def glr_Uaxes(self, position, U, prob, color, line_width):
"""Draw the anisotropic axies of the atom at the given probability.
"""
## rotate U
R = self.matrix[:3, :3]
Ur = numpy.dot(numpy.dot(R, U), numpy.transpose(R))
evals, evecs = linalg.eigenvectors(Ur)
def glr_Uaxes(self, position, U, prob, color, line_width):
"""Draw the anisotropic axies of the atom at the given probability.
"""
## rotate U
R = self.matrix[:3, :3]
Ur = numpy.dot(numpy.dot(R, U), numpy.transpose(R))
evals, evecs = linalg.eigenvectors(Ur)
def findQuaternionMatrix(collection, point_ref, conf1, conf2 = None, matrix = True ):
universe = collection.universe()
if conf1.universe != universe:
raise ValueError, "conformation is for a different universe"
if conf2 is None:
conf1, conf2 = conf2, conf1
else:
if conf2.universe != universe:
raise ValueError, "conformation is for a different universe"
ref = conf1
conf = conf2
weights = universe.masses()
weights = weights/collection.mass()
ref_cms = point_ref.position().array
pos = N.zeros((3,), N.Float)
pos = point_ref.position(conf).array
possq = 0.
cross = N.zeros((3, 3), N.Float)
for a in collection.atomList():
r = a.position(conf).array - pos
r_ref = a.position(ref).array-ref_cms
w = weights[a]
possq = possq + w*N.add.reduce(r*r) \
+ w*N.add.reduce(r_ref*r_ref)
cross = cross + w*r[:, N.NewAxis]*r_ref[N.NewAxis, :]
k = N.zeros((4, 4), N.Float)
k[0, 0] = -cross[0, 0]-cross[1, 1]-cross[2, 2]
k[0, 1] = cross[1, 2]-cross[2, 1]
k[0, 2] = cross[2, 0]-cross[0, 2]
k[0, 3] = cross[0, 1]-cross[1, 0]
k[1, 1] = -cross[0, 0]+cross[1, 1]+cross[2, 2]
k[1, 2] = -cross[0, 1]-cross[1, 0]
k[1, 3] = -cross[0, 2]-cross[2, 0]
k[2, 2] = cross[0, 0]-cross[1, 1]+cross[2, 2]
k[2, 3] = -cross[1, 2]-cross[2, 1]
k[3, 3] = cross[0, 0]+cross[1, 1]-cross[2, 2]
for i in range(1, 4):
for j in range(i):
k[i, j] = k[j, i]
k = 2.*k
for i in range(4):
k[i, i] = k[i, i] + possq - N.add.reduce(pos*pos)
import numpy.oldnumeric.linear_algebra as LinearAlgebra
e, v = LinearAlgebra.eigenvectors(k)
i = N.argmin(e)
v = v[i]
if v[0] < 0: v = -v
if e[i] <= 0.:
rms = 0.
else:
rms = N.sqrt(e[i])
if matrix:
emax = N.argmax(e)
QuatMatrix = v
return Quaternion.Quaternion(QuatMatrix),v, e, e[i],e[emax], rms
else:
return Quaternion.Quaternion(v), Vector(ref_cms), Vector(pos), rms
def diagonalization(self):
"""Returns the eigenvalues of a rank-2 tensor and a tensor
representing the rotation matrix to the diagonalized form."""
if self.rank == 2:
from numpy.oldnumeric.linear_algebra import eigenvectors
ev, vectors = eigenvectors(self.array)
return ev, Tensor(vectors)
else:
raise ValueError, 'Undefined operation'
def pca(M):
"Perform PCA on M, return eigenvectors and eigenvalues, sorted."
T, N = shape(M)
# if there are fewer rows T than columns N, use snapshot method
if T < N:
C = dot(M, t(M))
evals, evecsC = eigenvectors(C)
# HACK: make sure evals are all positive
evals = where(evals < 0, 0, evals)
evecs = 1. / sqrt(evals) * dot(t(M), t(evecsC))
else:
# calculate covariance matrix
K = 1. / T * dot(t(M), M)
evals, evecs = eigenvectors(K)
# sort the eigenvalues and eigenvectors, descending order
order = (argsort(evals)[::-1])
evecs = take(evecs, order, 1)
evals = take(evals, order)
return evals, t(evecs)
def calc_inertia_tensor(atom_iter, origin):
"""Calculate a moment-of-inertia tensor at the given origin assuming all
atoms have the same mass.
