Author: bugman
Date: Wed Oct 26 14:47:24 2011
New Revision: 14928
URL: http://svn.gna.org/viewcvs/relax?rev=14928&view=rev
Log:
Rearranged the back end of the structure.superimpose user function.
This is just to shift more code into the 'superimpose' module.
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=14928&r1=14927&r2=14928&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Wed Oct 26 14:47:24 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 kabsch
+from generic_fns.structure.superimpose import fit_to_first
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
@@ -510,47 +510,28 @@
for model in cdp.structure.model_loop():
models.append(model.num)
+ # Assemble the atomic coordinates of all models.
+ coord = []
+ for model in models:
+ coord.append([])
+ for pos in cdp.structure.atom_loop(atom_id=atom_id, model_num=model,
pos_flag=True):
+ coord[-1].append(pos[0])
+ coord[-1] = array(coord[-1])
+
# The different algorithms.
if method == 'fit to mean':
- superimpose_to_mean(models=models, atom_id=atom_id)
+ T, R, pivot = fit_to_mean(models=models, coord=coord)
elif method == 'fit to first':
- superimpose_to_first(models=models, atom_id=atom_id)
-
-
-def superimpose_to_first(models=None, atom_id=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 atom_id: The molecule, residue, and atom identifier string.
This matches the spin ID string format.
- @type atom_id: str or None
- """
-
- # Print out.
- print("\nSuperimposition of structural models %s using the 'fit to
first' algorithm." % models)
-
- # Assemble the atomic coordinates of the first model.
- coord_to = []
- for pos in cdp.structure.atom_loop(atom_id=atom_id, model_num=models[0],
pos_flag=True):
- coord_to.append(pos[0])
- coord_to = array(coord_to)
-
- # Loop over the ending models.
- for model in models[1:]:
- # Assemble the atomic coordinates.
- coord_from = []
- for pos in cdp.structure.atom_loop(atom_id=atom_id, model_num=model,
pos_flag=True):
- coord_from.append(pos[0])
- coord_from = array(coord_from)
-
- # Calculate the displacements (Kabsch algorithm).
- trans_vect, trans_dist, R, axis, angle, pivot =
kabsch(name_from='model %s'%models[0], name_to='model %s'%model,
coord_from=coord_from, coord_to=coord_to)
-
+ T, R, pivot = fit_to_first(models=models, coord=coord)
+
+
+ # Update to the new coordinates.
+ for i in range(len(models)):
# Translate the molecule first (the rotational pivot is defined in
the first model).
- translate(T=trans_vect, model=model)
+ translate(T=T[i], model=models[i])
# Rotate the molecule.
- rotate(R=R, origin=pivot, model=model)
+ rotate(R=R[i], origin=pivot[i], model=models[i])
def translate(T=None, model=None):
Modified: 1.3/generic_fns/structure/superimpose.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/superimpose.py?rev=14928&r1=14927&r2=14928&view=diff
==============================================================================
--- 1.3/generic_fns/structure/superimpose.py (original)
+++ 1.3/generic_fns/structure/superimpose.py Wed Oct 26 14:47:24 2011
@@ -25,7 +25,7 @@
# Python module imports.
from math import pi
-from numpy import diag, dot, float64, outer, sign, transpose, zeros
+from numpy import diag, dot, eye, float64, outer, sign, transpose, zeros
from numpy.linalg import det, norm, svd
# relax module import.
@@ -46,6 +46,39 @@
# Return.
return centroid
+
+
+def fit_to_first(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
first' algorithm." % models)
+
+ # Init (there is no transformation for the first model).
+ T_list = [zeros(3, float64)]
+ R_list = [eye(3, dtype=float64)]
+ pivot_list = [zeros(3, float64)]
+
+ # Loop over the ending models.
+ 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 kabsch(name_from=None, name_to=None, coord_from=None, coord_to=None,
centroid=None, verbosity=1):
r14928 - in /1.3/generic_fns/structure: main.py superimpose.py