def __init__(self, point1 = None, point2 = None, slab = None):
# Huaicai 4/23/05: added some comments below to help understand the code.
if slab:
# convert from 2d (x, y) coordinates into its 3d world (x, y, 0)
#coordinates(the lower-left and upper-right corner).
#In another word, the 3d coordinates minus the z offset of the plane
x = dot(A(point1), A(point2))
# Get the vector from upper-right point to the lower-left point
dx = subtract.reduce(x)
# Get the upper-left and lower right corner points
oc = x[1] + V(point2[0]*dot(dx,point2[0]),
point2[1]*dot(dx,point2[1]))
# Get the four 3d cooridinates on the bottom cookie-cutting plane
sq1 = cat(x,oc) + slab.normal*dot(slab.point, slab.normal)
# transfer the above 4 3d coordinates in parallel to get that on
#the top plane, put them together
sq1 = cat(sq1, sq1+slab.thickness*slab.normal)
self.data = V(maximum.reduce(sq1), minimum.reduce(sq1))
elif point2:
# just 2 3d points
self.data = V(maximum(point1, point2), minimum(point1, point2))
elif point1:
# list of points: could be 2d or 3d? +/- 1.8 to make the bounding
#box enclose the vDw ball of an atom?
self.data = V(maximum.reduce(point1) + BBOX_MARGIN,
minimum.reduce(point1) - BBOX_MARGIN)
else:
# a null bbox
self.data = None
def __init__(self, point1=None, point2=None, slab=None):
# Huaicai 4/23/05: added some comments below to help understand the code.
if slab:
# convert from 2d (x, y) coordinates into its 3d world (x, y, 0)
#coordinates(the lower-left and upper-right corner).
#In another word, the 3d coordinates minus the z offset of the plane
x = dot(A(point1), A(point2))
# Get the vector from upper-right point to the lower-left point
dx = subtract.reduce(x)
# Get the upper-left and lower right corner points
oc = x[1] + V(point2[0] * dot(dx, point2[0]),
point2[1] * dot(dx, point2[1]))
# Get the four 3d cooridinates on the bottom cookie-cutting plane
sq1 = cat(x, oc) + slab.normal * dot(slab.point, slab.normal)
# transfer the above 4 3d coordinates in parallel to get that on
#the top plane, put them together
sq1 = cat(sq1, sq1 + slab.thickness * slab.normal)
self.data = V(maximum.reduce(sq1), minimum.reduce(sq1))
elif point2:
# just 2 3d points
self.data = V(maximum(point1, point2), minimum(point1, point2))
elif point1:
# list of points: could be 2d or 3d? +/- 1.8 to make the bounding
#box enclose the vDw ball of an atom?
self.data = V(
maximum.reduce(point1) + BBOX_MARGIN,
minimum.reduce(point1) - BBOX_MARGIN)
else:
# a null bbox
self.data = None
def isin(self, pt):
return (minimum(pt,self.data[1]) == self.data[1] and
maximum(pt,self.data[0]) == self.data[0])
def isin(self, pt):
return (minimum(pt, self.data[1]) == self.data[1]
and maximum(pt, self.data[0]) == self.data[0])