"""
I = numpy.zeros((3, 3), float)
for atm in atom_iter:
x = atm.position - origin
I[0, 0] += x[1]**2 + x[2]**2
I[1, 1] += x[0]**2 + x[2]**2
I[2, 2] += x[0]**2 + x[1]**2
I[0, 1] += -x[0] * x[1]
I[1, 0] += -x[0] * x[1]
I[0, 2] += -x[0] * x[2]
I[2, 0] += -x[0] * x[2]
I[1, 2] += -x[1] * x[2]
I[2, 1] += -x[1] * x[2]
evals, evecs = linalg.eigenvectors(I)
## order the tensor such that the largest
## principal component is along the z-axis, and
## the second largest is along the y-axis
if evals[0] >= evals[1] and evals[0] >= evals[2]:
if evals[1] >= evals[2]:
R = numpy.array((evecs[2], evecs[1], evecs[0]), float)
else:
R = numpy.array((evecs[1], evecs[2], evecs[0]), float)
elif evals[1] >= evals[0] and evals[1] >= evals[2]:
if evals[0] >= evals[2]:
R = numpy.array((evecs[2], evecs[0], evecs[1]), float)
else:
R = numpy.array((evecs[0], evecs[2], evecs[1]), float)
elif evals[2] >= evals[0] and evals[2] >= evals[1]:
if evals[0] >= evals[1]:
R = numpy.array((evecs[1], evecs[0], evecs[2]), float)
else:
R = numpy.array((evecs[0], evecs[1], evecs[2]), float)
## make sure the tensor is right-handed
if numpy.allclose(linalg.determinant(R), -1.0):
I = numpy.identity(3, float)
I[0, 0] = -1.0
R = numpy.dot(I, R)
assert numpy.allclose(linalg.determinant(R), 1.0)
return R
def calc_inertia_tensor(atom_iter, origin):
"""Calculate a moment-of-inertia tensor at the given origin assuming all
atoms have the same mass.
"""
I = numpy.zeros((3,3), float)
for atm in atom_iter:
x = atm.position - origin
I[0,0] += x[1]**2 + x[2]**2
I[1,1] += x[0]**2 + x[2]**2
I[2,2] += x[0]**2 + x[1]**2
I[0,1] += - x[0]*x[1]
I[1,0] += - x[0]*x[1]
I[0,2] += - x[0]*x[2]
I[2,0] += - x[0]*x[2]
I[1,2] += - x[1]*x[2]
I[2,1] += - x[1]*x[2]
evals, evecs = linalg.eigenvectors(I)
## order the tensor such that the largest
## principal component is along the z-axis, and
## the second largest is along the y-axis
if evals[0] >= evals[1] and evals[0] >= evals[2]:
if evals[1] >= evals[2]:
R = numpy.array((evecs[2], evecs[1], evecs[0]), float)
else:
R = numpy.array((evecs[1], evecs[2], evecs[0]), float)
elif evals[1] >= evals[0] and evals[1] >= evals[2]:
if evals[0] >= evals[2]:
R = numpy.array((evecs[2], evecs[0], evecs[1]), float)
else:
R = numpy.array((evecs[0], evecs[2], evecs[1]), float)
elif evals[2] >= evals[0] and evals[2] >= evals[1]:
if evals[0] >= evals[1]:
R = numpy.array((evecs[1], evecs[0], evecs[2]), float)
else:
R = numpy.array((evecs[0], evecs[1], evecs[2]), float)
## make sure the tensor is right-handed
if numpy.allclose(linalg.determinant(R), -1.0):
I = numpy.identity(3, float)
I[0,0] = -1.0
R = numpy.dot(I, R)
assert numpy.allclose(linalg.determinant(R), 1.0)
return R
def PrincipalComponents(mat,reverseOrder=1):
""" do a principal components analysis
"""
import numpy.oldnumeric.linear_algebra as LinearAlgebra
covMat = FormCorrelationMatrix(mat)
eigenVals,eigenVects = LinearAlgebra.eigenvectors(covMat)
try:
eigenVals = eigenVals.real
except:
pass
try:
eigenVects = eigenVects.real
except:
pass
# and now sort:
ptOrder = numpy.argsort(eigenVals).tolist()
if reverseOrder:
ptOrder.reverse()
eigenVals = numpy.array([eigenVals[x] for x in ptOrder])
eigenVects = numpy.array([eigenVects[x] for x in ptOrder])
return eigenVals,eigenVects
def SuperimposePoints(src_points, dst_points):
"""Takes two 1:1 set of points and returns a 3x3 rotation matrix and
translation vector.
