Author: bugman
Date: Sun Oct 23 18:58:00 2011
New Revision: 14886
URL: http://svn.gna.org/viewcvs/relax?rev=14886&view=rev
Log:
Created the back end for the structure.rotate user function.
Modified:
1.3/generic_fns/structure/api_base.py
1.3/generic_fns/structure/internal.py
1.3/generic_fns/structure/main.py
Modified: 1.3/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/api_base.py?rev=14886&r1=14885&r2=14886&view=diff
==============================================================================
--- 1.3/generic_fns/structure/api_base.py (original)
+++ 1.3/generic_fns/structure/api_base.py Sun Oct 23 18:58:00 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2008-2010 Edward d'Auvergne
#
+# Copyright (C) 2008-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -459,6 +459,18 @@
model.mol[-1].file_model = orig_model_num[i]
+ def rotate(self, R=None, origin=None):
+ """Method stub for rotating a structure.
+
+ @keyword R: The forwards rotation matrix.
+ @type R: numpy 3D, rank-2 array
+ @keyword origin: The origin of the rotation.
+ @type origin: numpy 3D, rank-1 array
+ """
+
+ # Raise the error.
+ raise RelaxImplementError
+
def target_mol_name(self, set=None, target=None, index=None,
mol_num=None, file=None):
"""Add the new molecule name to the target data structure.
Modified: 1.3/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=14886&r1=14885&r2=14886&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Sun Oct 23 18:58:00 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2010 Edward d'Auvergne
#
+# Copyright (C) 2003-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -24,7 +24,7 @@
"""Module containing the internal relax structural object."""
# Python module imports.
-from numpy import array, float64, linalg, zeros
+from numpy import array, dot, float64, linalg, zeros
import os
from os import F_OK, access
from re import search
@@ -1020,6 +1020,34 @@
return True
+ def rotate(self, R=None, origin=None):
+ """Rotate the structural information about the given origin.
+
+ @keyword R: The forwards rotation matrix.
+ @type R: numpy 3D, rank-2 array
+ @keyword origin: The origin of the rotation.
+ @type origin: numpy 3D, rank-1 array
+ """
+
+ # Loop over the models.
+ for model in self.model_loop():
+ # Loop over the molecules.
+ for mol in model.mol:
+ # Loop over the atoms.
+ for i in range(len(mol.atom_num)):
+ # The origin to atom vector.
+ vect = array([mol.x[i], mol.y[i], mol.z[i]], float64) -
origin
+
+ # Rotation.
+ rot_vect = dot(R, vect)
+
+ # The new position.
+ pos = rot_vect + origin
+ mol.x[i] = pos[0]
+ mol.y[i] = pos[1]
+ mol.z[i] = pos[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=14886&r1=14885&r2=14886&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Sun Oct 23 18:58:00 2011
@@ -387,6 +387,34 @@
cdp.structure.load_xyz(file_path, read_mol=read_mol,
set_mol_name=set_mol_name, read_model=read_model,
set_model_num=set_model_num, verbosity=verbosity)
+def rotate(R=None, origin=None):
+ """Rotate the structural data about the origin by the specified forwards
rotation.
+
+ @keyword R: The forwards rotation matrix.
+ @type R: numpy 3D, rank-2 array or a 3x3 list of floats
+ @keyword origin: The origin of the rotation. If not supplied, the
origin will be set to [0, 0, 0].
+ @type origin: numpy 3D, rank-1 array or list of len 3 or None
+ """
+
+ # 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
+
+ # Set the origin if not supplied.
+ if origin == None:
+ origin = [0, 0, 0]
+
+ # Convert the args to numpy float data structures.
+ R = array(R, float64)
+ origin = array(origin, float64)
+
+ # Call the specific code.
+ cdp.structure.rotate(R=R, origin=origin)
+
+
def set_vector(spin=None, xh_vect=None):
"""Place the XH unit vector into the spin container object.
r14886 - in /1.3/generic_fns/structure: api_base.py internal.py main.py