def test_against_mathematica_two_overlap_atoms(self):
x=numpy.array([[2.920, -2.367, 1.693], [-0.770, -0.827, -0.417]], floattype)
y=numpy.array([[2.920, -2.367, 1.693], [-0.770, -0.827, -0.417]], floattype)
result_u = linear_algebra.find_u(x,y)
expected_u = [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]];
for i in range(len(result_u)):
self.assert_list_almost_equal(list(result_u[i]),expected_u[i])
def test_against_mathematica_three_arbitary_atoms(self):
x=numpy.array([[2.920, -2.367, 1.693], [-0.770, -0.827, -0.417], [-2.150, 3.193, -1.277]], floattype)
y=numpy.array([[1.663, -1.170, 3.567], [-1.197, -1.460, -0.523], [-0.467, 2.630, -3.043]], floattype)
result_u = linear_algebra.find_u(x,y)
expected_u = [[0.902737, -0.0539463, 0.426797], [0.23798, 0.8891, -0.390981], [-0.358373, 0.454522, 0.815462]]
for i in range(len(result_u)):
self.assert_list_almost_equal(list(result_u[i]),expected_u[i])
def test_against_mathematica_two_unit_atoms(self):
x=numpy.array([[1.0, 1.0, 1.0], [2.0, 1.0, 1.0]], floattype)
y=numpy.array([[1.0, 1.0, 1.0], [1.0, 2.0, 1.0]], floattype)
result_u = linear_algebra.find_u(x,y); print result_u
expected_u = [[0.0, 1.0, 0.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0]];
for i in range(len(result_u)):
self.assert_list_almost_equal(list(result_u[i]),expected_u[i])
def test_against_mathematica_six_arbitary_atoms(self):
x=numpy.array([[0.357, -12.123, 2.098], [1.209, 10.209, -50.082], [-1.098, 3.572, 2.982], \
[1.231, -1.230, 0.589], [12.398, -30.289, 19.482], [12.123, 0.980, 19.309]], floattype)
y=numpy.array([[90.380, 12.987, 0.392], [3.219, 83.390, 0.028], [0.002, 10.298, -18.820], \
[12.879, -10.298, 0.987], [0.986, 12.984, 0.367], [12.359, -12.402, 1.298]], floattype)
result_u = linear_algebra.find_u(x,y)
expected_u = [[0.121253, 0.025345, 0.992298], [-0.992602, 0.00937959, 0.12105], [-0.00623933, -0.999635, 0.0262948]]
for i in range(len(result_u)):
self.assert_list_almost_equal(list(result_u[i]),expected_u[i])
def test_find_u_unit(self):
x=numpy.array([[0,0,0],[1,0,0]], floattype)
y=numpy.array([[0,0,0],[0,1,0]], floattype)
rmx = linear_algebra.find_u(x,y)
result = numpy.dot(rmx,y.T)
result = result.T
self.assertEqual(len(result),len(x))
for i in range(len(x)):
self.assert_list_almost_equal(list(result[i]),x[i])
def test_find_u_rotate_pdb(self):
m1 = system.Molecule(0)
m2 = system.Molecule(1)
m1.read_pdb(PdbPath+"1CRN.pdb")
m2.read_pdb(modulePdbPath+"1CRN-rot.pdb")
coor_sub_m1 = m1.coor()[0]
coor_sub_m2 = m2.coor()[0]
u = linear_algebra.find_u(coor_sub_m1, coor_sub_m2)
result = numpy.array((numpy.matrix(u)*(numpy.matrix(coor_sub_m2).T)).T, numpy.float)
#print numpy.dot(result.reshape(1,-1)[0],coor_sub_m1.reshape(1,-1)[0])/numpy.sqrt(numpy.dot(coor_sub_m1.reshape(1,-1)[0],coor_sub_m1.reshape(1,-1)[0])*numpy.dot(result.reshape(1,-1)[0],result.reshape(1,-1)[0]))
#m3 = system.Molecule(2)
#m3.read_pdb('1CRN.pdb')
#m3._coor[0,:]=result
#m3.writepdb('1CRN-result.pdb',0,'w')
self.assertEqual(len(result),len(coor_sub_m1))
for i in range(len(coor_sub_m1)):
self.assert_list_almost_equal(list(result[i]),coor_sub_m1[i])
def align(self, other, self_basis, other_basis, **kwargs):
'''
Alignment of one object on top of another
"self" is aligned onto "other" using the basis
of molecule 2 to align onto the basis of molecule 1
and the transformation is then done to all the atoms of
molecule 2
self = molecule_2
other = molecule_1
self aligned to other
molecule_2 aligned to molecule_1
Parameters
----------
frame
integer : trajectory frame number to use
other
system object : molecule 1
self_basis
string : unique description of atoms used for alignment
other_basis
