def test_unit_arrays_3(self):
a=numpy.array([[1.0, 0.0, 0.0]],floattype)
b=numpy.array([[1.0, 0.0, 0.0],[0.0, 1.0, 0.0]],floattype).T
result = linear_algebra.matrix_multiply(a,b)[1]
expected = numpy.array([[1.0, 0.0]],floattype)
self.assert_list_almost_equal(result,expected)
result_error = linear_algebra.matrix_multiply(a,b)[0]
expected_error = []
self.assertEqual(result_error, expected_error)
def test_unit_arrays_3(self):
a = numpy.array([[1.0, 0.0, 0.0]], floattype)
b = numpy.array([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0]], floattype).T
result = linear_algebra.matrix_multiply(a, b)[1]
expected = numpy.array([[1.0, 0.0]], floattype)
self.assert_list_almost_equal(result, expected)
result_error = linear_algebra.matrix_multiply(a, b)[0]
expected_error = []
self.assertEqual(result_error, expected_error)
def test_zero(self):
a=numpy.array([[util.ZERO, -20.0, 80.0],[2.02, util.ZERO, 20.0]],floattype)
b=numpy.array([[1.23, 2.0, 20.0],[10.0, 21.0, util.ZERO]],floattype).T
result = linear_algebra.matrix_multiply(a,b)[1]
expected = numpy.array([[1560.0, -420.0],[402.4846, 20.2]],floattype)
print result
self.assert_list_almost_equal(result,expected)
result_error = linear_algebra.matrix_multiply(a,b)[0]
expected_error = []
self.assertEqual(result_error, expected_error)
def test_nan_inf(self):
a=numpy.array([[util.INF, -20.0, 80.0],[2.02, util.NAN, 20.0]],floattype)
b=numpy.array([[1.23, 2.0, 20.0],[10.0, 21.0, util.NAN]],floattype).T
result = linear_algebra.matrix_multiply(a,b)[1]
expected = numpy.array([[util.INF, util.NAN],[util.NAN, util.NAN]],floattype)
print result
self.assert_list_almost_equal(result,expected)
result_error = linear_algebra.matrix_multiply(a,b)[0]
expected_error = []
self.assertEqual(result_error, expected_error)
def test_arb_2(self):
a=numpy.array([[1.0168308, -1.35572028, -1.35362422],[-0.69958848, 1.66901076, 0.49978462]],floattype)
b=numpy.array([-20.69958848, 16.66901076, 20.49978462],floattype)
result = linear_algebra.matrix_multiply(a,b)[1]
expected = numpy.array([[-71.396],[52.547]],floattype)
print result
self.assert_list_almost_equal(result,expected,3)
result_error = linear_algebra.matrix_multiply(a,b)[0]
expected_error = []
self.assertEqual(result_error, expected_error)
def test_arb_1(self):
a=numpy.array([[12.0, -20.0, -80.0],[2.02, -901.0, 0.0]],floattype)
b=numpy.array([[1.23, 0.03, 20.0],[10.0, 1.0, 3.0]],floattype).T
result = linear_algebra.matrix_multiply(a,b)[1]
expected = numpy.array([[-1585.84, -140.0],[-24.5454, -880.8]],floattype)
print result
self.assert_list_almost_equal(result,expected)
result_error = linear_algebra.matrix_multiply(a,b)[0]
expected_error = []
self.assertEqual(result_error, expected_error)
def test_arb_2(self):
a = numpy.array([[1.0168308, -1.35572028, -1.35362422],
[-0.69958848, 1.66901076, 0.49978462]], floattype)
b = numpy.array([-20.69958848, 16.66901076, 20.49978462], floattype)
result = linear_algebra.matrix_multiply(a, b)[1]
expected = numpy.array([[-71.396], [52.547]], floattype)
print result
self.assert_list_almost_equal(result, expected, 3)
result_error = linear_algebra.matrix_multiply(a, b)[0]
expected_error = []
self.assertEqual(result_error, expected_error)
def test_arb_1(self):
a = numpy.array([[12.0, -20.0, -80.0], [2.02, -901.0, 0.0]], floattype)
b = numpy.array([[1.23, 0.03, 20.0], [10.0, 1.0, 3.0]], floattype).T
result = linear_algebra.matrix_multiply(a, b)[1]
