Author: bugman
Date: Wed Oct 26 12:24:24 2011
New Revision: 14925
URL: http://svn.gna.org/viewcvs/relax?rev=14925&view=rev
Log:
Implemented the back end of the structure.superimpose user function.
This only implements the 'fit to first' algorithm. The 'fit to mean' is yet
to be implemented.
Modified:
1.3/generic_fns/structure/internal.py
1.3/generic_fns/structure/main.py
1.3/generic_fns/structure/superimpose.py
Modified: 1.3/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=14925&r1=14924&r2=14925&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Wed Oct 26 12:24:24 2011
@@ -1044,6 +1044,27 @@
mol.z[i] = pos[2]
+ def translate(self, T=None, model=None):
+ """Displace the structural information by the given translation
vector.
+
+ @keyword T: The translation vector.
+ @type T: numpy 3D, rank-1 array
+ @keyword model: The model to rotate. If None, all models will
be rotated.
+ @type model: int
+ """
+
+ # Loop over the models.
+ for model_cont in self.model_loop(model):
+ # Loop over the molecules.
+ for mol in model_cont.mol:
+ # Loop over the atoms.
+ for i in range(len(mol.atom_num)):
+ # Translate.
+ mol.x[i] = mol.x[i] + T[0]
+ mol.y[i] = mol.y[i] + T[1]
+ mol.z[i] = mol.z[i] + T[2]
+
+
def write_pdb(self, file, model_num=None):
"""Method for the creation of a PDB file from the structural data.
Modified: 1.3/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=14925&r1=14924&r2=14925&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Wed Oct 26 12:24:24 2011
@@ -37,6 +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 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
@@ -487,6 +488,94 @@
spin.xh_vect = xh_vect
+def superimpose(models=None, method='fit to mean', atom_id=None):
+ """Superimpose a set of structural models.
+
+ @keyword models: The list of models to superimpose. If set to None,
then all models will be used.
+ @type models: list of int or None
+ @keyword method: The superimposition method. It must be one of 'fit
to mean' or 'fit to first'.
+ @type method: str
+ @keyword atom_id: The molecule, residue, and atom identifier string.
This matches the spin ID string format.
+ @type atom_id: str or None
+ """
+
+ # Check the method.
+ allowed = ['fit to mean', 'fit to first']
+ if method not in allowed:
+ raise RelaxError("The superimposition method '%s' is unknown. It
must be one of %s." % (method, allowed))
+
+ # Create a list of all models.
+ if models == None:
+ models = []
+ for model in cdp.structure.model_loop():
+ models.append(model.num)
+
+ # The different algorithms.
+ if method == 'fit to mean':
+ superimpose_to_mean(models=models, atom_id=atom_id)
+ 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)
+
+ # Translate the molecule first (the rotational pivot is defined in
the first model).
+ translate(T=trans_vect, model=model)
+
+ # Rotate the molecule.
+ rotate(R=R, origin=pivot, model=model)
+
+
+def translate(T=None, model=None):
+ """Shift the structural data by the specified translation vector.
+
+ @keyword T: The translation vector.
+ @type T: numpy rank-1, 3D array or list of float
+ @keyword model: The model to translate. If None, all models will be
rotated.
+ @type model: int
+ """
+
+ # Test if the current data pipe exists.
+ pipes.test()
+
+ # Test if the structure exists.
+ if not hasattr(cdp, 'structure') or not cdp.structure.num_models() or
not cdp.structure.num_molecules():
+ raise RelaxNoPdbError
+
+ # Convert the args to numpy float data structures.
+ T = array(T, float64)
+
+ # Call the specific code.
+ cdp.structure.translate(T=T, model=model)
+
+
def vectors(attached=None, spin_id=None, model=None, verbosity=1, ave=True,
unit=True):
"""Extract the bond vectors from the loaded structures and store them in
the spin container.
Modified: 1.3/generic_fns/structure/superimpose.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/superimpose.py?rev=14925&r1=14924&r2=14925&view=diff
==============================================================================
--- 1.3/generic_fns/structure/superimpose.py (original)
+++ 1.3/generic_fns/structure/superimpose.py Wed Oct 26 12:24:24 2011
@@ -64,8 +64,8 @@
@type coord_to: numpy rank-2, Nx3 array
@keyword centroid: An alternative position of the centroid, used
for studying pivoted systems.
@type centroid: list of float or numpy rank-1, 3D array
- @return: The translation vector T, translation distance
d, rotation matrix R, rotation axis r, and rotation angle theta.
- @rtype: numpy rank-1 3D array, float, numpy rank-2 3D
array, numpy rank-1 3D array, float
+ @return: The translation vector T, translation distance
d, rotation matrix R, rotation axis r, rotation angle theta, and the
rotational pivot defined as the centroid of the ending structure.
+ @rtype: numpy rank-1 3D array, float, numpy rank-2 3D
array, numpy rank-1 3D array, float, numpy rank-1 3D array
"""
# Calculate the centroids.
@@ -86,7 +86,7 @@
# Print out.
if verbosity >= 1:
- print("\n\nCalculating the rotational and translational
displacements from model %s to model %s.\n" % (name_from, name_to))
+ print("\n\nCalculating the rotational and translational
displacements from %s to %s using the Kabsch algorithm.\n" % (name_from,
name_to))
print("Start centroid: [%20.15f, %20.15f, %20.15f]" %
(centroid_from[0], centroid_from[1], centroid_from[2]))
print("End centroid: [%20.15f, %20.15f, %20.15f]" %
(centroid_to[0], centroid_to[1], centroid_to[2]))
print("Translation vector: [%20.15f, %20.15f, %20.15f]" %
(trans_vect[0], trans_vect[1], trans_vect[2]))
@@ -99,7 +99,7 @@
print("Rotation angle (deg): %.15f" % (angle / 2.0 / pi * 360.0))
# Return the data.
- return trans_vect, trans_dist, R, axis, angle
+ return trans_vect, trans_dist, R, axis, angle, centroid_to
def kabsch_rotation(coord_from=None, coord_to=None, centroid_from=None,
centroid_to=None):
r14925 - in /1.3/generic_fns/structure: internal.py main.py superimpose.py