def test_interpolate3D(self):
mat1=rotax([0,0,0], [0,0,1],30.0*degtorad)
mat2=rotax([0,0,0], [0,0,1],60.0*degtorad)
mat3=rotax([0,0,0], [0,0,1],90.0*degtorad)
# add translation (0,1,0) to mat2
mat2 = N.array([
[ 0.5 , 0.86602539, 0. , 0. ],
[-0.86602539, 0.5 , 0. , 0. ],
[ 0. , 0. , 1. , 0. ],
[ 0. , 1. , 0. , 1. ]],'f')
matList=[mat1, mat2, mat3]
indexList = [0.33333333, 0.66666666667, 1.0]
data = [[0.,0.,0.,1.],[1.0, 0.0, 0.0,1.0],[2.,0.,0.,1.]]
p=0.5
M = interpolate3DTransform(matList, indexList, p)
res=N.dot(data, M)[1]
self.assertEqual( self.diff(res[0], 0.70710677 ),True)
self.assertEqual(self.diff(res[1], 1.20710677 ),True) # 50% translation along Y axis
self.assertEqual(self.diff(res[2], 0.0),True)
p=1.5
M = interpolate3DTransform(matList, indexList, p)
res=N.dot(data, M)[1]
self.assertEqual(self.diff(res[0], -0.70710677 ),True)
self.assertEqual(self.diff(res[1], 0.70710677 ),True)
self.assertEqual(self.diff(res[2], 0.0),True)
def test_interpolate3D(self):
mat1 = rotax([0, 0, 0], [0, 0, 1], 30.0 * degtorad)
mat2 = rotax([0, 0, 0], [0, 0, 1], 60.0 * degtorad)
mat3 = rotax([0, 0, 0], [0, 0, 1], 90.0 * degtorad)
# add translation (0,1,0) to mat2
mat2 = N.array([[0.5, 0.86602539, 0., 0.], [-0.86602539, 0.5, 0., 0.],
[0., 0., 1., 0.], [0., 1., 0., 1.]], 'f')
matList = [mat1, mat2, mat3]
indexList = [0.33333333, 0.66666666667, 1.0]
data = [[0., 0., 0., 1.], [1.0, 0.0, 0.0, 1.0], [2., 0., 0., 1.]]
p = 0.5
M = interpolate3DTransform(matList, indexList, p)
res = N.dot(data, M)[1]
self.assertEqual(self.diff(res[0], 0.70710677), True)
self.assertEqual(self.diff(res[1], 1.20710677),
True) # 50% translation along Y axis
self.assertEqual(self.diff(res[2], 0.0), True)
p = 1.5
M = interpolate3DTransform(matList, indexList, p)
res = N.dot(data, M)[1]
self.assertEqual(self.diff(res[0], -0.70710677), True)
self.assertEqual(self.diff(res[1], 0.70710677), True)
self.assertEqual(self.diff(res[2], 0.0), True)
def __applyTorsion(self, node, parent_mtx):
"""Transform the subtree rooted at node.
The new torsion angle must be pre-set.
Children of the node are transformed recursively.
"""
# get rotation matrix for node
# my_mtx = self.rotax(node)
mtx = rotax( Numeric.array(node.a.coords),
Numeric.array(node.b.coords),
node.angle * self.rads_per_degree, transpose=1)
# node_mtx = Numeric.dot(parent_mtx, mtx)
node_mtx = self.mult4_3Mat(parent_mtx, mtx)
# set-up for the transformation
mm11 = node_mtx[0][0]; mm12 = node_mtx[0][1]; mm13 = node_mtx[0][2]
mm21 = node_mtx[1][0]; mm22 = node_mtx[1][1]; mm23 = node_mtx[1][2]
mm31 = node_mtx[2][0]; mm32 = node_mtx[2][1]; mm33 = node_mtx[2][2]
mm41 = node_mtx[3][0]; mm42 = node_mtx[3][1]; mm43 = node_mtx[3][2]
atomSet = node.atomSet
# transform the coordinates for the node
for i in node.atomRange:
x,y,z = node.coords[i][:3] # get origin-subtracted originals
c = atomSet[i].coords
c[0] = x*mm11 + y*mm21 + z*mm31 + mm41
c[1] = x*mm12 + y*mm22 + z*mm32 + mm42
c[2] = x*mm13 + y*mm23 + z*mm33 + mm43
# recurse through children
for child in node.children:
self.__applyTorsion(child, node_mtx)
def setValue(self, value):
#print 'Rotate by', value
mat = rotax((0, 0, 0), self.axis, value * math.pi / 180.)
