Author: semor
Date: Sun Feb 24 00:04:18 2008
New Revision: 5116
URL: http://svn.gna.org/viewcvs/relax?rev=5116&view=rev
Log:
Merged revisions
5056,5058-5060,5063,5065,5067,5069,5071,5074,5076,5079,5081,5085,5087,5089,5091-5115
via svnmerge from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.3
........
r5056 | bugman | 2008-02-20 09:42:33 -0500 (Wed, 20 Feb 2008) | 8 lines
Ported the r4503 revision from the N-state model branch.
The command used was:
svn merge -r4502:4503
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/N_state_model/ .
This file addition should happened in 1.3 line.
........
r5058 | bugman | 2008-02-20 12:23:52 -0500 (Wed, 20 Feb 2008) | 6 lines
Renamed rotation_matrix_zyz() to R_euler_zyz().
This name is more descriptive and is a better naming scheme for rotation
matrices constructed using
other inputs.
........
r5059 | bugman | 2008-02-20 12:53:03 -0500 (Wed, 20 Feb 2008) | 7 lines
Wrote a new function R_2vect() to generate a rotation matrix from 2 vectors.
This rotation matrix is not unique because of axially symmetry allowing the
rotation axis to be any
vector within the symmetry plane, so the cross product with the axis-angle
convention is used to
define this matrix.
........
r5060 | bugman | 2008-02-20 12:54:37 -0500 (Wed, 20 Feb 2008) | 6 lines
Started writing the generic_fns.structure.cone_edge() function.
This function generates a geometric shape constructed from atoms to be
embedded into a PDB file,
representing the outer edge of the cone.
........
r5063 | bugman | 2008-02-21 03:11:55 -0500 (Thu, 21 Feb 2008) | 3 lines
Added the missing import of the rotation matrix R_2vect() function.
........
r5065 | bugman | 2008-02-21 03:18:42 -0500 (Thu, 21 Feb 2008) | 3 lines
Completed the cone_pdb() function.
........
r5067 | bugman | 2008-02-21 03:21:22 -0500 (Thu, 21 Feb 2008) | 3 lines
Added a missing numpy import.
........
r5069 | bugman | 2008-02-21 03:23:03 -0500 (Thu, 21 Feb 2008) | 3 lines
Ok, now the norm() function was in numpy.linalg, not in numpy!
........
r5071 | bugman | 2008-02-21 03:39:59 -0500 (Thu, 21 Feb 2008) | 3 lines
Fix for the cone_edge() function. The atom position is now calculated.
........
r5074 | bugman | 2008-02-21 03:49:27 -0500 (Thu, 21 Feb 2008) | 3 lines
Created the generic_fns.structure.terminate() function for adding a TER
record.
........
r5076 | bugman | 2008-02-21 03:57:46 -0500 (Thu, 21 Feb 2008) | 3 lines
Updated the write_pdb_file() to accept the atomic_data object as an
argument.
........
r5079 | bugman | 2008-02-21 04:04:22 -0500 (Thu, 21 Feb 2008) | 3 lines
Added a few more entries into the get_chemical_name() function for the
parts of the cone object.
........
r5081 | bugman | 2008-02-21 04:14:46 -0500 (Thu, 21 Feb 2008) | 5 lines
Bug fix for the generate_vector_residues() function.
The chain_id arg should default to '' and not None.
........
r5085 | bugman | 2008-02-21 04:23:52 -0500 (Thu, 21 Feb 2008) | 3 lines
The circle part of the cone is now zipped up.
........
r5087 | bugman | 2008-02-21 04:30:40 -0500 (Thu, 21 Feb 2008) | 3 lines
In cone_edge(), added an atom for the apex of the cone and joined all other
atoms to it.
........
r5089 | bugman | 2008-02-21 04:54:10 -0500 (Thu, 21 Feb 2008) | 13 lines
Merged the N-state model branch back into the 1.3 line.
