Author: bugman
Date: Thu Apr 3 19:40:54 2014
New Revision: 22630
URL: http://svn.gna.org/viewcvs/relax?rev=22630&view=rev
Log:
Merged revisions 22056-22064 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/double_rotor
........
r22056 | bugman | 2014-01-28 11:23:50 +0100 (Tue, 28 Jan 2014) | 7 lines
Fixes for the calculation of the frame order matrix in the test data
generation base script.
The matrix generation now handles multiple modes of motion correctly. The
total rotation matrix is
constructed when looping over the modes by using the dot product of the
individual rotation to the
total, and then this is used to create the outer product, summed over all
states.
........
r22057 | bugman | 2014-01-28 11:24:33 +0100 (Tue, 28 Jan 2014) | 3 lines
Fix for the frame order test data generation base script for when the
distribution of structures is not created.
........
r22058 | bugman | 2014-01-28 11:25:13 +0100 (Tue, 28 Jan 2014) | 3 lines
The frame order test data generation base script now outputs the frame
order matrix to 8 places.
........
r22059 | bugman | 2014-01-28 11:30:02 +0100 (Tue, 28 Jan 2014) | 6 lines
Introduced the ROT_FILE flag to the frame order test data generation base
script.
This allows the 'rotations.bz2' file creation to be skipped, if set to
False. This file takes time
to create and is of limited use.
........
r22060 | bugman | 2014-01-28 18:27:35 +0100 (Tue, 28 Jan 2014) | 3 lines
Removed a duplicated state.save call in the frame order test data
generation base script.
........
r22061 | bugman | 2014-01-29 09:08:33 +0100 (Wed, 29 Jan 2014) | 8 lines
The save file created by the frame order test data generation base script
can now be bypassed.
When loading 1,000,000 PDB structures as models into the relax data store,
the RAM usage can go over
10 Gb. When trying to save this into a relax state file with the
state.save user function, the time
required can be over a day. Therefore the SAVE_STATE class variable has
been introduced to allow
the state.save call to be bypassed.
........
r22062 | bugman | 2014-01-29 11:33:18 +0100 (Wed, 29 Jan 2014) | 8 lines
Created the RDC and PCS back calculated test data for the CaM double rotor
frame order model.
This consists of a uniform distribution over both rotors, the first centred
in the C-domain and
the second in the N-domain, and the two axes being perpendicular to each
other along the CoM-CoM
axis. The distribution consists of 250000 rotated structures. The frame
order matrix for this
model is also given.
........
r22063 | bugman | 2014-01-29 11:48:16 +0100 (Wed, 29 Jan 2014) | 7 lines
Created a distribution of structures for the CaM double rotor frame order
model.
This is only for a distribution of 100 structures, to keep the file size to
a reasonable size. A
PyMOL *.pse file is also included to show the distribution together with
the rotor system and the
domain positions.
........
r22064 | bugman | 2014-01-29 16:21:58 +0100 (Wed, 29 Jan 2014) | 6 lines
Updated for the rotation() method of all the CaM frame order test data
generation scripts.
The motion_index argument is now accepted by all of the methods to allow
the base script to execute
correctly.
........