object = self.object
object.ConcatRotation(mat.flatten())
if isinstance(object, Camera):
object.Redraw()
def doit(self, atom1, atom2, angle, mov_atoms, returnVal=0):
mol = atom1.top
if mov_atoms is None:
mov_atoms = mol.subTree(atom1, atom2, mol.allAtoms)
assert len(mov_atoms)
mov_coords = Numeric.array(mov_atoms.coords)
lenCoords = len(mov_coords)
x = Numeric.array(atom1.coords)
y = Numeric.array(atom2.coords)
rot = (angle * 3.14159 / 180.) % (2 * Numeric.pi)
matrix = rotax(x, y, rot)
_ones = Numeric.ones(lenCoords, 'f')
_ones.shape = (lenCoords, 1)
mov_coords = Numeric.concatenate((mov_coords, _ones), 1)
newcoords = Numeric.dot(mov_coords, matrix)
nc = newcoords[:, :3].astype('f')
for i in range(lenCoords):
at = mov_atoms[i]
at._coords[at.conformation] = nc[i].tolist()
event = EditAtomsEvent('coords', mov_atoms)
self.vf.dispatchEvent(event)
#have to return nc for setTorsionGC
if returnVal:
return nc
def __applyTorsion(self, node, parent_mtx):
"""Transform the subtree rooted at node.
The new torsion angle must be pre-set.
Children of the node are transformed recursively.
"""
# get rotation matrix for node
# my_mtx = self.rotax(node)
mtx = rotax( Numeric.array(node.a.coords),
Numeric.array(node.b.coords),
node.angle * self.rads_per_degree, transpose=1)
# node_mtx = Numeric.dot(parent_mtx, mtx)
node_mtx = self.mult4_3Mat(parent_mtx, mtx)
# set-up for the transformation
mm11 = node_mtx[0][0]; mm12 = node_mtx[0][1]; mm13 = node_mtx[0][2]
mm21 = node_mtx[1][0]; mm22 = node_mtx[1][1]; mm23 = node_mtx[1][2]
mm31 = node_mtx[2][0]; mm32 = node_mtx[2][1]; mm33 = node_mtx[2][2]
mm41 = node_mtx[3][0]; mm42 = node_mtx[3][1]; mm43 = node_mtx[3][2]
atomSet = node.atomSet
# transform the coordinates for the node
for i in node.atomRange:
x,y,z = node.coords[i][:3] # get origin-subtracted originals
c = atomSet[i].coords
c[0] = x*mm11 + y*mm21 + z*mm31 + mm41
c[1] = x*mm12 + y*mm22 + z*mm32 + mm42
c[2] = x*mm13 + y*mm23 + z*mm33 + mm43
# recurse through children
for child in node.children:
self.__applyTorsion(child, node_mtx)
def setValue(self, value):
#print 'Rotate by', value
mat = rotax( (0,0,0), self.axis, value*math.pi/180.)