"""
num_points = src_points.shape[0]
## shift both sets of coordinates to their centroids
src_org = numpy.add.reduce(src_points) / float(src_points.shape[0])
dst_org = numpy.add.reduce(dst_points) / float(dst_points.shape[0])
X = numpy.add(src_points, -src_org)
Y = numpy.add(dst_points, -dst_org)
xy2n = 0.0
R = numpy.zeros((3,3), float)
for k in xrange(num_points):
x = X[k]
y = Y[k]
xy2n += numpy.add.reduce(x*x) + numpy.add.reduce(y*y)
R[0,0] += x[0]*y[0]
R[0,1] += x[0]*y[1]
R[0,2] += x[0]*y[2]
R[1,0] += x[1]*y[0]
R[1,1] += x[1]*y[1]
R[1,2] += x[1]*y[2]
R[2,0] += x[2]*y[0]
R[2,1] += x[2]*y[1]
R[2,2] += x[2]*y[2]
F = numpy.zeros((4,4), float)
F[0,0] = R[0,0] + R[1,1] + R[2,2]
F[0,1] = R[1,2] - R[2,1]
F[0,2] = R[2,0] - R[0,2]
F[0,3] = R[0,1] - R[1,0]
F[1,0] = F[0,1]
F[1,1] = R[0,0] - R[1,1] - R[2,2]
F[1,2] = R[0,1] + R[1,0]
F[1,3] = R[0,2] + R[2,0]
F[2,0] = F[0,2]
F[2,1] = F[1,2]
F[2,2] =-R[0,0] + R[1,1] - R[2,2]
F[2,3] = R[1,2] + R[2,1]
F[3,0] = F[0,3]
F[3,1] = F[1,3]
F[3,2] = F[2,3]
F[3,3] =-R[0,0] - R[1,1] + R[2,2]
evals, evecs = linalg.eigenvectors(F)
i = numpy.argmax(evals)
eval = evals[i]
evec = evecs[i]
msd = (xy2n - 2.0*eval) / num_points
if msd < 0.0:
rmsd = 0.0
else:
rmsd = math.sqrt(msd)
return SuperpositionResults(evec, src_org, dst_org, rmsd, num_points)
def rigidFit(self, mobileCoords):
"""
the rigidFit method computes the necessary
transformation matrices to superimpose the list of mobileCoords
onto the list of referenceCoords, and stores the resulting matrices
(rot, trans) <- rigidFit(mobileCoords)
Rigid body fit. Finds transformation (rot,trans) such that
r.m.s dist(x,rot*y+trans) --> min !
mobileCoords: cartesian coordinates of mobile structure (3,n) (input)
rot : rotation matrix (3,3) (output)
trans : translation vector (3) (output)
status: 0 if OK, 1 if singular problem (n<3 ...)
