Author: bugman
Date: Sun Mar 24 15:54:57 2013
New Revision: 19108
URL: http://svn.gna.org/viewcvs/relax?rev=19108&view=rev
Log:
Shifted the pipe_control.structure.statistics module to
lib.structure.statistics.
Added:
trunk/lib/structure/statistics.py
- copied unchanged from r19105,
trunk/pipe_control/structure/statistics.py
Removed:
trunk/pipe_control/structure/statistics.py
Modified:
trunk/lib/structure/__init__.py
trunk/lib/structure/superimpose.py
trunk/pipe_control/structure/__init__.py
trunk/pipe_control/structure/main.py
trunk/target_functions/ens_pivot_finder.py
Modified: trunk/lib/structure/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/__init__.py?rev=19108&r1=19107&r2=19108&view=diff
==============================================================================
--- trunk/lib/structure/__init__.py (original)
+++ trunk/lib/structure/__init__.py Sun Mar 24 15:54:57 2013
@@ -24,5 +24,6 @@
__all__ = [
'rotor',
+ 'statistics',
'superimpose'
]
Modified: trunk/lib/structure/superimpose.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/superimpose.py?rev=19108&r1=19107&r2=19108&view=diff
==============================================================================
--- trunk/lib/structure/superimpose.py (original)
+++ trunk/lib/structure/superimpose.py Sun Mar 24 15:54:57 2013
@@ -29,7 +29,7 @@
from numpy.linalg import det, norm, svd
# relax module import.
-from pipe_control.structure.statistics import calc_mean_structure
+from lib.structure.statistics import calc_mean_structure
from lib.geometry.rotations import R_to_axis_angle, R_to_euler_zyz
Modified: trunk/pipe_control/structure/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/__init__.py?rev=19108&r1=19107&r2=19108&view=diff
==============================================================================
--- trunk/pipe_control/structure/__init__.py (original)
+++ trunk/pipe_control/structure/__init__.py Sun Mar 24 15:54:57 2013
@@ -45,5 +45,4 @@
'pdb_read',
'pdb_write',
'scientific',
- 'statistics'
]
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=19108&r1=19107&r2=19108&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Sun Mar 24 15:54:57 2013
@@ -37,7 +37,7 @@
from pipe_control.structure.api_base import Displacements
from pipe_control.structure.internal import Internal
from pipe_control.structure.scientific import Scientific_data
-from pipe_control.structure.statistics import atomic_rmsd
+from lib.structure.statistics import atomic_rmsd
from lib.structure.superimpose import fit_to_first, fit_to_mean
from target_functions.ens_pivot_finder import Pivot_finder
from lib.errors import RelaxError, RelaxFileError, RelaxNoPdbError,
RelaxNoSequenceError
Removed: trunk/pipe_control/structure/statistics.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/statistics.py?rev=19107&view=auto
==============================================================================
--- trunk/pipe_control/structure/statistics.py (original)
+++ trunk/pipe_control/structure/statistics.py (removed)
@@ -1,111 +1,0 @@
-###############################################################################
-#
#
-# Copyright (C) 2011-2013 Edward d'Auvergne
#
-#
#
-# This file is part of the program relax (http://www.nmr-relax.com).
#
-#
#
-# This program is free software: you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation, either version 3 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# This program is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
-#
#
-###############################################################################
-
-# Module docstring.
-"""Module for handling all types of structural statistics."""
-
-# Python module imports.
-from numpy import float64, mean, sqrt, std, zeros
-from numpy.linalg import norm
-
-
-def atomic_rmsd(coord, verbosity=0):
- """Determine the RMSD for the given atomic coordinates.
-
- This is the per atom RMSD to the mean structure.
-
-
- @keyword coord: The array of molecular coordinates. The first
dimension corresponds to the model, the second the atom, the third the
coordinate.
- @type coord: rank-3 numpy array
- @return: The RMSD value.
- @rtype: float
- """
-
- # Init.
- M = len(coord)
- N = len(coord[0])
- model_rmsd = zeros(M, float64)
- mean_str = zeros((N, 3), float64)
-
- # Calculate the mean structure.
- calc_mean_structure(coord, mean_str)
-
- # Loop over the models.
- for i in range(M):
- # Loop over the atoms.
- for j in range(N):
- # The vector connecting the mean to model atom.
- vect = mean_str[j] - coord[i][j]
-
- # The atomic RMSD.
- model_rmsd[i] += norm(vect)**2
-
- # Normalise, and sqrt.
- model_rmsd[i] = sqrt(model_rmsd[i] / N)
-
- # Print out.
- if verbosity:
- print("Model %2s RMSD: %s" % (i, model_rmsd[i]))
-
- # Calculate the mean.
- rmsd_mean = mean(model_rmsd)
-
- # Calculate the normal non-biased standard deviation.
- try:
- rmsd_sd = std(model_rmsd, ddof=1)
-
- # Handle old numpy versions not having the ddof argument.
- except TypeError:
- rmsd_sd = std(model_rmsd) * sqrt(M / (M - 1.0))
-
- # Printout.
- if verbosity:
- print("\nGlobal RMSD: %s +/- %s" % (rmsd_mean, rmsd_sd))
-
- # Return the average RMSD.
- return rmsd_mean
-
-
-def calc_mean_structure(coord=None, mean=None):
- """Average the coordinates.
-
- @keyword coord: The list of coordinates of all models to
superimpose. The first index is the models, the second is the atomic
positions, and the third is the xyz coordinates.
- @type coord: list of numpy rank-2, Nx3 arrays
- @keyword mean: The data storage for the mean structure.
- @type mean: numpy rank-2, Nx3 array
- """
-
- # The number of atoms.
- N = len(coord[0])
- M = len(coord)
-
- # Clear the mean data structure.
- for i in range(N):
- mean[i] = [0.0, 0.0, 0.0]
-
- # Loop over the atoms.
- for i in range(N):
- # Loop over the models.
- for j in range(M):
- mean[i] += coord[j][i]
-
- # Average.
- mean[i] = mean[i] / M
Modified: trunk/target_functions/ens_pivot_finder.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/ens_pivot_finder.py?rev=19108&r1=19107&r2=19108&view=diff
==============================================================================
--- trunk/target_functions/ens_pivot_finder.py (original)
+++ trunk/target_functions/ens_pivot_finder.py Sun Mar 24 15:54:57 2013
@@ -26,7 +26,7 @@
from copy import deepcopy
# relax module import.
-from pipe_control.structure.statistics import atomic_rmsd
+from lib.structure.statistics import atomic_rmsd
from lib.structure.superimpose import fit_to_mean
r19108 - in /trunk: lib/structure/ pipe_control/structure/ target_functions/