Author: bugman
Date: Tue Sep 23 20:01:59 2014
New Revision: 25980
URL: http://svn.gna.org/viewcvs/relax?rev=25980&view=rev
Log:
Merged revisions 25971-25979 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r25971 | bugman | 2014-09-23 18:02:05 +0200 (Tue, 23 Sep 2014) | 8 lines
Created a special internal structural object selection object.
This will be used for massively speeding up the internal structural object.
The use of the
lib.selection module by the internal structural object is currently very
slow as a huge number of
calls to re.search() are required. The idea is to avoid this by using
lib.selection once to
populate this new selection object, and then reusing this object to loop
over molecules and atoms.
........
r25972 | bugman | 2014-09-23 18:05:23 +0200 (Tue, 23 Sep 2014) | 8 lines
Added the selection() method to the internal structural object.
This parses the atom ID string using the lib.selection module, loops over
the molecules and atoms,
performs matches using re.search() via lib.selection, and populates and
returns the new
Internal_selection object. This can be used to pre-process the atom ID
string to save huge amounts
of time.
........
r25973 | bugman | 2014-09-23 18:12:45 +0200 (Tue, 23 Sep 2014) | 5 lines
The internal structural object validate_models() method now accepts the
verbosity argument.
This is used to silence printouts.
........
r25974 | bugman | 2014-09-23 18:13:12 +0200 (Tue, 23 Sep 2014) | 3 lines
Missing import of the Internal_selection class.
........
r25975 | bugman | 2014-09-23 18:14:12 +0200 (Tue, 23 Sep 2014) | 3 lines
Indentation fix for the internal structural object validate_model() method.
........
r25976 | bugman | 2014-09-23 18:21:42 +0200 (Tue, 23 Sep 2014) | 5 lines
Fixes for the new structural object Internal_selection object.
The atom indices are not stored via the molecule index.
........
r25977 | bugman | 2014-09-23 18:43:56 +0200 (Tue, 23 Sep 2014) | 6 lines
Converted the rotate() and translate() structural object methods to use the
new selection object.
The atom_id arguments have been replaced with selection arguments.
Therefore all parts of relax
which call these methods must first call selection() to obtain the
Internal_selection instance.
........
r25978 | bugman | 2014-09-23 18:55:47 +0200 (Tue, 23 Sep 2014) | 5 lines
Created the structural object Internal_selection.mol_loop() method.
This is to simply quickly loop over all molecule indices of the selection
object.
........
r25979 | bugman | 2014-09-23 19:50:46 +0200 (Tue, 23 Sep 2014) | 8 lines
Converted all structural object methods to use the selection object rather
that atom ID strings.
This should have a significant impact on the speed of certain operations
within relax. The most
obvious effect will be a huge speed up of the interatom.define user
function. There should be speed
ups with a number of other user functions relating to structural
information. All parts of relax
have been updated for the change.
........
Added:
branches/frame_order_cleanup/lib/structure/internal/selection.py
- copied unchanged from r25979,
trunk/lib/structure/internal/selection.py
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/lib/structure/internal/__init__.py
branches/frame_order_cleanup/lib/structure/internal/object.py
branches/frame_order_cleanup/pipe_control/interatomic.py
branches/frame_order_cleanup/pipe_control/structure/main.py
branches/frame_order_cleanup/pipe_control/structure/mass.py
branches/frame_order_cleanup/test_suite/unit_tests/_pipe_control/_structure/test_internal.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_cleanup/lib/structure/internal/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/internal/__init__.py?rev=25980&r1=25979&r2=25980&view=diff
Modified: branches/frame_order_cleanup/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/internal/object.py?rev=25980&r1=25979&r2=25980&view=diff
Modified: branches/frame_order_cleanup/pipe_control/interatomic.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/interatomic.py?rev=25980&r1=25979&r2=25980&view=diff
Modified: branches/frame_order_cleanup/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/structure/main.py?rev=25980&r1=25979&r2=25980&view=diff
Modified: branches/frame_order_cleanup/pipe_control/structure/mass.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/structure/mass.py?rev=25980&r1=25979&r2=25980&view=diff
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/_pipe_control/_structure/test_internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/_pipe_control/_structure/test_internal.py?rev=25980&r1=25979&r2=25980&view=diff
r25980 - in /branches/frame_order_cleanup: ./ lib/structure/internal/ pipe_control/ pipe_control/structure/ test_suite/unit_...