Method: W.Kabsch, Acta Cryst. (1976). A32,922-923
W.Kabsch, Acta Cryst. (1978). A34,827-828
"""
if self.refCoords is None:
raise RuntimeError(" no reference coordinates specified")
refCoords = self.refCoords
if len(refCoords) != len(mobileCoords):
raise RuntimeError("input vector length mismatch")
refCoords = Numeric.array(refCoords)
mobileCoords = Numeric.array(mobileCoords)
#
# 1. Compute centroids:
refCentroid = Numeric.sum(refCoords)/ len(refCoords)
mobileCentroid = Numeric.sum(mobileCoords)/ len(mobileCoords)
#
# 2. Wolfgang Kabsch's method for rotation matrix rot:
rot = Numeric.identity(3).astype('f')
# LOOK how to modify that code.
for i in xrange(3):
for j in xrange(3):
rot[j][i] = Numeric.sum((refCoords[:,i]-refCentroid[i])*
(mobileCoords[:,j]-mobileCentroid[j]))
rotTransposed = Numeric.transpose(rot)
e = Numeric.dot(rot, rotTransposed)
evals, evecs = LinearAlgebra.eigenvectors(e)
ev = Numeric.identity(3).astype('d')
# set ev[0] to be the evec or the largest eigenvalue
# and ev[1] to be the evec or the second largest eigenvalue
eigenValues = list(evals)
discard = eigenValues.index(min(eigenValues))
i = j =0
while i<3:
if i==discard:
i = i + 1
continue
ev[j] = evecs[i]
j = j + 1
i = i + 1
evecs = ev
evecs[2][0] = evecs[0][1]*evecs[1][2] - evecs[0][2]*evecs[1][1]
evecs[2][1] = evecs[0][2]*evecs[1][0] - evecs[0][0]*evecs[1][2]
evecs[2][2] = evecs[0][0]*evecs[1][1] - evecs[0][1]*evecs[1][0]
b = Numeric.dot(evecs, rot)
norm = math.sqrt(b[0][0]*b[0][0] + b[0][1]*b[0][1] + b[0][2]*b[0][2])
if math.fabs(norm)<1.0e-20: return -1, -1
b[0] = b[0]/norm
norm = math.sqrt(b[1][0]*b[1][0] + b[1][1]*b[1][1] + b[1][2]*b[1][2])
if math.fabs(norm)<1.0e-20: return -1, -1
b[1] = b[1]/norm
# vvmult(b[0],b[1],b[2])
b[2][0] = b[0][1]*b[1][2] - b[0][2]*b[1][1]
b[2][1] = b[0][2]*b[1][0] - b[0][0]*b[1][2]
b[2][2] = b[0][0]*b[1][1] - b[0][1]*b[1][0]
# mtrans3(e)
e = evecs
tempo=e[0][1]; e[0][1]=e[1][0]; e[1][0]=tempo
tempo=e[0][2]; e[0][2]=e[2][0]; e[2][0]=tempo
tempo=e[1][2]; e[1][2]=e[2][1]; e[2][1]=tempo
# mmmult3(b,e,rot)
rot[0][0] = b[0][0]*e[0][0] + b[1][0]*e[0][1] + b[2][0]*e[0][2]
rot[0][1] = b[0][1]*e[0][0] + b[1][1]*e[0][1] + b[2][1]*e[0][2]
rot[0][2] = b[0][2]*e[0][0] + b[1][2]*e[0][1] + b[2][2]*e[0][2]
rot[1][0] = b[0][0]*e[1][0] + b[1][0]*e[1][1] + b[2][0]*e[1][2]
rot[1][1] = b[0][1]*e[1][0] + b[1][1]*e[1][1] + b[2][1]*e[1][2]
rot[1][2] = b[0][2]*e[1][0] + b[1][2]*e[1][1] + b[2][2]*e[1][2]
rot[2][0] = b[0][0]*e[2][0] + b[1][0]*e[2][1] + b[2][0]*e[2][2]
rot[2][1] = b[0][1]*e[2][0] + b[1][1]*e[2][1] + b[2][1]*e[2][2]
rot[2][2] = b[0][2]*e[2][0] + b[1][2]*e[2][1] + b[2][2]*e[2][2]
#
# Compute translation vector trans:
# mvmult3(rot,cy,cy);
trans3 = [0, 0, 0]
for i in range(3):
trans3[i] = mobileCentroid[0]*rot[0][i] + mobileCentroid[1]*rot[1][i] + \
mobileCentroid[2]*rot[2][i]
#bcopy(t3,cy,sizeof(t3));
#vvdiff(cx,cy,trans);
trans = ( refCentroid[0]-trans3[0], refCentroid[1]-trans3[1], refCentroid[2]-trans3[2] )