The command used was:
svn merge -r3692:HEAD
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/N_state_model/ .
Although the branch was not complete, the future changes to the N-state
model code will not affect
the rest of relax. However, the merger was done because this branch was
requiring significant
changes to the structural/PDB code (further abstractions and other API
improvements). This caused
a lot of individual changes to the generic_fns.stucture module being ported
to the branch using
svnmerge, just for debugging. The merger is best for both the branch and
the stability of the 1.3
line.
........
r5091 | bugman | 2008-02-21 05:05:46 -0500 (Thu, 21 Feb 2008) | 5 lines
Bug fix for the cone_pdb() function.
The average pivot-CoM vector is now the correct length.
........
r5092 | bugman | 2008-02-21 05:08:03 -0500 (Thu, 21 Feb 2008) | 3 lines
The pivot-CoM vector is now stored in the data pipe.
........
r5093 | bugman | 2008-02-21 05:10:01 -0500 (Thu, 21 Feb 2008) | 3 lines
Bug fix in the CoM() function. The variable unit_vector was being
referenced before it existed.
........
r5094 | bugman | 2008-02-21 05:15:46 -0500 (Thu, 21 Feb 2008) | 3 lines
The length of the pivot-CoM vector is now being used to specify the size of
the cone.
........
r5095 | bugman | 2008-02-21 05:23:02 -0500 (Thu, 21 Feb 2008) | 5 lines
Renaming of a number of variables for the CoM analysis.
These names are more logical.
........
r5096 | bugman | 2008-02-21 05:25:57 -0500 (Thu, 21 Feb 2008) | 3 lines
The ave pivot-CoM vector is now correctly calculated, and the full length
vect is now separate.
........
r5097 | bugman | 2008-02-21 05:28:16 -0500 (Thu, 21 Feb 2008) | 3 lines
Removed some debugging code.
........
r5098 | bugman | 2008-02-21 06:28:08 -0500 (Thu, 21 Feb 2008) | 3 lines
Removal of a few comments.
........
r5099 | bugman | 2008-02-21 06:39:20 -0500 (Thu, 21 Feb 2008) | 6 lines
Added code to the cone_pdb() function to generate the cone cap.
The generic_fns.structure.generate_vector_dist() doesn't exist yet though.
A few print out
statements were also added.
........
r5100 | bugman | 2008-02-21 06:42:06 -0500 (Thu, 21 Feb 2008) | 9 lines
Changed the residue numbering for the cone models.
The numbering is now:
1: Pivot point.
2: Average pivot-CoM vectors.
3: Cone outer edge.
4: Cone cap (for diffusion in a cone).
........
r5101 | bugman | 2008-02-21 06:52:24 -0500 (Thu, 21 Feb 2008) | 3 lines
Modified the cone_edge() function to accept a rotation matrix as an
argument.
........
r5102 | bugman | 2008-02-21 06:55:14 -0500 (Thu, 21 Feb 2008) | 5 lines
The rotation matrix is now calculated in the cone_pdb() function.
This avoids duplicated code in the generic_fns.structure module.
........
r5103 | bugman | 2008-02-21 06:56:35 -0500 (Thu, 21 Feb 2008) | 5 lines
Bug fix for the cone_pdb() function.
The rotation matrix args are 'R', not 'rotation'.
........
r5104 | bugman | 2008-02-21 07:01:44 -0500 (Thu, 21 Feb 2008) | 3 lines
The inc value has already been set as a variable, so no need to replicate
the number in cone_pdb().
........
r5105 | bugman | 2008-02-21 08:40:05 -0500 (Thu, 21 Feb 2008) | 6 lines
Shifted the code for generating the diffusion tensor geometric object into
generate_vector_dist().
The code has been abstracted so that it can also be used to generate cone
caps, or any other PDB
objects which can be generated by rotating and warping a sphere.
........
r5106 | bugman | 2008-02-21 08:44:31 -0500 (Thu, 21 Feb 2008) | 3 lines
A number of fixes for the new generate_vector_dist() function.