string : unique description of atoms used for alignment
kwargs
optional future arguments
Returns
-------
None
updated self._coor
Examples
-------
>>> import sasmol.system as system
>>> molecule_1 = system.Molecule('hiv1_gag.pdb')
>>> molecule_2 = system.Molecule('moved_and_rotated_hiv1_gag.pdb')
>>> frame = 0
>>> basis_1 = 'name[i] == "CA"'
>>> basis_2 = 'name[i] == "CA"'
>>> molecule_2.align(molecule_1, basis_1, basis_2)
>>> com_sub_2 = molecule_2.calculate_center_of_mass(frame)
Note
----
mass_check determines if mass is defined for the object so that
center of mass can be calculated
'''
frame = 0
### other = molecule_1 (reference)
error, other_mask = other.get_subset_mask(other_basis)
subset_other = sasmol.system.Molecule()
error = other.copy_molecule_using_mask(subset_other, other_mask, frame)
com_subset_other = subset_other.calculate_center_of_mass(frame)
subset_other.center(frame)
coor_subset_other = subset_other.coor()[frame]
### self = molecule_2 (to be aligned to other / molecule_1)
error, self_mask = self.get_subset_mask(self_basis)
subset_self = sasmol.system.Molecule()
error = self.copy_molecule_using_mask(subset_self, self_mask, frame)
com_subset_self = subset_self.calculate_center_of_mass(frame)
subset_self.center(frame)
coor_subset_self = subset_self.coor()[frame]
u = linear_algebra.find_u(coor_subset_self, coor_subset_other)
tao = numpy.transpose(self.coor()[frame] - com_subset_other)
error, nat2 = linear_algebra.matrix_multiply(u, tao)
ncoor = numpy.transpose(nat2) + com_subset_other
self._coor[frame, :] = ncoor
return
def align(self, other, self_basis, other_basis, **kwargs):
'''
Alignment of one object on top of another
"self" is aligned onto "other" using the basis
of molecule 2 to align onto the basis of molecule 1
and the transformation is then done to all the atoms of
molecule 2
self = molecule_2
other = molecule_1
self aligned to other
molecule_2 aligned to molecule_1
Parameters
----------
frame
integer : trajectory frame number to use
other
system object : molecule 1
self_basis
string : unique description of atoms used for alignment
other_basis
string : unique description of atoms used for alignment
kwargs
optional future arguments
Returns
-------
None
updated self._coor
Examples
-------
>>> import sasmol.system as system
>>> molecule_1 = system.Molecule('hiv1_gag.pdb')
>>> molecule_2 = system.Molecule('moved_and_rotated_hiv1_gag.pdb')
>>> frame = 0
>>> basis_1 = 'name[i] == "CA"'
>>> basis_2 = 'name[i] == "CA"'
>>> molecule_2.align(molecule_1, basis_1, basis_2)
>>> com_sub_2 = molecule_2.calculate_center_of_mass(frame)
Note
----
mass_check determines if mass is defined for the object so that
center of mass can be calculated
'''
frame = 0
### other = molecule_1 (reference)
error, other_mask = other.get_subset_mask(other_basis)
subset_other = sasmol.system.Molecule()
error = other.copy_molecule_using_mask(subset_other, other_mask, frame)
com_subset_other = subset_other.calculate_center_of_mass(frame)
subset_other.center(frame)
coor_subset_other = subset_other.coor()[frame]
### self = molecule_2 (to be aligned to other / molecule_1)
error, self_mask = self.get_subset_mask(self_basis)
subset_self = sasmol.system.Molecule()
error = self.copy_molecule_using_mask(subset_self, self_mask, frame)
com_subset_self = subset_self.calculate_center_of_mass(frame)
subset_self.center(frame)
coor_subset_self = subset_self.coor()[frame]
u = linear_algebra.find_u(coor_subset_self, coor_subset_other)
tao = numpy.transpose(self.coor()[frame] - com_subset_other)
error, nat2 = linear_algebra.matrix_multiply(u, tao)
ncoor = numpy.transpose(nat2) + com_subset_other
self._coor[frame, :] = ncoor
return