#
# That's it...
self.rotationMatrix = rot
self.translationMatrix = trans
self.superimposed = 1
def rigidFit(self, mobileCoords):
"""
the rigidFit method computes the necessary
transformation matrices to superimpose the list of mobileCoords
onto the list of referenceCoords, and stores the resulting matrices
(rot, trans) <- rigidFit(mobileCoords)
Rigid body fit. Finds transformation (rot,trans) such that
r.m.s dist(x,rot*y+trans) --> min !
mobileCoords: cartesian coordinates of mobile structure (3,n) (input)
rot : rotation matrix (3,3) (output)
trans : translation vector (3) (output)
status: 0 if OK, 1 if singular problem (n<3 ...)
Method: W.Kabsch, Acta Cryst. (1976). A32,922-923
W.Kabsch, Acta Cryst. (1978). A34,827-828
"""
if self.refCoords is None:
raise RuntimeError(" no reference coordinates specified")
refCoords = self.refCoords
if len(refCoords) != len(mobileCoords):
raise RuntimeError("input vector length mismatch")
refCoords = Numeric.array(refCoords)
mobileCoords = Numeric.array(mobileCoords)
#
# 1. Compute centroids:
refCentroid = Numeric.sum(refCoords) / len(refCoords)
mobileCentroid = Numeric.sum(mobileCoords) / len(mobileCoords)
#
# 2. Wolfgang Kabsch's method for rotation matrix rot:
rot = Numeric.identity(3).astype('f')
# LOOK how to modify that code.
for i in xrange(3):
for j in xrange(3):
rot[j][i] = Numeric.sum(
(refCoords[:, i] - refCentroid[i]) *
(mobileCoords[:, j] - mobileCentroid[j]))
rotTransposed = Numeric.transpose(rot)
e = Numeric.dot(rot, rotTransposed)
evals, evecs = LinearAlgebra.eigenvectors(e)
ev = Numeric.identity(3).astype('d')
# set ev[0] to be the evec or the largest eigenvalue
# and ev[1] to be the evec or the second largest eigenvalue
eigenValues = list(evals)
discard = eigenValues.index(min(eigenValues))
i = j = 0
while i < 3:
if i == discard:
i = i + 1
continue
ev[j] = evecs[i]
j = j + 1
i = i + 1
evecs = ev
evecs[2][0] = evecs[0][1] * evecs[1][2] - evecs[0][2] * evecs[1][1]
evecs[2][1] = evecs[0][2] * evecs[1][0] - evecs[0][0] * evecs[1][2]
evecs[2][2] = evecs[0][0] * evecs[1][1] - evecs[0][1] * evecs[1][0]
b = Numeric.dot(evecs, rot)
norm = math.sqrt(b[0][0] * b[0][0] + b[0][1] * b[0][1] +
b[0][2] * b[0][2])
if math.fabs(norm) < 1.0e-20: return -1, -1
b[0] = b[0] / norm
norm = math.sqrt(b[1][0] * b[1][0] + b[1][1] * b[1][1] +
b[1][2] * b[1][2])
if math.fabs(norm) < 1.0e-20: return -1, -1
b[1] = b[1] / norm
# vvmult(b[0],b[1],b[2])
b[2][0] = b[0][1] * b[1][2] - b[0][2] * b[1][1]
b[2][1] = b[0][2] * b[1][0] - b[0][0] * b[1][2]
b[2][2] = b[0][0] * b[1][1] - b[0][1] * b[1][0]
# mtrans3(e)
e = evecs
tempo = e[0][1]
e[0][1] = e[1][0]
e[1][0] = tempo
tempo = e[0][2]
e[0][2] = e[2][0]