object = self.object
object.ConcatRotation(mat.flatten())
if isinstance(object, Camera):
object.Redraw()
def mouseMove(self, event):
# simple trackball, only works inside cirle
# creates an XY rotation defined by pts intersecting the spheres
xc = event.x - self.xm
yc = self.ym - event.y
# compute the intersection point between
xc2 = xc*xc
yc2 = yc*yc
z2 = self.r2-xc2-yc2
if z2 < 0:
lInvMag = 1./math.sqrt(xc2 + yc2)
xc *= lInvMag * (self.r)
yc *= lInvMag * (self.r)
z2 = 0
# compute rotation angle
a = self.lastPt3D
b = (xc, yc, math.sqrt(z2))
ang = math.acos((a[0]*b[0]+a[1]*b[1]+a[2]*b[2])/self.r2)
if self.mode=='XY':
#compute rotation axis
rotaxis = Numeric.array( (a[1]*b[2] - a[2]*b[1],
a[2]*b[0] - a[0]*b[2],
a[0]*b[1] - a[1]*b[0] ), 'f' )
elif self.mode=='X': rotaxis = Numeric.array( (1.,0.,0.), 'f')
elif self.mode=='Y': rotaxis = Numeric.array( (0.,1.,0.), 'f')
elif self.mode=='Z': rotaxis = Numeric.array( (0.,0.,1.), 'f')
mat = rotax( self.zeros, rotaxis, ang )
self.lastPt3D = b
self.updateVector(mat)
def mouseMove(self, event):
# simple trackball, only works inside cirle
# creates an XY rotation defined by pts intersecting the spheres
xc = event.x - self.xm
yc = self.ym - event.y
# compute the intersection point between
xc2 = xc * xc
yc2 = yc * yc
z2 = self.r2 - xc2 - yc2
if z2 < 0:
lInvMag = 1. / math.sqrt(xc2 + yc2)
xc *= lInvMag * (self.r)
yc *= lInvMag * (self.r)
z2 = 0
# compute rotation angle
a = self.lastPt3D
b = (xc, yc, math.sqrt(z2))
ang = math.acos((a[0] * b[0] + a[1] * b[1] + a[2] * b[2]) / self.r2)
if self.mode == 'XY':
#compute rotation axis
rotaxis = numpy.array(
(a[1] * b[2] - a[2] * b[1], a[2] * b[0] - a[0] * b[2],
a[0] * b[1] - a[1] * b[0]), 'f')
elif self.mode == 'X':
rotaxis = numpy.array((1., 0., 0.), 'f')
elif self.mode == 'Y':
rotaxis = numpy.array((0., 1., 0.), 'f')
elif self.mode == 'Z':
rotaxis = numpy.array((0., 0., 1.), 'f')
mat = rotax(self.zeros, rotaxis, ang)
self.lastPt3D = b
self.updateVector(mat)
def doit(self, atom1, atom2, angle, mov_atoms, returnVal=0):
mol = atom1.top
if mov_atoms is None:
mov_atoms = mol.subTree(atom1, atom2, mol.allAtoms)
assert len(mov_atoms)
mov_coords = Numeric.array(mov_atoms.coords)
lenCoords = len(mov_coords)
x = Numeric.array(atom1.coords)
y = Numeric.array(atom2.coords)
rot = (angle * 3.14159/180.)%(2 * Numeric.pi)
matrix = rotax(x, y, rot)
_ones = Numeric.ones(lenCoords, 'f')
_ones.shape = (lenCoords,1)
mov_coords = Numeric.concatenate((mov_coords, _ones),1)
newcoords = Numeric.dot(mov_coords, matrix)
nc = newcoords[:,:3].astype('f')
for i in range(lenCoords):
at = mov_atoms[i]
at._coords[at.conformation] = nc[i].tolist()
event = EditAtomsEvent('coords', mov_atoms)
self.vf.dispatchEvent(event)
#have to return nc for setTorsionGC
if returnVal:
return nc
def rotateObject():
from mglutil.math.rotax import rotax
from math import sin, cos, pi, sqrt, fabs
import random
degtorad = pi/180.
point1 = [random.random()*8-4, random.random()*8-4.,random.random()*10-5]
point2 = [random.random()*8-4, random.random()*8-4.,random.random()*10-5.]
angle = random.random()*360.
transf = rotax(point1, point2, angle*degtorad, transpose=1)
from mglutil.math.rotax import mat_to_axis_angle
vector , pp, angle = mat_to_axis_angle(transf)
from FlexTree.FTMotions import FTMotion_Hinge
motion = FTMotion_Hinge(axis={'vector':vector,'point':pp})
motion.configure(angle=angle)
m1=Numeric.array(motion.getMatrix()).ravel()
m2=transf.ravel()
bSame = True
for i in range(len(m1)):
if fabs(m1[i]-m2[i]) > 1e-4:
bSame = False
assert (bSame, True)
def getRotMatrix(self, shape=(4,4), transpose = None):
"""return the rotation matrix as a array of shape shape.