........
r5107 | bugman | 2008-02-21 08:46:04 -0500 (Thu, 21 Feb 2008) | 3 lines
The call to generate_vector_dist() from cone_pdb() now passes in the 'CON'
residue name.
........
r5108 | bugman | 2008-02-21 09:19:04 -0500 (Thu, 21 Feb 2008) | 6 lines
Bug fix in the generate_vector_dist() function.
The centre of the distribution is called 'centre' and not 'R', as it used
to be for the diffusion
tensor.
........
r5109 | bugman | 2008-02-21 09:21:30 -0500 (Thu, 21 Feb 2008) | 3 lines
Docstring fix for the generate_vector_dist() function.
........
r5110 | bugman | 2008-02-21 10:05:02 -0500 (Thu, 21 Feb 2008) | 3 lines
The max_angle arg is now being respected. The generate_vector_dist() is
complete.
........
r5111 | bugman | 2008-02-21 10:18:33 -0500 (Thu, 21 Feb 2008) | 5 lines
Wrote the stitch_cap_to_cone() to join the cap of a cone to the cone edge.
This is being called from the specific_fns.n_state_model.cone_pdb()
function.
........
r5112 | bugman | 2008-02-21 10:19:00 -0500 (Thu, 21 Feb 2008) | 3 lines
Removed some debugging code.
........
r5113 | bugman | 2008-02-21 10:20:36 -0500 (Thu, 21 Feb 2008) | 3 lines
Modified the cone_pdb() function so that the cone edge and cap are now the
same residue.
........
r5114 | bugman | 2008-02-21 10:22:18 -0500 (Thu, 21 Feb 2008) | 3 lines
Modified the cone_edge() function to accept the residue name as an argument.
........
r5115 | bugman | 2008-02-21 11:25:16 -0500 (Thu, 21 Feb 2008) | 5 lines
Bug fix for the generic_fns.sequence.load_PDB_sequence() function.
The function no longer fails if a chain or segment id is present in the PDB
file.
........
Added:
branches/consistency_tests_1.3/data/align_tensor.py
- copied unchanged from r5115, 1.3/data/align_tensor.py
branches/consistency_tests_1.3/generic_fns/align_tensor.py
- copied unchanged from r5115, 1.3/generic_fns/align_tensor.py
branches/consistency_tests_1.3/maths_fns/n_state_model.py
- copied unchanged from r5115, 1.3/maths_fns/n_state_model.py
branches/consistency_tests_1.3/maths_fns/rotation_matrix.py
- copied unchanged from r5115, 1.3/maths_fns/rotation_matrix.py
branches/consistency_tests_1.3/prompt/align_tensor.py
- copied unchanged from r5115, 1.3/prompt/align_tensor.py
branches/consistency_tests_1.3/prompt/n_state_model.py
- copied unchanged from r5115, 1.3/prompt/n_state_model.py
branches/consistency_tests_1.3/sample_scripts/N_state_model.py
- copied unchanged from r5115, 1.3/sample_scripts/N_state_model.py
branches/consistency_tests_1.3/specific_fns/n_state_model.py
- copied unchanged from r5115, 1.3/specific_fns/n_state_model.py
branches/consistency_tests_1.3/test_suite/system_tests/n_state_model.py
- copied unchanged from r5115,
1.3/test_suite/system_tests/n_state_model.py
branches/consistency_tests_1.3/test_suite/system_tests/scripts/5_state_xz.py
- copied unchanged from r5115,
1.3/test_suite/system_tests/scripts/5_state_xz.py
branches/consistency_tests_1.3/test_suite/unit_tests/_data/test_align_tensor.py
- copied unchanged from r5115,
1.3/test_suite/unit_tests/_data/test_align_tensor.py
branches/consistency_tests_1.3/test_suite/unit_tests/_generic_fns/test_align_tensor.py
- copied unchanged from r5115,
1.3/test_suite/unit_tests/_generic_fns/test_align_tensor.py
branches/consistency_tests_1.3/test_suite/unit_tests/_maths_fns/test_n_state_model.py
- copied unchanged from r5115,
1.3/test_suite/unit_tests/_maths_fns/test_n_state_model.py
