relax SVN archive

Deletion of the frame_order.domain_to_pdb user function.

The redesign of the frame_order.pdb_model user function will make frame_order.domain_to_pdb
obsolete. The user function is ugly anyway as it forces a user to create a separate PDB file for
each domain.

Modifications to the frame_order.pdb_model user function backend.

Modified the visualisation() method of the frame order auto-analysis.

This is to use the renamed frame_order.pdb_model user function, as well as the yet to be renamed
pymol.cone_pdb -> pymol.frame_order user function.

Started to remodel the frame_order.pdb_model user function.

The dist_file argument has been added for the creation of a special distribution of models spanning
the frame order dynamics.

Renamed the frame_order.cone_pdb user function to frame_order.pdb_model.

This is because it will be used for the rigid and rotor models as well as the isotropic and
pseudo-elliptic cone models.

Silenced the PCS and RDC warnings during Monte Carlo simulations for the frame order analysis.

Fix for the assembly of the simulation parameter vector in the frame order analysis.

The frame order specific analysis _assemble_param_vector() method was broken when creating the
parameter vector for the Monte Carlo simulations.

Merged revisions 18822-18828 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r18822 | bugman | 2013-03-13 18:24:47 +0100 (Wed, 13 Mar 2013) | 9 lines

Fix for a strange and extremely rare typo bug in the model-free specific analysis code.

This was identified by Manish Chaubey <manish dott chaubey att tuebingen dott mpg dott de> in the
message at http://thread.gmane.org/gmane.science.nmr.relax.user/1422.

This only occurs if a relaxation data error of zero is encountered and is a bug in the RelaxError
message explaining the problem with the data.
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r18823 | bugman | 2013-03-14 17:54:01 +0100 (Thu, 14 Mar 2013) | 5 lines

Created the front end for the new structure.create_rotor_pdb user function.

This will be used to create a PDB representation of a rotor motional model.
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r18824 | bugman | 2013-03-14 19:35:40 +0100 (Thu, 14 Mar 2013) | 3 lines

Added file, directory and overwrite force arguments to the structure.create_rotor_pdb user function.
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r18825 | bugman | 2013-03-14 19:59:45 +0100 (Thu, 14 Mar 2013) | 3 lines

Started to implement the backend of the structure.create_rotor_pdb user function.
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r18826 | bugman | 2013-03-15 10:32:04 +0100 (Fri, 15 Mar 2013) | 3 lines

The internal structural object MolContainer.add_atom() method now returns the index of the new atom.
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r18827 | bugman | 2013-03-15 10:59:10 +0100 (Fri, 15 Mar 2013) | 3 lines

Created the internal structural object MolContainer.last_residue() method.
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r18828 | bugman | 2013-03-15 11:21:12 +0100 (Fri, 15 Mar 2013) | 5 lines

Fully implemented the structure.create_rotor_pdb user function.

For this, the generic_fns.structure.geometric.create_rotor_propellers() function was created.
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Fully implemented the structure.create_rotor_pdb user function.

For this, the generic_fns.structure.geometric.create_rotor_propellers() function was created.

Created the internal structural object MolContainer.last_residue() method.