Author: bugman
Date: Wed Nov 25 18:37:58 2015
New Revision: 28100
URL: http://svn.gna.org/viewcvs/relax?rev=28100=rev
Log:
Basic implementation of the structure.pca user function back end.
This is the new pca() function of the pipe_control.structure.main module. It
simply performs some
checks,
Author: bugman
Date: Wed Nov 25 18:38:40 2015
New Revision: 28119
URL: http://svn.gna.org/viewcvs/relax?rev=28119=rev
Log:
Fixes and improvements for the graphs produced by the structure.pca user
function.
The different sets are now correctly created, and are now labelled in the plots.
Author: bugman
Date: Wed Nov 25 18:38:25 2015
New Revision: 28113
URL: http://svn.gna.org/viewcvs/relax?rev=28113=rev
Log:
Improved the graphs in the backend of the structure.pca user function.
The graphs are now clustered so that different models of the same structure in
the same data pipe
are
Author: bugman
Date: Wed Nov 25 18:38:04 2015
New Revision: 28103
URL: http://svn.gna.org/viewcvs/relax?rev=28103=rev
Log:
Implemented the SVD algorithm for the PCA analysis in the relax library.
This simply calls numpy.linalg.svd().
Modified:
trunk/lib/structure/pca.py
Modified:
Author: bugman
Date: Wed Nov 25 18:38:12 2015
New Revision: 28107
URL: http://svn.gna.org/viewcvs/relax?rev=28107=rev
Log:
Added the 'format' and 'dir' arguments to the structure.pca user function.
This is to the front and back ends.
Modified:
trunk/pipe_control/structure/main.py
Author: bugman
Date: Wed Nov 25 18:38:37 2015
New Revision: 28118
URL: http://svn.gna.org/viewcvs/relax?rev=28118=rev
Log:
Improved the printouts from the relax library principle component analysis.
This is in the pca_analysis() function of the lib.structure.pca module.
Modified:
Author: bugman
Date: Wed Nov 25 18:37:53 2015
New Revision: 28097
URL: http://svn.gna.org/viewcvs/relax?rev=28097=rev
Log:
Added a file to the test suite shared data to help implement the PCA structural
analysis.
This is the N-domain of the CaM-IQ complex used in a frame order analysis. It
is
Author: bugman
Date: Wed Nov 25 18:37:55 2015
New Revision: 28098
URL: http://svn.gna.org/viewcvs/relax?rev=28098=rev
Log:
Created the structure.pca user function front end.
This is currently modelled on the structure.rmsd user function framework.
Modified:
trunk/user_functions/structure.py
Author: bugman
Date: Wed Nov 25 18:38:23 2015
New Revision: 28112
URL: http://svn.gna.org/viewcvs/relax?rev=28112=rev
Log:
Created an initial Structure.test_pca system test.
This executes the new structure.pca user function, and checks if data is stored
in cdp.structure.
Added:
Author: bugman
Date: Wed Nov 25 18:38:34 2015
New Revision: 28117
URL: http://svn.gna.org/viewcvs/relax?rev=28117=rev
Log:
Created the Structure.test_pca_observers system test.
This is for testing the new observer structures concept of the structure.pca
user function.
Added:
Author: bugman
Date: Wed Nov 25 18:38:14 2015
New Revision: 28108
URL: http://svn.gna.org/viewcvs/relax?rev=28108=rev
Log:
Modified the assemble_structural_coordinates() method to return more
information.
This is from the pipe_control.structure.main module. The 'lists' boolean
argument is now
Author: bugman
Date: Wed Nov 25 18:38:27 2015
New Revision: 28114
URL: http://svn.gna.org/viewcvs/relax?rev=28114=rev
Log:
Expanded the Structure.test_pca system test checks to compare to the values
from Gromacs.
Modified:
trunk/test_suite/system_tests/structure.py
Modified:
Author: bugman
Date: Wed Nov 25 18:09:01 2015
New Revision: 28095
URL: http://svn.gna.org/viewcvs/relax?rev=28095=rev
Log:
Modified the internal structural object to be less influenced by the format of
the PDB.