Added:
trunk/test_suite/shared_data/frame_order/cam/double_rotor/distribution.pdb.gz
- copied unchanged from r22064,
branches/double_rotor/test_suite/shared_data/frame_order/cam/double_rotor/distribution.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/double_rotor/distribution.pse.bz2
- copied unchanged from r22064,
branches/double_rotor/test_suite/shared_data/frame_order/cam/double_rotor/distribution.pse.bz2
trunk/test_suite/shared_data/frame_order/cam/double_rotor/frame_order_matrix
- copied unchanged from r22064,
branches/double_rotor/test_suite/shared_data/frame_order/cam/double_rotor/frame_order_matrix
trunk/test_suite/shared_data/frame_order/cam/double_rotor/generate_distribution.log.bz2
- copied unchanged from r22064,
branches/double_rotor/test_suite/shared_data/frame_order/cam/double_rotor/generate_distribution.log.bz2
trunk/test_suite/shared_data/frame_order/cam/double_rotor/generate_distribution.py
- copied unchanged from r22064,
branches/double_rotor/test_suite/shared_data/frame_order/cam/double_rotor/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/double_rotor/pcs_dy.txt
- copied unchanged from r22064,
branches/double_rotor/test_suite/shared_data/frame_order/cam/double_rotor/pcs_dy.txt
trunk/test_suite/shared_data/frame_order/cam/double_rotor/pcs_er.txt
- copied unchanged from r22064,
branches/double_rotor/test_suite/shared_data/frame_order/cam/double_rotor/pcs_er.txt
trunk/test_suite/shared_data/frame_order/cam/double_rotor/pcs_tb.txt
- copied unchanged from r22064,
branches/double_rotor/test_suite/shared_data/frame_order/cam/double_rotor/pcs_tb.txt
trunk/test_suite/shared_data/frame_order/cam/double_rotor/pcs_tm.txt
- copied unchanged from r22064,
branches/double_rotor/test_suite/shared_data/frame_order/cam/double_rotor/pcs_tm.txt
trunk/test_suite/shared_data/frame_order/cam/double_rotor/rdc_dy.txt
- copied unchanged from r22064,
branches/double_rotor/test_suite/shared_data/frame_order/cam/double_rotor/rdc_dy.txt
trunk/test_suite/shared_data/frame_order/cam/double_rotor/rdc_er.txt
- copied unchanged from r22064,
branches/double_rotor/test_suite/shared_data/frame_order/cam/double_rotor/rdc_er.txt
trunk/test_suite/shared_data/frame_order/cam/double_rotor/rdc_tb.txt
- copied unchanged from r22064,
branches/double_rotor/test_suite/shared_data/frame_order/cam/double_rotor/rdc_tb.txt
trunk/test_suite/shared_data/frame_order/cam/double_rotor/rdc_tm.txt
- copied unchanged from r22064,
branches/double_rotor/test_suite/shared_data/frame_order/cam/double_rotor/rdc_tm.txt
Modified:
trunk/ (props changed)
trunk/test_suite/shared_data/frame_order/cam/free_rotor/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/generate_base.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/rotor/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/rotor2/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/rotor_2_state/generate_distribution.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor/generate_distribution.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor/generate_distribution.py?rev=22630&r1=22629&r2=22630&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/generate_distribution.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor2/generate_distribution.py?rev=22630&r1=22629&r2=22630&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/generate_distribution.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/generate_distribution.py?rev=22630&r1=22629&r2=22630&view=diff
Modified: trunk/test_suite/shared_data/frame_order/cam/generate_base.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/generate_base.py?rev=22630&r1=22629&r2=22630&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/iso_cone/generate_distribution.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/iso_cone/generate_distribution.py?rev=22630&r1=22629&r2=22630&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/generate_distribution.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/generate_distribution.py?rev=22630&r1=22629&r2=22630&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/generate_distribution.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/generate_distribution.py?rev=22630&r1=22629&r2=22630&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/generate_distribution.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/generate_distribution.py?rev=22630&r1=22629&r2=22630&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/generate_distribution.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/generate_distribution.py?rev=22630&r1=22629&r2=22630&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/generate_distribution.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/generate_distribution.py?rev=22630&r1=22629&r2=22630&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/generate_distribution.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/generate_distribution.py?rev=22630&r1=22629&r2=22630&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/generate_distribution.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/generate_distribution.py?rev=22630&r1=22629&r2=22630&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/rotor/generate_distribution.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor/generate_distribution.py?rev=22630&r1=22629&r2=22630&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/rotor2/generate_distribution.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor2/generate_distribution.py?rev=22630&r1=22629&r2=22630&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/rotor_2_state/generate_distribution.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor_2_state/generate_distribution.py?rev=22630&r1=22629&r2=22630&view=diff
r22630 - in /trunk: ./ test_suite/shared_data/frame_order/cam/ test_suite/shared_data/frame_order/cam/double_rotor/ test_sui...