relax SVN archive

svn+ssh://semor@.../svn/relax/1.3

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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@.../svn/relax/branches/N_state_model/ .

This file addition should happened in 1.3 line.
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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.
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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.
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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.
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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.
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r5065 | bugman | 2008-02-21 03:18:42 -0500 (Thu, 21 Feb 2008) | 3 lines

Completed the cone_pdb() function.
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r5067 | bugman | 2008-02-21 03:21:22 -0500 (Thu, 21 Feb 2008) | 3 lines

Added a missing numpy import.
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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!
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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@.../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.
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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.
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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.
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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.
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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.
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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.
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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.
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r5097 | bugman | 2008-02-21 05:28:16 -0500 (Thu, 21 Feb 2008) | 3 lines

Removed some debugging code.
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r5098 | bugman | 2008-02-21 06:28:08 -0500 (Thu, 21 Feb 2008) | 3 lines

Removal of a few comments.
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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.
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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).
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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.
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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.
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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'.
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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().
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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.
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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.
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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.
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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.
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r5109 | bugman | 2008-02-21 09:21:30 -0500 (Thu, 21 Feb 2008) | 3 lines

Docstring fix for the generate_vector_dist() function.
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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.
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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.
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r5112 | bugman | 2008-02-21 10:19:00 -0500 (Thu, 21 Feb 2008) | 3 lines

Removed some debugging code.
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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.
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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.
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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.
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