"""
try:
assert( shape in [ (3,3), (4,4), (9,), (16,)] )
except:
raise ValueError('shape must be (3,3), (4,4), (9,) or (16,)')
# get the inverse 4x4 from rotax
mtx = rotax.rotax(numpy.array([0.,0.,0.],'f'),self.pure,2*numpy.arccos(self.real))
# strip if necessary
if shape in ((3,3),(9,)):
mtx = [x[:3] for x in mtx]
mtx = mtx[:3]
if not transpose:
return numpy.reshape(numpy.transpose(mtx),shape)
else:
return numpy.reshape(mtx,shape)
def setRelativeTorsion(atom1, atom2, angle): #mov_atoms=None):
#rat1, rat2, ??30degrees??
mol = atom1.top
if mov_atoms is None:
mov_atoms = mol.subTree(atom1, atom2, mol.allAtoms)
assert len(mov_atoms)
mov_coords = Numeric.array(mov_atoms.coords)
lenCoords = len(mov_coords)
x = Numeric.array(atom1.coords)
y = Numeric.array(atom2.coords)
rot = (angle * 3.14159/180.)%(2 * Numeric.pi)
matrix = rotax(x, y, rot)
_ones = Numeric.ones(lenCoords, 'f')
_ones.shape = (lenCoords,1)
mov_coords = Numeric.concatenate((mov_coords, _ones),1)
newcoords = Numeric.dot(mov_coords, matrix)
nc = newcoords[:,:3].astype('f')
for i in range(lenCoords):
at = mov_atoms[i]
at._coords[at.conformation] = nc[i].tolist()
def setRelativeTorsion(atom1, atom2, angle): #mov_atoms=None):
#rat1, rat2, ??30degrees??
mol = atom1.top
if mov_atoms is None:
mov_atoms = mol.subTree(atom1, atom2, mol.allAtoms)
assert len(mov_atoms)
mov_coords = Numeric.array(mov_atoms.coords)
lenCoords = len(mov_coords)
x = Numeric.array(atom1.coords)
y = Numeric.array(atom2.coords)
rot = (angle * 3.14159 / 180.) % (2 * Numeric.pi)
matrix = rotax(x, y, rot)
_ones = Numeric.ones(lenCoords, 'f')
_ones.shape = (lenCoords, 1)
mov_coords = Numeric.concatenate((mov_coords, _ones), 1)
newcoords = Numeric.dot(mov_coords, matrix)
nc = newcoords[:, :3].astype('f')
for i in range(lenCoords):
at = mov_atoms[i]
at._coords[at.conformation] = nc[i].tolist()
def getRotMatrix(self, shape=(4,4), transpose = None):
"""return the rotation matrix as a Numeric array of shape shape.
