def screwMotion(self):
l = self.vector.length()
if l == 0.:
return Geometry.Vector(0.,0.,0.), \
Geometry.Vector(0.,0.,1.), 0., 0.
else:
return Geometry.Vector(0., 0., 0.), self.vector / l, 0., l
def screwMotion(self):
axis, angle = self.rotation().axisAndAngle()
d = self.vector*axis
x = d*axis-self.vector
if abs(angle) < 1.e-9:
r0 = Geometry.Vector(0., 0., 0.)
angle = 0.
else:
r0 = -0.5*((N.cos(0.5*angle)/N.sin(0.5*angle))*axis.cross(x)+x)
return r0, axis, angle, d
def asVector(self):
"""
@returns: an equivalent vector object
@rtype: L{Scientific.Geometry.Vector}
@raises ValueError: if rank > 1
"""
from Scientific import Geometry
if self.rank == 1:
return Geometry.Vector(self.array)
else:
raise ValueError('rank > 1')
def screwMotion(self):
axis, angle = self.rotation().axisAndAngle()
d = self.vector * axis
if d < 0.:
d = -d
axis = -axis
angle = -angle
if abs(angle) < 1.e-9:
r0 = Geometry.Vector(0., 0., 0.)
angle = 0.
else:
x = d * axis - self.vector
r0 = -0.5 * (
(N.cos(0.5 * angle) / N.sin(0.5 * angle)) * axis.cross(x) + x)
return r0, axis, angle % (2. * N.pi), d
def axisAndAngle(self):
"""
@returns: the axis (a normalized vector) and angle (in radians).
The angle is in the interval (-pi, pi]
@rtype: (L{Scientific.Geometry.Vector}, C{float})
"""
asym = -self.tensor.asymmetricalPart()
axis = Geometry.Vector(asym[1, 2], asym[2, 0], asym[0, 1])
sine = axis.length()
if abs(sine) > 1.e-10:
axis = axis / sine
projector = axis.dyadicProduct(axis)
cosine = (self.tensor - projector).trace() / (3. - axis * axis)
angle = angleFromSineAndCosine(sine, cosine)
else:
t = 0.5 * (self.tensor + Geometry.delta)
i = N.argmax(t.diagonal().array)
axis = (t[i] / N.sqrt(t[i, i])).asVector()
angle = 0.
if t.trace() < 2.:
angle = N.pi
return axis, angle
junk = co_file.readline()
testline = co_file.readline()
while testline != "":
# Eliminate white space and split line
in_str = testline.strip()
in_str = in_str.split()
#Convert coordinates based on atom type
if (in_str[0] == "H" and len(H1) == len(H2)):
#Convert coordinates to vectors for the H1's
H1.append(
Geo.Vector(float(in_str[1]), float(in_str[2]), float(in_str[3])))
print "H1"
elif (in_str[0] == "H" and len(H2) == (len(H1) - 1)):
#Convert coordinates to vectors for the H2's
H2.append(
Geo.Vector(float(in_str[1]), float(in_str[2]), float(in_str[3])))
print "H2"
elif (in_str[0] == "O"):
#Convert coordinates to vectors for the O's
Oxy.append(
Geo.Vector(float(in_str[1]), float(in_str[2]), float(in_str[3])))
print "O"
def screwMotion(self):
axis, angle = self.axisAndAngle()
return Geometry.Vector(0., 0., 0.), axis, angle, 0.
def translation(self):
return Translation(Geometry.Vector(0., 0., 0.))
def inverse(self):
return LinearTransformation(self.tensor.inverse(), -self.vector)
# Utility functions
def angleFromSineAndCosine(y, x):
return atan2(y, x)
def mod_angle(angle, mod):
return (angle + mod / 2.) % mod - mod / 2
# Test code
if __name__ == '__main__':
t = Translation(Geometry.Vector(1., -2., 0))
r = Rotation(Geometry.Vector(0.1, -2., 0.5), 1.e-10)
q = r.asQuaternion()
angles = r.threeAngles(Geometry.Vector(1., 0., 0.),
Geometry.Vector(0., 1., 0.),
Geometry.Vector(0., 0., 1.))
c = t * r
print c.screwMotion()
s = Scaling(2.)
all = s * t * r
print all(Geometry.ex)
junk = xyz_file.readline()
junk = xyz_file.readline()
while 1:
line = xyz_file.readline()
if not line: break
x, y, z = map(float, string.split(line)[1:]) #ignore atom label
cage_type = string.split(line)[0] #get the atom type
#Convert coordinates based on atom type
if (cage_type == "Ar(Small)"):
#Convert coordinates to vectors for the Small Cages
small_cages.append(Geo.Vector(x,y,z))
elif (cage_type == "Kr(Large)"):
#Convert coordinates to vectors for the Large Cages
large_cages.append(Geo.Vector(x,y,z))
else:
raise CorrelationError("Can't parse file. Encountered strange cage centre type: " + cage_type + " Only 'Ar(Small)' and 'Kr(Large)' accepted.")
xyz_file.close()
print "Read in Cage Centre locations. There are %d small and %d large cages." % (len(small_cages), len(large_cages))