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SVN archive Commit Log


Commit Date  
[r2701] by bugman

Removed a number of unused import statements in the Molmol prompt interface file.

2006-10-29 07:48:29 Tree
[r2700] by bugman

Created the user function 'molmol.tensor_pdb()' for displaying the diffusion tensor in Molmol.

The function takes the pre-generated diffusion tensor PDB file, created with the user function
'pdb.create_tensor_pdb()', and displays it in Molmol over the loaded structure.

2006-10-29 07:42:32 Tree
[r2699] by bugman

Improvements to the docstring of the 'molmol.ribbon()' user function.

2006-10-29 06:39:04 Tree
[r2698] by bugman

Created the user function 'molmol.ribbon()'.

This function applies the Molmol ribbon style and is equivalent to clicking on 'ribbon' in the
Molmol side menu.

2006-10-29 06:37:48 Tree
[r2697] by bugman

Implemented the 'molmol.command()' user function.

The user function did previously exist, but it hadn't been implemented in the generic code. The
user function was calling the wrong function 'self.write' in 'generic_fns/molmol.py'.

2006-10-29 06:14:07 Tree
[r2696] by bugman

Improvements to the printed out messages of the 'pdb.create_tensor_pdb()' user function.

2006-10-29 05:56:37 Tree
[r2695] by bugman

Changed the CONECT record algorithm (for the tensor PDB) to allow more than four bonded atoms.

Multiple CONECT records are now generated for an atom if it is bonded to more than 4 other atoms.

2006-10-29 05:51:32 Tree
[r2694] by bugman

Sorted the HETATM and CONECT records by atomic number in the tensor PDB file.

2006-10-29 05:18:29 Tree
[r2693] by bugman

Because of the diffusion tensor symmetry, the axes where extended in both the pos and neg directions.

2006-10-29 05:10:07 Tree
[r2692] by bugman

Improved the docstring of the user function 'pdb.create_tensor_pdb()'.

I've made it more clear that the units of the diffusion tensor are rates, not times. This is to
help users to not be confused with the fact that being parallel to the long axis of the tensor means
that the bond is moving faster!

2006-10-29 04:54:29 Tree
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