"""
try:
assert( shape in [ (3,3), (4,4), (9,), (16,)] )
except:
raise ValueError('shape must be (3,3), (4,4), (9,) or (16,)')
# get the inverse 4x4 from rotax
mtx = rotax.rotax(N.array([0.,0.,0.],'f'),self.pure,2*N.arccos(self.real))
# strip if necessary
if shape in ((3,3),(9,)):
mtx = map(lambda x: x[:3],mtx)
mtx = mtx[:3]
if not transpose:
return N.reshape(N.transpose(mtx),shape)
else:
return N.reshape(mtx,shape)
def getMatrices(self):
matrices = []
r = self.hrise
v = self.vector
p = self.point
rv = (r*v[0], r*v[1], r*v[2])
## does not work .. some weird problem with the angle (MS)
# build one increment of transformation
## R = Transformation(
## trans=[rv[0], rv[1], rv[2]],
## quaternion=[v[0], v[1], v[2], self.angle*180/math.pi])
## T = Transformation(trans=self.point)
## transform1 = T * R * T.inverse()
## transform = T * R * T.inverse()
## matrices.append( transform.getMatrix() )
## for i in range(self.copies-1):
## transform = transform*transform1
## matrices.append( transform.getMatrix() )
# build rotation and translation matrix about helical axis going
# rot matrix C style
R = rotax( p, [p[0]+v[0], p[1]+v[1], p[2]+v[2]],
self.angle, False)
riseMat = Numeric.identity(4).astype('f')
riseMat[:3, 3] = rv # add the rise
transform = Numeric.dot(riseMat, R)
N = Numeric
matrices.append( N.identity(4).astype('f'))
for i in range(1,self.copies):
mat = matrices[i-1]
mat = Numeric.dot(mat, transform)
matrices.append(mat)
return matrices
## Automatically adapted for numpy.oldnumeric Jul 23, 2007 by
#
# collection of standard 4x4 rotation matrices
# about the X, Y and Z axis of 10, 30, 45, 90, 180 degrees
#
rotations = {
}
import math, numpy.oldnumeric as Numeric
from mglutil.math.rotax import rotax
orig = Numeric.array( (0,0,0), 'f')
X = Numeric.array( (1,0,0), 'f')
Y = Numeric.array( (0,1,0), 'f')
Z = Numeric.array( (0,0,1), 'f')
for angle in [1, 5, 10, 30, 45, 90, 180]:
rotations['X'+str(angle)] = rotax( orig, X, angle*math.pi/180.)
rotations['X-'+str(angle)] = rotax( orig, X, -angle*math.pi/180.)
for angle in [1, 5, 10, 30, 45, 90, 180]:
rotations['Y'+str(angle)] = rotax( orig, Y, angle*math.pi/180.)
rotations['Y-'+str(angle)] = rotax( orig, Y, -angle*math.pi/180.)
for angle in [1, 5, 10, 30, 45, 90, 180]:
rotations['Z'+str(angle)] = rotax( orig, Z, angle*math.pi/180.)
rotations['Z-'+str(angle)] = rotax( orig, Z, -angle*math.pi/180.)
else:
print 'Sorry! Unable to write this filetype->', filetype
center = Numeric.add.reduce(mol.allAtoms.coords)/len(mol.allAtoms)
crds = Numeric.array(mol.allAtoms.coords)
center = Numeric.add.reduce(crds)/len(mol.allAtoms)
crds = crds - center
crds = crds.tolist()
mol.allAtoms.updateCoords(crds)
lenCoords = len(crds)
#rotate the atoms here
if axis is not None and angle is not None:
rot = (float(angle)* 3.14159/180.)%(2 * Numeric.pi)
x = Numeric.array([0.,0.,0.])
y = Numeric.array(map(float,axis.split(',')))
matrix = rotax(x,y, rot)
_ones = Numeric.ones(lenCoords, 'f')
_ones.shape = (lenCoords,1)
mov_coords = Numeric.concatenate((crds, _ones),1)
newcoords = Numeric.dot(mov_coords, matrix)
nc = newcoords[:,:3].astype('f')
for i in range(lenCoords):
mol.allAtoms[i]._coords[0] = nc[i].tolist()
else:
if rotation=='z':
#for rotation around z-axis:
for a in mol.allAtoms:
a._coords[0][0] = -1.*a._coords[0][0]
a._coords[0][1] = -1.*a._coords[0][1]
elif rotation=='y':
#for rotation around y-axis:
def getMatrices(self):
pt1 = self.point
v1 = self.vector
r1 = self.hrise
pt2 = self.point2
v2 = self.vector2
r2 = self.hrise2
nbCopies = self.copies
matrices1 = [] # overall helical transfomations