The PDB serial number is now intelligently handled, in that it is reset to 1
when a
Author: bugman
Date: Wed Nov 25 18:09:04 2015
New Revision: 28096
URL: http://svn.gna.org/viewcvs/relax?rev=28096=rev
Log:
Updates to the Noe and Structure system test classes for the internal
structural object changes.
The serial number can now be reset, and the chain ID information is no
Author: bugman
Date: Wed Nov 25 18:38:06 2015
New Revision: 28104
URL: http://svn.gna.org/viewcvs/relax?rev=28104=rev
Log:
The PCA analysis in the relax library now calculates the per structure
projections along the PCs.
Modified:
trunk/lib/structure/pca.py
Modified:
Author: bugman
Date: Wed Nov 25 18:38:18 2015
New Revision: 28110
URL: http://svn.gna.org/viewcvs/relax?rev=28110=rev
Log:
Added the Gromacs PCA results for the distribution.pdb file.
This includes a script used to execute all parts of Gromacs and all output
files.
Added:
Author: bugman
Date: Wed Nov 25 18:38:21 2015
New Revision: 28111
URL: http://svn.gna.org/viewcvs/relax?rev=28111=rev
Log:
Updated the Gromacs PCA results for the newest Gromacs version (5.1.1).
Modified:
trunk/test_suite/shared_data/structures/pca/gromacs/average.pdb
Author: bugman
Date: Wed Nov 25 18:38:29 2015
New Revision: 28115
URL: http://svn.gna.org/viewcvs/relax?rev=28115=rev
Log:
A weighted mean structure can now be calculated.
This is for the calc_mean_structure() function of the relax library module
lib.structure.statistics.
Weights can now be
Author: bugman
Date: Wed Nov 25 18:37:56 2015
New Revision: 28099
URL: http://svn.gna.org/viewcvs/relax?rev=28099=rev
Log:
Fix for the structure.pca user function front end.
The PCA name was misspelt as PCS.
Modified:
trunk/user_functions/structure.py
Modified:
Author: bugman
Date: Wed Nov 25 18:38:10 2015
New Revision: 28106
URL: http://svn.gna.org/viewcvs/relax?rev=28106=rev
Log:
The PCA values and vectors, and the per structure projections are now being
stored.
This is in the structure.pca user function backend in the
pipe_control.structure.main
Author: bugman
Date: Wed Nov 25 18:38:08 2015
New Revision: 28105
URL: http://svn.gna.org/viewcvs/relax?rev=28105=rev
Log:
The PCA analysis function in the relax library is now returning data.
This includes the PCA values and vectors, and the per structure projections.
Modified:
Author: bugman
Date: Wed Nov 25 18:38:02 2015
New Revision: 28102
URL: http://svn.gna.org/viewcvs/relax?rev=28102=rev
Log:
Added the 'algorithm' and 'num_modes' arguments to the structure.pca user
function.
These are passed all the way into the relax library backend.
Modified:
Author: bugman
Date: Wed Nov 25 18:38:32 2015
New Revision: 28116
URL: http://svn.gna.org/viewcvs/relax?rev=28116=rev
Log:
Added support for 'observer' structures in the structure.pca user function.
This allows a subset of the structures used in the PC analysis to have zero
weight so that these
Author: bugman
Date: Wed Nov 25 18:38:00 2015
New Revision: 28101
URL: http://svn.gna.org/viewcvs/relax?rev=28101=rev
Log:
Partial implemented of the PCA analysis in the relax library.
This is for the new structure.pca user function. The lib.structure.pca module
has been created, and
the
Author: bugman
Date: Wed Nov 25 18:38:15 2015
New Revision: 28109
URL: http://svn.gna.org/viewcvs/relax?rev=28109=rev
Log:
The structure.pca user function now creates graphs of the PC projections.
This includes PC1 vs. PC2, PC2 vs. PC3, etc.
Modified:
trunk/pipe_control/structure/main.py
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