def rotate(self,R):
"""Performs rotation operation by the rotation matrix R."""
from BioNanoLEGO.DenseMatrix import dot
# FIXME: this assignment is ugly in my opinion
new_coords = dot(R,self.coords)
self.coords = array([new_coords[0,0],new_coords[0,1],new_coords[0,2]])
return
def getDistance(self,other):
"""Calculates the distance between two atoms."""
from math import sqrt
from BioNanoLEGO.DenseMatrix import dot
# Displacement between two atoms
disp_atoms = self.coords-other.coords
return sqrt(dot(disp_atoms,disp_atoms))
def getSquareDist(self,other):
"""Calculates the square distance between two atoms."""
from BioNanoLEGO.DenseMatrix import dot
# Displacement between two atoms
disp_atoms = self.coords-other.coords
return dot(disp_atoms,disp_atoms)