matrices2 = [] # local helical transformations
rv1 = (r1*v1[0], r1*v1[1], r1*v1[2]) # tanslation vector 1
rv2 = (r2*v2[0], r2*v2[1], r2*v2[2]) # tanslation vector 2
# rotation matrix for helix 1
R = rotax( pt1, [pt1[0]+v1[0], pt1[1]+v1[1], pt1[2]+v1[2]],
self.angle, False)
# rise transformation for helix 1
riseMat1 = numpy.identity(4).astype('f')
riseMat1[:3, 3] = rv1 # add the rise
# helical step for helix 1
transform1 = numpy.dot(riseMat1, R)
# first transformation is didentity for both helices
matrices1.append( numpy.identity(4).astype('f') )
matrices2.append( numpy.identity(4).astype('f') )
ang2 = self.angle2 # angle for helix 2
# loop over number of copies
for i in range(1,nbCopies):
# take previous transfromation
mat = matrices1[i-1]
# add 1 helic step for overall helix
mat = numpy.dot(mat, transform1)
# save this in transformation for overall helix
matrices1.append(mat)
# move the point defining local helix along first helical axis
p2t = (pt2[0]+(i*rv1[0]), pt2[1]+(i*rv1[1]), pt2[2]+(i*rv1[2]))
# build local helix rotation
R = rotax( p2t, [p2t[0]+v2[0], p2t[1]+v2[1], p2t[2]+v2[2]],
ang2, False)
# build local helix raise
riseMat2 = numpy.identity(4).astype('f')
riseMat2[:3, 3] = rv2 # add the rise
# build helical step for local helix
transform2 = numpy.dot(riseMat2, R)
mat = matrices2[i-1]
# apply step to previous helical step
mat = numpy.dot(mat, transform2)
matrices2.append(mat)
# combine the overall helix wioth the local helix
results = []
results.append(numpy.identity(4).astype('f') )
for i in range(1,nbCopies):
results.append( numpy.dot(matrices2[i], matrices1[i]) )
return results
else:
print('Sorry! Unable to write this filetype->', filetype)
center = numpy.add.reduce(mol.allAtoms.coords) / len(mol.allAtoms)
crds = numpy.array(mol.allAtoms.coords)
center = numpy.add.reduce(crds) / len(mol.allAtoms)
crds = crds - center
crds = crds.tolist()
mol.allAtoms.updateCoords(crds)
lenCoords = len(crds)
#rotate the atoms here
if axis is not None and angle is not None:
rot = (float(angle) * 3.14159 / 180.) % (2 * numpy.pi)
x = numpy.array([0., 0., 0.])
y = numpy.array(list(map(float, axis.split(','))))
matrix = rotax(x, y, rot)
_ones = numpy.ones(lenCoords, 'f')
_ones.shape = (lenCoords, 1)
mov_coords = numpy.concatenate((crds, _ones), 1)
newcoords = numpy.dot(mov_coords, matrix)
nc = newcoords[:, :3].astype('f')
for i in range(lenCoords):
mol.allAtoms[i]._coords[0] = nc[i].tolist()
else:
if rotation == 'z':
#for rotation around z-axis:
for a in mol.allAtoms:
a._coords[0][0] = -1. * a._coords[0][0]
a._coords[0][1] = -1. * a._coords[0][1]
elif rotation == 'y':
#for rotation around y-axis:
## Automatically adapted for numpy.oldnumeric Jul 23, 2007 by
#
# collection of standard 4x4 rotation matrices
# about the X, Y and Z axis of 10, 30, 45, 90, 180 degrees
#
rotations = {}
import math, numpy.oldnumeric as Numeric
from mglutil.math.rotax import rotax
orig = Numeric.array((0, 0, 0), 'f')
X = Numeric.array((1, 0, 0), 'f')
Y = Numeric.array((0, 1, 0), 'f')
Z = Numeric.array((0, 0, 1), 'f')
for angle in [1, 5, 10, 30, 45, 90, 180]:
rotations['X' + str(angle)] = rotax(orig, X, angle * math.pi / 180.)
rotations['X-' + str(angle)] = rotax(orig, X, -angle * math.pi / 180.)
for angle in [1, 5, 10, 30, 45, 90, 180]:
rotations['Y' + str(angle)] = rotax(orig, Y, angle * math.pi / 180.)
rotations['Y-' + str(angle)] = rotax(orig, Y, -angle * math.pi / 180.)
for angle in [1, 5, 10, 30, 45, 90, 180]:
rotations['Z' + str(angle)] = rotax(orig, Z, angle * math.pi / 180.)
rotations['Z-' + str(angle)] = rotax(orig, Z, -angle * math.pi / 180.)