relax SVN archive

Added links to the reference page in the side menu.

Merged revisions 5117 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

........
r5117 | bugman | 2008-03-21 13:49:16 +0100 (Fri, 21 Mar 2008) | 6 lines

Fix for bug #11004 (https://gna.org/bugs/?11004).

The division by zero is now caught and avoided, but this bug has been triggered by a deeper problem
which is likely to uncover additional bugs.
........

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

........
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!
........
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.
........
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@.../svn/relax/branches/N_state_model
........
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.
........
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.
........
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.
........
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.
........
r5010 | bugman | 2008-02-15 11:42:55 +0100 (Fri, 15 Feb 2008) | 3 lines

Added some missing imports.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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().
........
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.
........
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.
........
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@.../svn/relax/branches/N_state_model/ .

This file addition should happened in 1.3 line.
........
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.
........
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.
........
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.
........
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.
........
r5065 | bugman | 2008-02-21 09:18:42 +0100 (Thu, 21 Feb 2008) | 3 lines

Completed the cone_pdb() function.
........
r5067 | bugman | 2008-02-21 09:21:22 +0100 (Thu, 21 Feb 2008) | 3 lines

Added a missing numpy import.
........
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!
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
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@.../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 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.
........
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.
........
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.
........
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.
........
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.
........
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.
........
r5097 | bugman | 2008-02-21 11:28:16 +0100 (Thu, 21 Feb 2008) | 3 lines

Removed some debugging code.
........
r5098 | bugman | 2008-02-21 12:28:08 +0100 (Thu, 21 Feb 2008) | 3 lines

Removal of a few comments.
........
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.
........
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).
........
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.
........
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.
........
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'.
........
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().
........
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.
........
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.
........
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.
........
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.
........
r5109 | bugman | 2008-02-21 15:21:30 +0100 (Thu, 21 Feb 2008) | 3 lines

Docstring fix for the generate_vector_dist() function.
........
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.
........
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.
........
r5112 | bugman | 2008-02-21 16:19:00 +0100 (Thu, 21 Feb 2008) | 3 lines

Removed some debugging code.
........
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.
........
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.
........
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.
........

Fix for bug #11004 (https://gna.org/bugs/?11004).

The division by zero is now caught and avoided, but this bug has been triggered by a deeper problem
which is likely to uncover additional bugs.

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@.../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@.../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@.../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.
........

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.

Modified the cone_edge() function to accept the residue name as an argument.

Modified the cone_pdb() function so that the cone edge and cap are now the same residue.

Removed some debugging code.

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.