Author: bugman
Date: Wed Oct 26 15:43:14 2011
New Revision: 14929
URL: http://svn.gna.org/viewcvs/relax?rev=14929&view=rev
Log:
Implemented the 'fit to mean' algorithm for the structure.superimpose user
function.
Modified:
1.3/generic_fns/structure/main.py
1.3/generic_fns/structure/superimpose.py
Modified: 1.3/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=14929&r1=14928&r2=14929&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Wed Oct 26 15:43:14 2011
@@ -37,7 +37,7 @@
from generic_fns.structure.api_base import Displacements
from generic_fns.structure.internal import Internal
from generic_fns.structure.scientific import Scientific_data
-from generic_fns.structure.superimpose import fit_to_first
+from generic_fns.structure.superimpose import fit_to_first, fit_to_mean
from relax_errors import RelaxError, RelaxFileError, RelaxNoPdbError,
RelaxNoSequenceError
from relax_io import get_file_path, open_write_file, write_spin_data
from relax_warnings import RelaxWarning, RelaxNoPDBFileWarning,
RelaxZeroVectorWarning
Modified: 1.3/generic_fns/structure/superimpose.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/superimpose.py?rev=14929&r1=14928&r2=14929&view=diff
==============================================================================
--- 1.3/generic_fns/structure/superimpose.py (original)
+++ 1.3/generic_fns/structure/superimpose.py Wed Oct 26 15:43:14 2011
@@ -24,12 +24,40 @@
"""Module for handling all types of structural superimpositions."""
# Python module imports.
+from copy import deepcopy
from math import pi
from numpy import diag, dot, eye, float64, outer, sign, transpose, zeros
from numpy.linalg import det, norm, svd
# relax module import.
from maths_fns.rotation_matrix import R_to_axis_angle
+
+
+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 coord: 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
def find_centroid(coords):
@@ -71,6 +99,89 @@
for i in range(1, len(models)):
# Calculate the displacements (Kabsch algorithm).
trans_vect, trans_dist, R, axis, angle, pivot =
kabsch(name_from='model %s'%models[0], name_to='model %s'%models[i],
coord_from=coord[i], coord_to=coord[0])
+
+ # Store the transforms.
+ T_list.append(trans_vect)
+ R_list.append(R)
+ pivot_list.append(pivot)
+
+ # Return the transform data.
+ return T_list, R_list, pivot_list
+
+
+def fit_to_mean(models=None, coord=None):
+ """Superimpose a set of structural models using the fit to first
algorithm.
+
+ @keyword models: The list of models to superimpose.
+ @type models: list of int
+ @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
+ @return: The lists of translation vectors, rotation matrices,
and rotation pivots.
+ @rtype: list of numpy rank-1 3D arrays, list of numpy rank-2
3D arrays, list of numpy rank-1 3D arrays
+ """
+
+ # Print out.
+ print("\nSuperimposition of structural models %s using the 'fit to mean'
algorithm." % models)
+
+ # Duplicate the coordinates.
+ orig_coord = deepcopy(coord)
+
+ # Initialise the displacement lists.
+ T_list = []
+ R_list = []
+ pivot_list = []
+
+ # Initialise the mean structure.
+ N = len(coord[0])
+ mean = zeros((N, 3), float64)
+
+ # Iterative fitting to mean.
+ converged = False
+ iter = 0
+ while not converged:
+ # Print out.
+ print("\nIteration %i of the algorithm." % iter)
+ print("%-10s%-25s%-25s" % ("Model", "Translation (Angstrom)",
"Rotation (deg)"))
+
+ # Calculate the mean structure.
+ calc_mean_structure(coord, mean)
+
+ # Fit each model to the mean.
+ converged = True
+ for i in range(len(models)):
+ # Calculate the displacements (Kabsch algorithm).
+ trans_vect, trans_dist, R, axis, angle, pivot =
kabsch(name_from='model %s'%models[0], name_to='mean', coord_from=coord[i],
coord_to=mean, verbosity=0)
+
+ # Table print out.
+ print("%-10i%25.3g%25.3g" % (i, trans_dist, angle))
+
+ # Shift the coordinates.
+ print coord[i][0]
+ for j in range(N):
+ # Translate.
+ coord[i][j] += trans_vect
+
+ # The pivot to atom vector.
+ coord[i][j] -= pivot
+
+ # Rotation.
+ coord[i][j] = dot(R, coord[i][j])
+
+ # The new position.
+ coord[i][j] += pivot
+ print coord[i][0]
+
+ # Convergence test.
+ if trans_dist > 1e-10 or angle > 1e-10:
+ converged = False
+
+ # Increment the iteration number.
+ iter += 1
+
+ # Perform the fit once from the original coordinates to obtain the full
transforms.
+ for i in range(len(models)):
+ # Calculate the displacements (Kabsch algorithm).
+ trans_vect, trans_dist, R, axis, angle, pivot =
kabsch(name_from='model %s'%models[0], name_to='model %s'%models[i],
coord_from=orig_coord[i], coord_to=mean)
# Store the transforms.
T_list.append(trans_vect)
r14929 - in /1.3/generic_fns/structure: main.py superimpose.py