e[2][0] = tempo
tempo = e[1][2]
e[1][2] = e[2][1]
e[2][1] = tempo
# mmmult3(b,e,rot)
rot[0][0] = b[0][0] * e[0][0] + b[1][0] * e[0][1] + b[2][0] * e[0][2]
rot[0][1] = b[0][1] * e[0][0] + b[1][1] * e[0][1] + b[2][1] * e[0][2]
rot[0][2] = b[0][2] * e[0][0] + b[1][2] * e[0][1] + b[2][2] * e[0][2]
rot[1][0] = b[0][0] * e[1][0] + b[1][0] * e[1][1] + b[2][0] * e[1][2]
rot[1][1] = b[0][1] * e[1][0] + b[1][1] * e[1][1] + b[2][1] * e[1][2]
rot[1][2] = b[0][2] * e[1][0] + b[1][2] * e[1][1] + b[2][2] * e[1][2]
rot[2][0] = b[0][0] * e[2][0] + b[1][0] * e[2][1] + b[2][0] * e[2][2]
rot[2][1] = b[0][1] * e[2][0] + b[1][1] * e[2][1] + b[2][1] * e[2][2]
rot[2][2] = b[0][2] * e[2][0] + b[1][2] * e[2][1] + b[2][2] * e[2][2]
#
# Compute translation vector trans:
# mvmult3(rot,cy,cy);
trans3 = [0, 0, 0]
for i in range(3):
trans3[i] = mobileCentroid[0]*rot[0][i] + mobileCentroid[1]*rot[1][i] + \
mobileCentroid[2]*rot[2][i]
#bcopy(t3,cy,sizeof(t3));
#vvdiff(cx,cy,trans);
trans = (refCentroid[0] - trans3[0], refCentroid[1] - trans3[1],
refCentroid[2] - trans3[2])
#
# That's it...
self.rotationMatrix = rot
self.translationMatrix = trans
self.superimposed = 1
def SuperimposePoints(src_points, dst_points):
"""Takes two 1:1 set of points and returns a 3x3 rotation matrix and
translation vector.
"""
num_points = src_points.shape[0]
## shift both sets of coordinates to their centroids
src_org = numpy.add.reduce(src_points) / float(src_points.shape[0])
dst_org = numpy.add.reduce(dst_points) / float(dst_points.shape[0])
X = numpy.add(src_points, -src_org)
Y = numpy.add(dst_points, -dst_org)
xy2n = 0.0
R = numpy.zeros((3, 3), float)
for k in xrange(num_points):
x = X[k]
y = Y[k]
xy2n += numpy.add.reduce(x * x) + numpy.add.reduce(y * y)
R[0, 0] += x[0] * y[0]
R[0, 1] += x[0] * y[1]
R[0, 2] += x[0] * y[2]
R[1, 0] += x[1] * y[0]
R[1, 1] += x[1] * y[1]
R[1, 2] += x[1] * y[2]
R[2, 0] += x[2] * y[0]
R[2, 1] += x[2] * y[1]
R[2, 2] += x[2] * y[2]
F = numpy.zeros((4, 4), float)
F[0, 0] = R[0, 0] + R[1, 1] + R[2, 2]
F[0, 1] = R[1, 2] - R[2, 1]
F[0, 2] = R[2, 0] - R[0, 2]
F[0, 3] = R[0, 1] - R[1, 0]
F[1, 0] = F[0, 1]
F[1, 1] = R[0, 0] - R[1, 1] - R[2, 2]
F[1, 2] = R[0, 1] + R[1, 0]
F[1, 3] = R[0, 2] + R[2, 0]
F[2, 0] = F[0, 2]
F[2, 1] = F[1, 2]
F[2, 2] = -R[0, 0] + R[1, 1] - R[2, 2]
F[2, 3] = R[1, 2] + R[2, 1]
F[3, 0] = F[0, 3]
F[3, 1] = F[1, 3]
F[3, 2] = F[2, 3]
F[3, 3] = -R[0, 0] - R[1, 1] + R[2, 2]
evals, evecs = linalg.eigenvectors(F)
i = numpy.argmax(evals)
eval = evals[i]
evec = evecs[i]
msd = (xy2n - 2.0 * eval) / num_points
if msd < 0.0:
rmsd = 0.0
else:
rmsd = math.sqrt(msd)
return SuperpositionResults(evec, src_org, dst_org, rmsd, num_points)