Author: bugman
Date: Fri Jan 20 11:31:09 2012
New Revision: 15198
URL: http://svn.gna.org/viewcvs/relax?rev=15198&view=rev
Log:
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.
Modified:
branches/spec_api/auto_analyses/dauvergne_protocol.py
branches/spec_api/auto_analyses/stereochem_analysis.py
branches/spec_api/data/mol_res_spin.py
branches/spec_api/generic_fns/dasha.py
branches/spec_api/generic_fns/diffusion_tensor.py
branches/spec_api/generic_fns/grace.py
branches/spec_api/generic_fns/minimise.py
branches/spec_api/generic_fns/palmer.py
branches/spec_api/generic_fns/pdc.py
branches/spec_api/gui/user_functions/molmol.py
branches/spec_api/gui/user_functions/pymol.py
branches/spec_api/maths_fns/mf.py
branches/spec_api/opendx/base_map.py
branches/spec_api/prompt/dx.py
branches/spec_api/prompt/grace.py
branches/spec_api/prompt/model_free.py
branches/spec_api/prompt/molmol.py
branches/spec_api/prompt/pymol_control.py
branches/spec_api/prompt/value.py
branches/spec_api/sample_scripts/consistency_tests.py
branches/spec_api/sample_scripts/generate_ri.py
branches/spec_api/sample_scripts/jw_mapping.py
branches/spec_api/sample_scripts/model_free/cv.py
branches/spec_api/sample_scripts/model_free/dasha.py
branches/spec_api/sample_scripts/model_free/dauvergne_protocol.py
branches/spec_api/sample_scripts/model_free/diff_min.py
branches/spec_api/sample_scripts/model_free/map.py
branches/spec_api/sample_scripts/model_free/mf_multimodel.py
branches/spec_api/sample_scripts/model_free/molmol_plot.py
branches/spec_api/sample_scripts/model_free/palmer.py
branches/spec_api/sample_scripts/model_free/remap.py
branches/spec_api/sample_scripts/model_free/single_model.py
branches/spec_api/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py
branches/spec_api/specific_fns/model_free/__init__.py
branches/spec_api/specific_fns/model_free/bmrb.py
branches/spec_api/specific_fns/model_free/macro_base.py
branches/spec_api/specific_fns/model_free/main.py
branches/spec_api/specific_fns/model_free/mf_minimise.py
branches/spec_api/specific_fns/model_free/results.py
branches/spec_api/specific_fns/n_state_model.py
branches/spec_api/test_suite/gui_tests/model_free.py
branches/spec_api/test_suite/shared_data/frame_order/free_rotor/back_calc.py
branches/spec_api/test_suite/shared_data/frame_order/free_rotor/tensor_fit.py
branches/spec_api/test_suite/shared_data/frame_order/free_rotor2/back_calc.py
branches/spec_api/test_suite/shared_data/frame_order/free_rotor2/tensor_fit.py
branches/spec_api/test_suite/shared_data/frame_order/iso_cone_free_rotor/back_calc.py
branches/spec_api/test_suite/shared_data/frame_order/iso_cone_free_rotor/tensor_fit.py
branches/spec_api/test_suite/shared_data/frame_order/iso_cone_free_rotor2/back_calc.py
branches/spec_api/test_suite/shared_data/frame_order/iso_cone_free_rotor2/tensor_fit.py
branches/spec_api/test_suite/shared_data/frame_order/rigid/back_calc.py
branches/spec_api/test_suite/shared_data/frame_order/rigid/tensor_fit.py
branches/spec_api/test_suite/shared_data/frame_order/rotor/back_calc.py
branches/spec_api/test_suite/shared_data/frame_order/rotor/tensor_fit.py
branches/spec_api/test_suite/shared_data/frame_order/rotor2/back_calc.py
branches/spec_api/test_suite/shared_data/frame_order/rotor2/tensor_fit.py
branches/spec_api/test_suite/shared_data/frame_order/rotor_2_state/back_calc.py
branches/spec_api/test_suite/shared_data/frame_order/rotor_2_state/tensor_fit.py
branches/spec_api/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3.bz2
branches/spec_api/test_suite/shared_data/model_free/sphere/create_ri.py
branches/spec_api/test_suite/system_tests/dasha.py
branches/spec_api/test_suite/system_tests/generic.py
branches/spec_api/test_suite/system_tests/model_free.py
branches/spec_api/test_suite/system_tests/palmer.py
branches/spec_api/test_suite/system_tests/scripts/dasha.py
branches/spec_api/test_suite/system_tests/scripts/diff_tensor/ri_back_calc.py
branches/spec_api/test_suite/system_tests/scripts/diff_tensor/tensor_opt.py
branches/spec_api/test_suite/system_tests/scripts/model_free/bug_15050.py
branches/spec_api/test_suite/system_tests/scripts/model_free/bug_18790_negative_error.py
branches/spec_api/test_suite/system_tests/scripts/model_free/bugs_12582_12591_12607.py
branches/spec_api/test_suite/system_tests/scripts/model_free/create_m4.py
branches/spec_api/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
branches/spec_api/test_suite/system_tests/scripts/model_free/generate_ri.py
branches/spec_api/test_suite/system_tests/scripts/model_free/omp_model_free.py
branches/spec_api/test_suite/system_tests/scripts/model_free/opendx_s2_te_rex.py
branches/spec_api/test_suite/system_tests/scripts/model_free/opt_setup_S2_0_970_te_2048_Rex_0_149.py
branches/spec_api/test_suite/system_tests/scripts/model_free/opt_setup_local_tm_10_S2_0_8_te_40.py
branches/spec_api/test_suite/system_tests/scripts/model_free/opt_tm_fns.py
branches/spec_api/test_suite/system_tests/scripts/n_state_model/align_fit.py
branches/spec_api/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
branches/spec_api/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
branches/spec_api/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
branches/spec_api/test_suite/system_tests/scripts/n_state_model/monte_carlo_testing.py
branches/spec_api/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py
branches/spec_api/test_suite/system_tests/scripts/n_state_model/pcs_to_rdc.py
branches/spec_api/test_suite/system_tests/scripts/n_state_model/populations.py
branches/spec_api/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py
