Author: bugman
Date: Wed Nov 25 18:37:58 2015
New Revision: 28100
URL: http://svn.gna.org/viewcvs/relax?rev=28100&view=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, assembles the atomic coordinates, and the passes control to the relax
library pca_analysis()
function of the currently unimplemented lib.structure.pca module.
Modified:
trunk/pipe_control/structure/main.py
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=28100&r1=28099&r2=28100&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Wed Nov 25 18:37:58 2015
@@ -42,6 +42,7 @@
from lib.structure.internal.coordinates import assemble_atomic_coordinates,
assemble_coord_array, loop_coord_structures
from lib.structure.internal.displacements import Displacements
from lib.structure.internal.object import Internal
+from lib.structure.pca import pca_analysis
from lib.structure.represent.diffusion_tensor import diffusion_tensor
from lib.structure.statistics import atomic_rmsd
from lib.structure.superimpose import fit_to_first, fit_to_mean
@@ -1001,6 +1002,29 @@
# Set the number of states for use in the specific analyses.
cdp.N = len(from_mols)
+
+
+def pca(pipes=None, models=None, molecules=None, atom_id=None):
+ """PCA analysis of the motions between all the loaded models.
+
+ @keyword pipes: The data pipes to determine the RMSD for.
+ @type pipes: None or list of str
+ @keyword models: The list of models to determine the RMSD for. The
number of elements must match the pipes argument. If set to None, then all
models will be used.
+ @type models: None or list of lists of int
+ @keyword molecules: The list of molecules to determine the RMSD for. The
number of elements must match the pipes argument.
+ @type molecules: None or list of lists of str
+ @keyword atom_id: The atom identification string of the coordinates of
interest. This matches the spin ID string format.
+ @type atom_id: str or None
+ """
+
+ # Checks.
+ check_pipe()
+
+ # Assemble the structural coordinates.
+ coord, ids, mol_names, res_names, res_nums, atom_names, elements =
assemble_structural_coordinates(pipes=pipes, models=models,
molecules=molecules, atom_id=atom_id)
+
+ # Perform the PCA analysis.
+ pca_analysis(coord=coord)
def read_gaussian(file=None, dir=None, set_mol_name=None, set_model_num=None,
verbosity=1, fail=True):
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