relax SVN archive

The ellipsoidal diff tensor check in check_ellipsoid() now functions better.

The diffusion elements are scaled down to the order of 1 so that the assertAlmostEqual() calls do
not fail with tiny machine precision differences.

The ellipsoidal diff tensor relaxation data was not fully regenerated in r11056.

The spheroid diffusion tensor optimisation test now checks the values.

The simulation of PDB coordinate truncation now occurs after vector scaling by r.

This should now be a more accurate representation and allow relax to find these values exactly.

The unit bond vectors are now normalised using the numpy.linalg.norm() function.

Fixes for the tests of the spheroid diffusion tensor.

Modified the spheroid diffusion tensor data generation so that Z is the symmetry axis.

This will allow direct mapping of Euler angles to spherical angles!

Path fix for the relax installation directory.

This corresponds to the shifting of this string into __main__.install_path at r11000 of the 1.3
line. This problem was identified by Michael Bieri at
https://mail.gna.org/public/relax-devel/2010-03/msg00060.html (Message-id:
<4BAFE29C.7090907@...>).

1.3 branch was merged into bieri_gui branch to update recent improvements.
- Diese und die folgenden Zeilen werden ignoriert --

_M .
M prompt/deselect.py
M prompt/frq.py
M prompt/jw_mapping.py
M prompt/pipe.py
M prompt/__init__.py
M prompt/base_class.py
M prompt/minimisation.py
M prompt/residue.py
M prompt/structure.py
M prompt/spectrum.py
M prompt/relax_data.py
M prompt/model_selection.py
M prompt/sequence.py
M prompt/spin.py
M prompt/view.py
M prompt/value.py
M prompt/relax_fit.py
M prompt/select.py
M prompt/palmer.py
M prompt/dasha.py
M prompt/diffusion_tensor.py
M prompt/state.py
M prompt/align_tensor.py
M prompt/fix.py
M prompt/vmd.py
M prompt/temperature.py
M prompt/molmol.py
M prompt/pymol_control.py
M prompt/model_free.py
M prompt/results.py
M prompt/monte_carlo.py
M prompt/interpreter.py
M prompt/molecule.py
M prompt/eliminate.py
M prompt/rdc.py
M prompt/angles.py
M prompt/dx.py
M prompt/n_state_model.py
M prompt/noe.py
M prompt/grace.py
M prompt/consistency_tests.py
M prompt/pcs.py
M prompt/frame_order.py
M generic_fns/__init__.py
M generic_fns/structure/internal.py
M generic_fns/structure/geometric.py
M generic_fns/diffusion_tensor.py
M generic_fns/pymol_control.py
M docs/latex/fetch_docstrings.py
A + test_suite/shared_data/diffusion_tensor
A + test_suite/shared_data/diffusion_tensor/ellipsoid
A + test_suite/shared_data/diffusion_tensor/ellipsoid/R2.800.out
A + test_suite/shared_data/diffusion_tensor/ellipsoid/uniform.pdb
A + test_suite/shared_data/diffusion_tensor/ellipsoid/NOE.500.out
A + test_suite/shared_data/diffusion_tensor/ellipsoid/generate_data.py
A + test_suite/shared_data/diffusion_tensor/ellipsoid/NOE.600.out
A + test_suite/shared_data/diffusion_tensor/ellipsoid/R1.500.out
A + test_suite/shared_data/diffusion_tensor/ellipsoid/NOE.700.out
A + test_suite/shared_data/diffusion_tensor/ellipsoid/R1.600.out
A + test_suite/shared_data/diffusion_tensor/ellipsoid/R2.500.out
A + test_suite/shared_data/diffusion_tensor/ellipsoid/NOE.800.out
A + test_suite/shared_data/diffusion_tensor/ellipsoid/R1.700.out
A + test_suite/shared_data/diffusion_tensor/ellipsoid/R2.600.out
A + test_suite/shared_data/diffusion_tensor/ellipsoid/R1.800.out
A + test_suite/shared_data/diffusion_tensor/ellipsoid/R2.700.out
A + test_suite/shared_data/diffusion_tensor/__init__.py
A + test_suite/shared_data/diffusion_tensor/sphere
A + test_suite/shared_data/diffusion_tensor/sphere/R2.800.out
A + test_suite/shared_data/diffusion_tensor/sphere/uniform.pdb
A + test_suite/shared_data/diffusion_tensor/sphere/NOE.500.out
A + test_suite/shared_data/diffusion_tensor/sphere/generate_data.py
A + test_suite/shared_data/diffusion_tensor/sphere/NOE.600.out
A + test_suite/shared_data/diffusion_tensor/sphere/R1.500.out
A + test_suite/shared_data/diffusion_tensor/sphere/NOE.700.out
A + test_suite/shared_data/diffusion_tensor/sphere/R1.600.out
A + test_suite/shared_data/diffusion_tensor/sphere/R2.500.out
A + test_suite/shared_data/diffusion_tensor/sphere/NOE.800.out
A + test_suite/shared_data/diffusion_tensor/sphere/R1.700.out
A + test_suite/shared_data/diffusion_tensor/sphere/R2.600.out
A + test_suite/shared_data/diffusion_tensor/sphere/R1.800.out
A + test_suite/shared_data/diffusion_tensor/sphere/R2.700.out
A + test_suite/shared_data/diffusion_tensor/generate_data.py
A + test_suite/shared_data/diffusion_tensor/spheroid
A + test_suite/shared_data/diffusion_tensor/spheroid/R2.800.out