branches/consistency_tests_1.3/test_suite/unit_tests/_prompt/test_align_tensor.py
- copied unchanged from r5115,
1.3/test_suite/unit_tests/_prompt/test_align_tensor.py
branches/consistency_tests_1.3/test_suite/unit_tests/_prompt/test_n_state_model.py
- copied unchanged from r5115,
1.3/test_suite/unit_tests/_prompt/test_n_state_model.py
branches/consistency_tests_1.3/test_suite/unit_tests/_specific_fns/test_n_state_model.py
- copied unchanged from r5115,
1.3/test_suite/unit_tests/_specific_fns/test_n_state_model.py
branches/consistency_tests_1.3/test_suite/unit_tests/align_tensor_testing_base.py
- copied unchanged from r5115,
1.3/test_suite/unit_tests/align_tensor_testing_base.py
branches/consistency_tests_1.3/test_suite/unit_tests/n_state_model_testing_base.py
- copied unchanged from r5115,
1.3/test_suite/unit_tests/n_state_model_testing_base.py
Modified:
branches/consistency_tests_1.3/ (props changed)
branches/consistency_tests_1.3/generic_fns/pipes.py
branches/consistency_tests_1.3/generic_fns/sequence.py
branches/consistency_tests_1.3/generic_fns/structure.py
branches/consistency_tests_1.3/maths_fns/chi2.py
branches/consistency_tests_1.3/prompt/interpreter.py
branches/consistency_tests_1.3/prompt/pipe.py
branches/consistency_tests_1.3/prompt/value.py
branches/consistency_tests_1.3/relax_errors.py
branches/consistency_tests_1.3/specific_fns/__init__.py
branches/consistency_tests_1.3/specific_fns/setup.py
branches/consistency_tests_1.3/test_suite/system_tests/__init__.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/consistency_tests_1.3/generic_fns/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/generic_fns/pipes.py?rev=5116&r1=5115&r2=5116&view=diff
Modified: branches/consistency_tests_1.3/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/generic_fns/sequence.py?rev=5116&r1=5115&r2=5116&view=diff
Modified: branches/consistency_tests_1.3/generic_fns/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/generic_fns/structure.py?rev=5116&r1=5115&r2=5116&view=diff
Modified: branches/consistency_tests_1.3/maths_fns/chi2.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/maths_fns/chi2.py?rev=5116&r1=5115&r2=5116&view=diff
Modified: branches/consistency_tests_1.3/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/prompt/interpreter.py?rev=5116&r1=5115&r2=5116&view=diff
Modified: branches/consistency_tests_1.3/prompt/pipe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/prompt/pipe.py?rev=5116&r1=5115&r2=5116&view=diff
Modified: branches/consistency_tests_1.3/prompt/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/prompt/value.py?rev=5116&r1=5115&r2=5116&view=diff
Modified: branches/consistency_tests_1.3/relax_errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/relax_errors.py?rev=5116&r1=5115&r2=5116&view=diff
Modified: branches/consistency_tests_1.3/specific_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/specific_fns/__init__.py?rev=5116&r1=5115&r2=5116&view=diff
Modified: branches/consistency_tests_1.3/specific_fns/setup.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/specific_fns/setup.py?rev=5116&r1=5115&r2=5116&view=diff
Modified: branches/consistency_tests_1.3/test_suite/system_tests/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/test_suite/system_tests/__init__.py?rev=5116&r1=5115&r2=5116&view=diff
r5116 - in /branches/consistency_tests_1.3: ./ data/ generic_fns/ maths_fns/ prompt/ sample_scripts/ specific_fns/ test_suit...