py
1.3/test_suite/system_tests/scripts/diff_tensor/ri_back_calc.py
1.3/test_suite/system_tests/scripts/diff_tensor/tensor_opt.py
1.3/test_suite/system_tests/scripts/jw_mapping.py
1.3/test_suite/system_tests/scripts/model_free/bug_15050.py
1.3/test_suite/system_tests/scripts/model_free/bug_18790_negative_error.py
1.3/test_suite/system_tests/scripts/model_free/bugs_12582_12591_12607.py
1.3/test_suite/system_tests/scripts/model_free/create_m4.py
1.3/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
1.3/test_suite/system_tests/scripts/model_free/generate_ri.py
1.3/test_suite/system_tests/scripts/model_free/omp_model_free.py
1.3/test_suite/system_tests/scripts/model_free/opendx_s2_te_rex.py
1.3/test_suite/system_tests/scripts/model_free/opt_setup_S2_0_970_te_2048_Rex_0_149.py
1.3/test_suite/system_tests/scripts/model_free/opt_setup_local_tm_10_S2_0_8_te_40.py
1.3/test_suite/system_tests/scripts/model_free/opt_tm_fns.py
1.3/test_suite/system_tests/scripts/n_state_model/align_fit.py
1.3/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
1.3/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
1.3/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
1.3/test_suite/system_tests/scripts/n_state_model/monte_carlo_testing.py
1.3/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py
1.3/test_suite/system_tests/scripts/n_state_model/pcs_to_rdc.py
1.3/test_suite/system_tests/scripts/n_state_model/populations.py
1.3/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py
1.3/test_suite/system_tests/scripts/noe.py
1.3/test_suite/system_tests/scripts/palmer.py
1.3/test_suite/system_tests/scripts/palmer_omp.py
1.3/test_suite/system_tests/scripts/relax_fit.py
1.3/test_suite/unit_tests/_generic_fns/test_value.py
1.3/test_suite/unit_tests/_prompt/test_value.py
1.3/test_suite/unit_tests/value_testing_base.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: 1.3/arg_check.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/arg_check.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/auto_analyses/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/auto_analyses/dauvergne_protocol.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/auto_analyses/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/auto_analyses/relax_fit.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/auto_analyses/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/auto_analyses/stereochem_analysis.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/data/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/mol_res_spin.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/generic_fns/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/dasha.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/generic_fns/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/diffusion_tensor.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/generic_fns/grace.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/grace.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/generic_fns/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/minimise.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/generic_fns/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/palmer.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/generic_fns/pdc.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pdc.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/gui/user_functions/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/gui/user_functions/molmol.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/gui/user_functions/pymol.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/gui/user_functions/pymol.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/maths_fns/mf.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/maths_fns/mf.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/opendx/base_map.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/opendx/base_map.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/prompt/dx.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/dx.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/prompt/grace.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/grace.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/prompt/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/model_free.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/prompt/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/molmol.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/prompt/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/pymol_control.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/prompt/value.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/value.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/sample_scripts/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/consistency_tests.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/sample_scripts/generate_ri.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/generate_ri.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/sample_scripts/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/jw_mapping.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/sample_scripts/model_free/cv.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/model_free/cv.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/sample_scripts/model_free/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/model_free/dasha.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/sample_scripts/model_free/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/model_free/dauvergne_protocol.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/sample_scripts/model_free/diff_min.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/model_free/diff_min.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/sample_scripts/model_free/map.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/model_free/map.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/sample_scripts/model_free/mf_multimodel.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/model_free/mf_multimodel.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/sample_scripts/model_free/molmol_plot.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/model_free/molmol_plot.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/sample_scripts/model_free/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/model_free/palmer.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/sample_scripts/model_free/remap.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/model_free/remap.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/sample_scripts/model_free/single_model.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/model_free/single_model.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/n_state_model/conformation_analysis_rdc%2Bpcs.py?rev=15206&r1=15205&r2=15206&view=diff
Modified: 1.3/sample_scripts/noe.py
[... 230 lines stripped ...]
r15206 - in /1.3: ./ auto_analyses/ data/ generic_fns/ gui/user_functions/ maths_fns/ opendx/ prompt/ sample_scripts/ sample...