A + test_suite/shared_data/diffusion_tensor/spheroid/uniform.pdb
A + test_suite/shared_data/diffusion_tensor/spheroid/NOE.500.out
A + test_suite/shared_data/diffusion_tensor/spheroid/generate_data.py
A + test_suite/shared_data/diffusion_tensor/spheroid/NOE.600.out
A + test_suite/shared_data/diffusion_tensor/spheroid/R1.500.out
A + test_suite/shared_data/diffusion_tensor/spheroid/NOE.700.out
A + test_suite/shared_data/diffusion_tensor/spheroid/R1.600.out
A + test_suite/shared_data/diffusion_tensor/spheroid/R2.500.out
A + test_suite/shared_data/diffusion_tensor/spheroid/NOE.800.out
A + test_suite/shared_data/diffusion_tensor/spheroid/R1.700.out
A + test_suite/shared_data/diffusion_tensor/spheroid/R2.600.out
A + test_suite/shared_data/diffusion_tensor/spheroid/R1.800.out
A + test_suite/shared_data/diffusion_tensor/spheroid/R2.700.out
M test_suite/shared_data/align_data/CaM/generate_data.py
M test_suite/shared_data/align_data/CaM/pre_bleach.py
M test_suite/shared_data/structures/diff_tensors/spheroid.pdb
M test_suite/shared_data/structures/diff_tensors/ellipsoid.pdb
M test_suite/shared_data/structures/diff_tensors/sphere.pdb
M test_suite/shared_data/saved_states/create_peak_heights_T2_ncyc1.py
A + test_suite/shared_data/__init__.py
M test_suite/unit_tests/_prompt/test_pymol.py
M test_suite/unit_tests/_generic_fns/_structure/test_internal.py
M test_suite/unit_tests/_generic_fns/_structure/test_scientific.py
M test_suite/unit_tests/relax_data_testing_base.py
M test_suite/unit_tests/sequence_testing_base.py
M test_suite/unit_tests/_specific_fns/_model_free/test_main.py
M test_suite/unit_tests/state_testing_base.py
M test_suite/unit_tests/unit_test_runner.py
M test_suite/system_tests/model_elimination.py
M test_suite/system_tests/load_spins.py
M test_suite/system_tests/jw_mapping.py
M test_suite/system_tests/peak_lists.py
M test_suite/system_tests/noe_restraints.py
M test_suite/system_tests/scripts/palmer_omp.py
M test_suite/system_tests/scripts/jw_mapping.py
M test_suite/system_tests/scripts/load_spins_from_small_molecule.py
M test_suite/system_tests/scripts/tylers_peptide.py
M test_suite/system_tests/scripts/bug_14872_unicode_selection.py
M test_suite/system_tests/scripts/frame_order/opt_rigid_rand_rot.py
M test_suite/system_tests/scripts/bugs_12582_12591_12607.py
M test_suite/system_tests/scripts/local_tm_model_elimination.py
M test_suite/system_tests/scripts/opt_setup_S2_0_970_te_2048_Rex_0_149.py
M test_suite/system_tests/scripts/create_m4.py
M test_suite/system_tests/scripts/1UBQ_relax_fit.py
M test_suite/system_tests/scripts/latex_mf_table.py
M test_suite/system_tests/scripts/opendx_s2_te_rex.py
M test_suite/system_tests/scripts/angles.py
M test_suite/system_tests/scripts/model_free/bug_14941_local_tm_global_selection.py
M test_suite/system_tests/scripts/model_free/bug_15050.py
A + test_suite/system_tests/scripts/diff_tensor
A + test_suite/system_tests/scripts/diff_tensor/ri_back_calc.py
A + test_suite/system_tests/scripts/diff_tensor/tensor_opt.py
M test_suite/system_tests/scripts/omp_model_free.py
M test_suite/system_tests/scripts/relax_fit.py
M test_suite/system_tests/scripts/dasha.py
M test_suite/system_tests/scripts/palmer.py
M test_suite/system_tests/scripts/noe.py
M test_suite/system_tests/scripts/consistency_tests.py
M test_suite/system_tests/scripts/generate_ri.py
M test_suite/system_tests/scripts/xh_vector_dist.py
M test_suite/system_tests/scripts/n_state_model/align_fit.py
M test_suite/system_tests/scripts/n_state_model/phthalic_acid_noes.py
M test_suite/system_tests/scripts/n_state_model/stereochem_analysis.py
M test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
M test_suite/system_tests/structure.py
M test_suite/system_tests/model_free.py
M test_suite/system_tests/results.py
M test_suite/system_tests/model_selection.py
M test_suite/system_tests/sequence.py
M test_suite/system_tests/angles.py
M test_suite/system_tests/generic.py
M test_suite/system_tests/n_state_model.py
M test_suite/system_tests/relax_fit.py
M test_suite/system_tests/diffusion_tensor.py
M test_suite/system_tests/dasha.py
M test_suite/system_tests/palmer.py
M test_suite/system_tests/noe.py
M test_suite/system_tests/consistency_tests.py
M test_suite/system_tests/unit_vectors.py
M test_suite/system_tests/frame_order.py
M test_suite/test_suite_runner.py
M auto_analyses/__init__.py
M auto_analyses/dauvergne_protocol.py
A + auto_analyses/noe.py
M relax

Improvement for the relaxation data back-calculated for the diffusion tensors.

The back-calculated relaxation data now taked the truncation of the atom positions in the PDB into
account.