relax / SVN archive Commit Log

Commit	Date
[r2714] by bugman Ported r2713 from the 'tensor_pdb' branch. The command used was: $ svn merge -r2712:2713 svn+ssh://bugman@.../svn/relax/branches/tensor_pdb/ This adds the text "re-run relax with the '--debug' flag" to the RelaxFault error class.	2006-10-31 08:10:59	Tree
[r2713] by bugman Added the text "re-run relax with the '--debug' flag" to the RelaxFault error class.	2006-10-31 08:04:22	Tree
[r2712] by bugman Added RelaxImplementError for raising an error when code is executed which hasn't been implemented. The PyMOL macro functions now call this error.	2006-10-31 08:03:15	Tree
[r2711] by bugman Changed all references from Molmol to PyMOL in the PyMOL code. The macro fns raise RelaxErrors. The 'self.macro_exec()' and 'self.write()' functions raise RelaxErrors saying that the functions have not been implemented yet. The 'pymol.cartoon()' user function has been shifted to the top of the function list in the 'prompt/pymol.py' file.	2006-10-31 08:02:16	Tree
[r2710] by bugman Implemented the 'pymol.tensor_pdb()' user function. The numerous Molmol commands have been replaced by a single PyMOL load command.	2006-10-31 08:01:00	Tree
[r2709] by bugman Implemented the 'pymol.cartoon()' user function. This was modified from the 'molmol.ribbon()' user function. The molmol commands have been replaced with commands to hide everything, show the cartoon, and colour the cartoon by secondary structure.	2006-10-31 07:59:50	Tree
[r2708] by bugman The 'pymol.view()' user function now works. A number of calls to pipes located at 'self.relax.data.molmol' where changed to 'self.relax.data.pymol'. The Molmol 'InitAll' and loading functions where changed to the PyMOL equivalents. Now PyMOL executes and opens up the PDB file.	2006-10-31 07:57:07	Tree
[r2707] by bugman Ported r2705 and r2706 from the 1.2 line. The command used was: $ svn merge -r2704:2706 svn+ssh://bugman@.../svn/relax/1.2 This fixes bug #7583 (https://gna.org/bugs/?7583) and fixes a problem with one of the comments in 'specific_fns/model_free.py'.	2006-10-31 07:31:08	Tree
[r2706] by bugman Fix for bug #7583 (https://gna.org/bugs/?7583). The problem was to statements 'if len(file_data[i]) != 4:' followed by 'continue'. These tests were to avoid lines which contain no data, however it causes failures if there are not exactly for columns! Now the minimum number of columns, based on the given column numbers, is tested for.	2006-10-31 07:27:04	Tree
[r2705] by bugman Emphasised the looping over the minimisation instances and fixed an incorrect comment. The incorrect comment stated 'Require at least as many data points as params to prevent under-fitting'. It should say over-fitting.	2006-10-31 07:23:34	Tree

[r2714] by bugman

Ported r2713 from the 'tensor_pdb' branch.

The command used was:
$ svn merge -r2712:2713 svn+ssh://bugman@.../svn/relax/branches/tensor_pdb/

This adds the text "re-run relax with the '--debug' flag" to the RelaxFault error class.

2006-10-31 08:10:59

Tree

[r2713] by bugman

Added the text "re-run relax with the '--debug' flag" to the RelaxFault error class.

2006-10-31 08:04:22

Tree

[r2712] by bugman

Added RelaxImplementError for raising an error when code is executed which hasn't been implemented.

The PyMOL macro functions now call this error.

2006-10-31 08:03:15

Tree

[r2711] by bugman

Changed all references from Molmol to PyMOL in the PyMOL code. The macro fns raise RelaxErrors.

The 'self.macro_exec()' and 'self.write()' functions raise RelaxErrors saying that the functions
have not been implemented yet. The 'pymol.cartoon()' user function has been shifted to the top of
the function list in the 'prompt/pymol.py' file.

2006-10-31 08:02:16

Tree

[r2710] by bugman

Implemented the 'pymol.tensor_pdb()' user function.

The numerous Molmol commands have been replaced by a single PyMOL load command.

2006-10-31 08:01:00

Tree

[r2709] by bugman

Implemented the 'pymol.cartoon()' user function.

This was modified from the 'molmol.ribbon()' user function. The molmol commands have been replaced
with commands to hide everything, show the cartoon, and colour the cartoon by secondary structure.

2006-10-31 07:59:50

Tree

[r2708] by bugman

The 'pymol.view()' user function now works.

A number of calls to pipes located at 'self.relax.data.molmol' where changed to
'self.relax.data.pymol'. The Molmol 'InitAll' and loading functions where changed to the PyMOL
equivalents. Now PyMOL executes and opens up the PDB file.

2006-10-31 07:57:07

Tree

[r2707] by bugman

Ported r2705 and r2706 from the 1.2 line.

The command used was:
$ svn merge -r2704:2706 svn+ssh://bugman@.../svn/relax/1.2

This fixes bug #7583 (https://gna.org/bugs/?7583) and fixes a problem with one of the comments in
'specific_fns/model_free.py'.

2006-10-31 07:31:08

Tree

[r2706] by bugman

Fix for bug #7583 (https://gna.org/bugs/?7583).

The problem was to statements 'if len(file_data[i]) != 4:' followed by 'continue'. These tests were
to avoid lines which contain no data, however it causes failures if there are not exactly for
columns! Now the minimum number of columns, based on the given column numbers, is tested for.

2006-10-31 07:27:04

Tree

[r2705] by bugman

Emphasised the looping over the minimisation instances and fixed an incorrect comment.

The incorrect comment stated 'Require at least as many data points as params to prevent
under-fitting'. It should say over-fitting.

2006-10-31 07:23:34

Tree

relax SVN archive

Molecular dynamics by NMR data analysis

SVN archive Commit Log