branches/spec_api/test_suite/system_tests/scripts/palmer.py
branches/spec_api/test_suite/system_tests/scripts/palmer_omp.py
branches/spec_api/test_suite/unit_tests/_generic_fns/test_value.py
branches/spec_api/test_suite/unit_tests/_prompt/test_value.py
branches/spec_api/test_suite/unit_tests/value_testing_base.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/spec_api/auto_analyses/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/auto_analyses/dauvergne_protocol.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/auto_analyses/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/auto_analyses/stereochem_analysis.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/data/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/data/mol_res_spin.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/generic_fns/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/generic_fns/dasha.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/generic_fns/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/generic_fns/diffusion_tensor.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/generic_fns/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/generic_fns/grace.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/generic_fns/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/generic_fns/minimise.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/generic_fns/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/generic_fns/palmer.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/generic_fns/pdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/generic_fns/pdc.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/gui/user_functions/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/gui/user_functions/molmol.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/gui/user_functions/pymol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/gui/user_functions/pymol.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/maths_fns/mf.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/maths_fns/mf.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/opendx/base_map.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/opendx/base_map.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/prompt/dx.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/prompt/dx.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/prompt/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/prompt/grace.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/prompt/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/prompt/model_free.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/prompt/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/prompt/molmol.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/prompt/pymol_control.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/prompt/pymol_control.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/prompt/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/prompt/value.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/sample_scripts/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/sample_scripts/consistency_tests.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/sample_scripts/generate_ri.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/sample_scripts/generate_ri.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/sample_scripts/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/sample_scripts/jw_mapping.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/sample_scripts/model_free/cv.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/sample_scripts/model_free/cv.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/sample_scripts/model_free/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/sample_scripts/model_free/dasha.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/sample_scripts/model_free/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/sample_scripts/model_free/dauvergne_protocol.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/sample_scripts/model_free/diff_min.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/sample_scripts/model_free/diff_min.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/sample_scripts/model_free/map.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/sample_scripts/model_free/map.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/sample_scripts/model_free/mf_multimodel.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/sample_scripts/model_free/mf_multimodel.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/sample_scripts/model_free/molmol_plot.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/sample_scripts/model_free/molmol_plot.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/sample_scripts/model_free/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/sample_scripts/model_free/palmer.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/sample_scripts/model_free/remap.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/sample_scripts/model_free/remap.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/sample_scripts/model_free/single_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/sample_scripts/model_free/single_model.py?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/sample_scripts/n_state_model/conformation_analysis_rdc+pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/sample_scripts/n_state_model/conformation_analysis_rdc%2Bpcs.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/specific_fns/model_free/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/specific_fns/model_free/__init__.