expected = numpy.array([[-1585.84, -140.0], [-24.5454, -880.8]],
floattype)
print result
self.assert_list_almost_equal(result, expected)
result_error = linear_algebra.matrix_multiply(a, b)[0]
expected_error = []
self.assertEqual(result_error, expected_error)
def test_zero(self):
a = numpy.array([[util.ZERO, -20.0, 80.0], [2.02, util.ZERO, 20.0]],
floattype)
b = numpy.array([[1.23, 2.0, 20.0], [10.0, 21.0, util.ZERO]],
floattype).T
result = linear_algebra.matrix_multiply(a, b)[1]
expected = numpy.array([[1560.0, -420.0], [402.4846, 20.2]], floattype)
print result
self.assert_list_almost_equal(result, expected)
result_error = linear_algebra.matrix_multiply(a, b)[0]
expected_error = []
self.assertEqual(result_error, expected_error)
def test_nan_inf(self):
a = numpy.array([[util.INF, -20.0, 80.0], [2.02, util.NAN, 20.0]],
floattype)
b = numpy.array([[1.23, 2.0, 20.0], [10.0, 21.0, util.NAN]],
floattype).T
result = linear_algebra.matrix_multiply(a, b)[1]
expected = numpy.array([[util.INF, util.NAN], [util.NAN, util.NAN]],
floattype)
print result
self.assert_list_almost_equal(result, expected)
result_error = linear_algebra.matrix_multiply(a, b)[0]
expected_error = []
self.assertEqual(result_error, expected_error)
def rotate(self, frame, axis, theta, **kwargs):
'''
Simple rotation about the x, y, or z axis.
Parameters
----------
frame
integer : trajectory frame number to use
axis
string : 'x', 'y', or 'z'
theta
float : angle in radians
kwargs
optional future arguments
Returns
-------
None
updated self._coor
Examples
-------
>>> import sasmol.system as system ; import math
>>> molecule = system.Molecule('hiv1_gag.pdb')
>>> frame = 0 ; axis = 'x' ; theta = 45.0 * math.pi / 180.0
>>> molecule.rotate(frame, axis, theta)
Note
----------
Calculations are carried out using radians
'''
cs = numpy.cos(theta)
si = numpy.sin(theta)
if(axis == 'x'):
mat = numpy.array(
[[1.0, 0.0, 0.0], [0.0, cs, -si], [0.0, si, cs]])
elif(axis == 'y'):
mat = numpy.array(
[[cs, 0.0, si], [0.0, 1.0, 0.0], [-si, 0.0, cs]])
elif(axis == 'z'):
mat = numpy.array(
[[cs, -si, 0.0], [si, cs, 0.0], [0.0, 0.0, 1.0]])
coordt = self._coor[frame, :].T
error, matrix_product = linear_algebra.matrix_multiply(mat, coordt)
ncoord = matrix_product.T
self._coor[frame, :] = ncoord
return
def rotate(self, frame, axis, theta, **kwargs):
'''
Simple rotation about the x, y, or z axis.
Parameters
----------
frame
integer : trajectory frame number to use
axis
string : 'x', 'y', or 'z'
theta
float : angle in radians
kwargs
optional future arguments
Returns
-------
None
updated self._coor
Examples
-------
>>> import sasmol.system as system ; import math
>>> molecule = system.Molecule('hiv1_gag.pdb')
>>> frame = 0 ; axis = 'x' ; theta = 45.0 * math.pi / 180.0
>>> molecule.rotate(frame, axis, theta)
Note
----------
Calculations are carried out using radians
'''
cs = numpy.cos(theta)
si = numpy.sin(theta)
if (axis == 'x'):
mat = numpy.array([[1.0, 0.0, 0.0], [0.0, cs, -si], [0.0, si, cs]])
elif (axis == 'y'):
mat = numpy.array([[cs, 0.0, si], [0.0, 1.0, 0.0], [-si, 0.0, cs]])
elif (axis == 'z'):
mat = numpy.array([[cs, -si, 0.0], [si, cs, 0.0], [0.0, 0.0, 1.0]])
coordt = self._coor[frame, :].T
error, matrix_product = linear_algebra.matrix_multiply(mat, coordt)
ncoord = matrix_product.T
self._coor[frame, :] = ncoord
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
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
