Author: bugman
Date: Fri Mar 21 14:07:28 2008
New Revision: 5118
URL: http://svn.gna.org/viewcvs/relax?rev=5118&view=rev
Log:
Blocked revisions
4970-4971,5003,5005-5006,5008-5010,5013,5015-5023,5033-5037,5040-5045,5047,5056,5058-5060,5063,5065,5067,5069,5071,5074,5076,5079,5081,5085,5087,5089,5091-5115
via svnmerge
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r4970 | bugman | 2008-02-13 14:27:32 +0100 (Wed, 13 Feb 2008) | 5 lines
Separated the set up of the specific code into the setup.py module.
The design was crap! It causes massive circular import headaches!
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r4971 | bugman | 2008-02-13 14:30:07 +0100 (Wed, 13 Feb 2008) | 3 lines
Fixes for the imports of the get_specific_fn function.
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r5003 | bugman | 2008-02-15 10:28:40 +0100 (Fri, 15 Feb 2008) | 6 lines
Merged in r4999 to r5002 from the N_state_model branch as they should have
gone into the 1.3 line!
The command used was:
svn merge -r4998:5002
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/N_state_model
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r5005 | bugman | 2008-02-15 11:06:25 +0100 (Fri, 15 Feb 2008) | 3 lines
Modified the centre_of_mass() function to use obey the selections in the
mol-res-spin structure.
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r5006 | bugman | 2008-02-15 11:10:27 +0100 (Fri, 15 Feb 2008) | 3 lines
Converted the generic_fns.structure.centre_of_mass() docstring to epydoc
format.
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r5008 | bugman | 2008-02-15 11:36:16 +0100 (Fri, 15 Feb 2008) | 3 lines
Added select flags to the molecule and residue container and list data
structures.
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r5009 | bugman | 2008-02-15 11:37:58 +0100 (Fri, 15 Feb 2008) | 3 lines
Converted all the select variables of the mol-res-spin structures to
booleans.
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r5010 | bugman | 2008-02-15 11:42:55 +0100 (Fri, 15 Feb 2008) | 3 lines
Added some missing imports.
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r5013 | bugman | 2008-02-15 12:21:59 +0100 (Fri, 15 Feb 2008) | 5 lines
Bug fix for the generic_fns.structure.centre_of_mass() function.
The fetching of molecular, residue, and spin containers is now done
correctly.
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r5015 | bugman | 2008-02-19 11:44:18 +0100 (Tue, 19 Feb 2008) | 3 lines
Converted the angles.py sample script to the new relax design.
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r5016 | bugman | 2008-02-19 11:44:42 +0100 (Tue, 19 Feb 2008) | 3 lines
Converted the cv.py sample script to the new relax design.
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r5017 | bugman | 2008-02-19 11:45:25 +0100 (Tue, 19 Feb 2008) | 3 lines
A small comment fix for the cv.py sample script.
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r5018 | bugman | 2008-02-19 11:47:57 +0100 (Tue, 19 Feb 2008) | 3 lines
Converted the dasha.py sample script to the new relax design.
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r5019 | bugman | 2008-02-19 11:50:03 +0100 (Tue, 19 Feb 2008) | 3 lines
Converted the diff_min.py sample script to the new relax design.
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r5020 | bugman | 2008-02-19 11:51:00 +0100 (Tue, 19 Feb 2008) | 3 lines
Converted the diff_tensor.py sample script to the new relax design.
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r5021 | bugman | 2008-02-19 13:26:36 +0100 (Tue, 19 Feb 2008) | 3 lines
Created the spin_index_loop() fn for looping over spins and returning the
mol-res-spin indecies.
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r5022 | bugman | 2008-02-19 13:30:01 +0100 (Tue, 19 Feb 2008) | 3 lines
Converted the full_analysis.py sample script to the new relax design.
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r5023 | bugman | 2008-02-19 14:18:04 +0100 (Tue, 19 Feb 2008) | 3 lines
Converted the generate_ri.py sample script to the new relax design.
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r5033 | bugman | 2008-02-20 09:23:23 +0100 (Wed, 20 Feb 2008) | 5 lines
Fixes for the generic_fns.structure.atom_add() function.
The atomic_data dictionary is now expected to be passed into the function.
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r5034 | bugman | 2008-02-20 09:24:01 +0100 (Wed, 20 Feb 2008) | 5 lines
Fixes for the generic_fns.structure.atom_connect() function.
The atomic_data dictionary is now expected to be passed into the function.
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r5035 | bugman | 2008-02-20 09:31:00 +0100 (Wed, 20 Feb 2008) | 3 lines
Shifted all the relative atomic mass values into the physical_constants
module.
