relax / SVN archive Commit Log

Commit	Date
[r26322] by bugman Created the Periodic_table.has_element() method for the lib.periodic_table module. This is used to simply check if a given symbol exists as an atom in the periodic table.	2014-10-21 11:52:10	Tree
[r26321] by bugman Bug fix for the structure.align user function for when no data pipes are supplied.	2014-10-21 06:58:14	Tree
[r26320] by bugman The compression level for results files can now be set in the frame order auto-analysis. This is via the new argument results_compress_type, which is used to set the compress_type argument of the results.write user function. The results reading parts of the auto-analysis have been updated to allow uncompressed, bzip2 compressed, and gzip compressed files to be handled.	2014-10-20 14:45:49	Tree
[r26319] by bugman The intermediate results are no longer stored in the Frame_order.test_auto_analysis system test. This drops the test timing on one system from ~190 seconds to ~50 seconds.	2014-10-20 14:24:11	Tree
[r26318] by bugman The intermediate results storing can now be turned off in the frame order auto-analysis. The new store_intermediate Boolean argument has been added to the analysis to allow the storage of these results to be turned on or off.	2014-10-20 14:23:08	Tree
[r26317] by bugman The grid search can now be skipped for the rigid model in the frame order auto-analysis. If the input 3D structures are close to the real solution, the grid search over the translational and rotation parameters of the rigid model could be skipped. This speeds up the analysis and can help find the real solution in problematic cases.	2014-10-20 13:15:21	Tree
[r26316] by bugman Created the Optimisation.has_grid() method for the frame order auto-analysis. This is used to test if the optimisation settings object has a grid search defined.	2014-10-20 13:11:58	Tree
[r26315] by bugman Speed up of the Frame_order.test_auto_analysis system test. The splitting of the rigid model grid search into rotation and translation parts has been reactivated.	2014-10-20 12:45:24	Tree
[r26314] by bugman The splitting of the rigid model grid search into rotation and translation parts is now optional. In the frame order auto-analysis, the rigid_grid_split argument has been introduced. The alternating algorithm of performing a grid search over the rotational space followed by translation is now optional and turned off by default. The reason is because the global minimum is sometimes missed with this shortcut algorithm.	2014-10-20 09:52:52	Tree
[r26313] by bugman The simulation is now turned of for intermediate results in the frame order auto-analysis. The intermediate results are only for checking, so for these the full pseudo-Brownian dynamics simulations are not required. The simulation flag has been introduced into the results_output() method of the auto-analysis to control this.	2014-10-20 07:54:11	Tree

[r26322] by bugman

Created the Periodic_table.has_element() method for the lib.periodic_table module.

This is used to simply check if a given symbol exists as an atom in the periodic table.

2014-10-21 11:52:10

Tree

[r26321] by bugman

Bug fix for the structure.align user function for when no data pipes are supplied.

2014-10-21 06:58:14

Tree

[r26320] by bugman

The compression level for results files can now be set in the frame order auto-analysis.

This is via the new argument results_compress_type, which is used to set the compress_type argument
of the results.write user function. The results reading parts of the auto-analysis have been
updated to allow uncompressed, bzip2 compressed, and gzip compressed files to be handled.

2014-10-20 14:45:49

Tree

[r26319] by bugman

The intermediate results are no longer stored in the Frame_order.test_auto_analysis system test.

This drops the test timing on one system from ~190 seconds to ~50 seconds.

2014-10-20 14:24:11

Tree

[r26318] by bugman

The intermediate results storing can now be turned off in the frame order auto-analysis.

The new store_intermediate Boolean argument has been added to the analysis to allow the storage of
these results to be turned on or off.

2014-10-20 14:23:08

Tree

[r26317] by bugman

The grid search can now be skipped for the rigid model in the frame order auto-analysis.

If the input 3D structures are close to the real solution, the grid search over the translational
and rotation parameters of the rigid model could be skipped. This speeds up the analysis and can
help find the real solution in problematic cases.

2014-10-20 13:15:21

Tree

[r26316] by bugman

Created the Optimisation.has_grid() method for the frame order auto-analysis.

This is used to test if the optimisation settings object has a grid search defined.

2014-10-20 13:11:58

Tree

[r26315] by bugman

Speed up of the Frame_order.test_auto_analysis system test.

The splitting of the rigid model grid search into rotation and translation parts has been
reactivated.

2014-10-20 12:45:24

Tree

[r26314] by bugman

The splitting of the rigid model grid search into rotation and translation parts is now optional.

In the frame order auto-analysis, the rigid_grid_split argument has been introduced. The
alternating algorithm of performing a grid search over the rotational space followed by translation
is now optional and turned off by default. The reason is because the global minimum is sometimes
missed with this shortcut algorithm.

2014-10-20 09:52:52

Tree

[r26313] by bugman

The simulation is now turned of for intermediate results in the frame order auto-analysis.

The intermediate results are only for checking, so for these the full pseudo-Brownian dynamics
simulations are not required. The simulation flag has been introduced into the results_output()
method of the auto-analysis to control this.

2014-10-20 07:54:11

Tree

relax SVN archive

Molecular dynamics by NMR data analysis

SVN archive Commit Log