relax / SVN archive Commit Log

Commit	Date
[r26326] by bugman Fixes for the Structure.test_load_spins_multi_mol system test. The call to the structure.load_spins user function has also been modified so that all 3 spins are loaded at the same time.	2014-10-21 13:55:05	Tree
[r26325] by bugman Created the Structure.test_load_spins_multi_mol system test. This is to test yet to be implemented functionality of the structure.load_spins user function. This is the loading of spin information similar, but not necessarily identical molecules all loaded into the same structural model. For this, the from_mols argument will be added.	2014-10-21 12:43:36	Tree
[r26324] by bugman Modified the internal structural object backend for the structure.read_pdb user function. The MolContainer._det_pdb_element() method for handling PDB files with missing element information has been updated to use the Periodic_table.has_element() method to check if the PDB atom name corresponds to any atoms in the periodic table. This allows for far greater support for HETATOMS and all of the metals.	2014-10-21 12:17:49	Tree
[r26323] by bugman Added 4 unit tests to the _lib.test_periodic_table module for the Periodic_table.has_element() method.	2014-10-21 11:57:05	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

[r26326] by bugman

Fixes for the Structure.test_load_spins_multi_mol system test.

The call to the structure.load_spins user function has also been modified so that all 3 spins are
loaded at the same time.

2014-10-21 13:55:05

Tree

[r26325] by bugman

Created the Structure.test_load_spins_multi_mol system test.

This is to test yet to be implemented functionality of the structure.load_spins user function. This
is the loading of spin information similar, but not necessarily identical molecules all loaded into
the same structural model. For this, the from_mols argument will be added.

2014-10-21 12:43:36

Tree

[r26324] by bugman

Modified the internal structural object backend for the structure.read_pdb user function.

The MolContainer._det_pdb_element() method for handling PDB files with missing element information
has been updated to use the Periodic_table.has_element() method to check if the PDB atom name
corresponds to any atoms in the periodic table. This allows for far greater support for HETATOMS
and all of the metals.

2014-10-21 12:17:49

Tree

[r26323] by bugman

Added 4 unit tests to the _lib.test_periodic_table module for the Periodic_table.has_element() method.

2014-10-21 11:57:05

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

relax SVN archive

Molecular dynamics by NMR data analysis

SVN archive Commit Log