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r5036 | bugman | 2008-02-20 09:32:44 +0100 (Wed, 20 Feb 2008) | 3 lines
Updated the docstring of the generic_fns.structure.atomic_mass() function
to epydoc format.
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r5037 | bugman | 2008-02-20 09:36:10 +0100 (Wed, 20 Feb 2008) | 6 lines
Updated the generic_fns.structure.autoscale_tensor() function.
The docstring was changed to epydoc format, the default method changed from
None to 'mass', and a
few comments were added.
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r5040 | bugman | 2008-02-20 11:03:41 +0100 (Wed, 20 Feb 2008) | 7 lines
Created the new function generic_fns.structure.generate_vector_residues().
This new function should allow greater flexibility for creating PDB
representations of any type of
vector (and its MC sims). It will also replace the
generate_spheroid_axes() and
generate_ellipsoid_axes() functions.
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r5041 | bugman | 2008-02-20 11:56:31 +0100 (Wed, 20 Feb 2008) | 3 lines
All calls to generic_fns.structure.atom_add() now have the atomic_data
object passed into it.
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r5042 | bugman | 2008-02-20 11:57:33 +0100 (Wed, 20 Feb 2008) | 3 lines
All calls to generic_fns.structure.atom_connect() now have the atomic_data
object passed into it.
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r5043 | bugman | 2008-02-20 12:11:34 +0100 (Wed, 20 Feb 2008) | 3 lines
Converted the generic_fns.structure.create_diff_tensor_pdb() to the new
relax design.
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r5044 | bugman | 2008-02-20 14:19:39 +0100 (Wed, 20 Feb 2008) | 5 lines
Removed the calls to generate_spheroid_axes() and generate_ellipsoid_axes()
fns.
These have been replaced with calls to generate_vector_residues().
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r5045 | bugman | 2008-02-20 14:20:43 +0100 (Wed, 20 Feb 2008) | 3 lines
Deleted the generate_spheroid_axes() and generate_ellipsoid_axes() fns.
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r5047 | bugman | 2008-02-20 14:39:00 +0100 (Wed, 20 Feb 2008) | 5 lines
Bug fix for the generate_vector_residues() function.
The variable 'pdb_vect' no longer exists.
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r5056 | bugman | 2008-02-20 15:42:33 +0100 (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.
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r5058 | bugman | 2008-02-20 18:23:52 +0100 (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 18:53:03 +0100 (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 18:54:37 +0100 (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 09:11:55 +0100 (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 09:18:42 +0100 (Thu, 21 Feb 2008) | 3 lines
Completed the cone_pdb() function.
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r5067 | bugman | 2008-02-21 09:21:22 +0100 (Thu, 21 Feb 2008) | 3 lines
Added a missing numpy import.
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r5069 | bugman | 2008-02-21 09:23:03 +0100 (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 09:39:59 +0100 (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 09:49:27 +0100 (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 09:57:46 +0100 (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 10:04:22 +0100 (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 10:14:46 +0100 (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 10:23:52 +0100 (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 10:30:40 +0100 (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 10:54:10 +0100 (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.
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r5091 | bugman | 2008-02-21 11:05:46 +0100 (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 11:08:03 +0100 (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 11:10:01 +0100 (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 11:15:46 +0100 (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 11:23:02 +0100 (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 11:25:57 +0100 (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 11:28:16 +0100 (Thu, 21 Feb 2008) | 3 lines
Removed some debugging code.
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r5098 | bugman | 2008-02-21 12:28:08 +0100 (Thu, 21 Feb 2008) | 3 lines
Removal of a few comments.
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r5099 | bugman | 2008-02-21 12:39:20 +0100 (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 12:42:06 +0100 (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 12:52:24 +0100 (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 12:55:14 +0100 (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 12:56:35 +0100 (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 13:01:44 +0100 (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 14:40:05 +0100 (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 14:44:31 +0100 (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 14:46:04 +0100 (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 15:19:04 +0100 (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 15:21:30 +0100 (Thu, 21 Feb 2008) | 3 lines
Docstring fix for the generate_vector_dist() function.
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r5110 | bugman | 2008-02-21 16:05:02 +0100 (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 16:18:33 +0100 (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 16:19:00 +0100 (Thu, 21 Feb 2008) | 3 lines
Removed some debugging code.
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r5113 | bugman | 2008-02-21 16:20:36 +0100 (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 16:22:18 +0100 (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 17:25:16 +0100 (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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Modified:
1.2/ (props changed)
Propchange: 1.2/
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Binary property 'svnmerge-blocked' - no diff available.
r5118 - /1.2/