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/specific_fns/model_free/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/specific_fns/model_free/bmrb.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/specific_fns/model_free/macro_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/specific_fns/model_free/macro_base.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/specific_fns/model_free/main.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/specific_fns/model_free/mf_minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/specific_fns/model_free/mf_minimise.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/specific_fns/model_free/results.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/specific_fns/model_free/results.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/specific_fns/n_state_model.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/test_suite/gui_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/gui_tests/model_free.py?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/test_suite/shared_data/frame_order/free_rotor/back_calc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/shared_data/frame_order/free_rotor/back_calc.py?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/test_suite/shared_data/frame_order/free_rotor/tensor_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/shared_data/frame_order/free_rotor/tensor_fit.py?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/test_suite/shared_data/frame_order/free_rotor2/back_calc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/shared_data/frame_order/free_rotor2/back_calc.py?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/test_suite/shared_data/frame_order/free_rotor2/tensor_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/shared_data/frame_order/free_rotor2/tensor_fit.py?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/test_suite/shared_data/frame_order/iso_cone_free_rotor/back_calc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/shared_data/frame_order/iso_cone_free_rotor/back_calc.py?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/test_suite/shared_data/frame_order/iso_cone_free_rotor/tensor_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/shared_data/frame_order/iso_cone_free_rotor/tensor_fit.py?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/test_suite/shared_data/frame_order/iso_cone_free_rotor2/back_calc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/shared_data/frame_order/iso_cone_free_rotor2/back_calc.py?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/test_suite/shared_data/frame_order/iso_cone_free_rotor2/tensor_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/shared_data/frame_order/iso_cone_free_rotor2/tensor_fit.py?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/test_suite/shared_data/frame_order/rigid/back_calc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/shared_data/frame_order/rigid/back_calc.py?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/test_suite/shared_data/frame_order/rigid/tensor_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/shared_data/frame_order/rigid/tensor_fit.py?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/test_suite/shared_data/frame_order/rotor/back_calc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/shared_data/frame_order/rotor/back_calc.py?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/test_suite/shared_data/frame_order/rotor/tensor_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/shared_data/frame_order/rotor/tensor_fit.py?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/test_suite/shared_data/frame_order/rotor2/back_calc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/shared_data/frame_order/rotor2/back_calc.py?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/test_suite/shared_data/frame_order/rotor2/tensor_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/shared_data/frame_order/rotor2/tensor_fit.py?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/test_suite/shared_data/frame_order/rotor_2_state/back_calc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/shared_data/frame_order/rotor_2_state/back_calc.py?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/test_suite/shared_data/frame_order/rotor_2_state/tensor_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/shared_data/frame_order/rotor_2_state/tensor_fit.py?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3.bz2?rev=15198&r1=15197&r2=15198&view=diff
Modified:
branches/spec_api/test_suite/shared_data/model_free/sphere/create_ri.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/shared_data/model_free/sphere/create_ri.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/test_suite/system_tests/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/system_tests/dasha.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/test_suite/system_tests/generic.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/system_tests/generic.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/system_tests/model_free.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/test_suite/system_tests/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/system_tests/palmer.py?rev=15198&r1=15197&r2=15198&view=diff
Modified: branches/spec_api/test_suite/system_tests/scripts/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/spec_api/test_suite/system_tests/scripts/dasha.py?rev=15198&r1=15197&r2=15198&view=diff
[... 81 lines stripped ...]
r15198 - in /branches/spec_api: auto_analyses/ data/ generic_fns/ gui/user_functions/ maths_fns/ opendx/ prompt/ sample_scri...