def test_inf_2(self):
a = numpy.array([util.INF, 3.0, 0.0], floattype)
b = numpy.array([util.INF, 1.2, 2.3], floattype)
c = numpy.array([0.3, util.INF, 29.02], floattype)
d = numpy.array([2.1, 1.0, 29.02], floattype)
result = sasmath.dihedral_angle(a, b, c, d)
self.assertTrue(numpy.isnan(result) or numpy.isinf(result))
def test_nan(self):
a = numpy.array([util.NAN, 3.0, 0.0], floattype)
b = numpy.array([6.0, util.NAN, 2.0], floattype)
c = numpy.array([util.NAN, 1.0, 0.0], floattype)
d = numpy.array([2.1, 1.0, 29.02], floattype)
result = sasmath.dihedral_angle(a, b, c, d)
self.assertTrue(numpy.isnan(result))
def test_arb_1(self):
a = numpy.array([23.0, 0.0, 0.0], floattype)
b = numpy.array([0.0, 0.0, 0.0], floattype)
c = numpy.array([0.0, 12.0, 0.0], floattype)
d = numpy.array([0.0, 212.0, -20.0], floattype)
result = sasmath.dihedral_angle(a, b, c, d)
expected = 90.0
self.assertAlmostEqual(result, expected)
def test_same_plane_1(self):
a = numpy.array([1.0, 0.0, 0.0], floattype)
b = numpy.array([0.0, 0.0, 0.0], floattype)
c = numpy.array([0.0, 1.0, 0.0], floattype)
d = numpy.array([1.0, 1.0, 0.0], floattype)
result = sasmath.dihedral_angle(a, b, c, d)
expected = 0.0
self.assertAlmostEqual(result, expected)
def test_all_zero_arrays(self):
a = numpy.array([0.0, 0.0, 0.0], floattype)
b = numpy.array([0.0, 0.0, 0.0], floattype)
c = numpy.array([0.0, 0.0, 0.0], floattype)
d = numpy.array([0.0, 0.0, 0.0], floattype)
result = sasmath.dihedral_angle(a, b, c, d)
expected = 180.0
self.assertAlmostEqual(result, expected)
def test_zero(self):
a = numpy.array([util.ZERO, 3.0, 0.0], floattype)
b = numpy.array([6.0, util.ZERO, 2.0], floattype)
c = numpy.array([6.7, 1.0, util.ZERO], floattype)
d = numpy.array([2.1, 1.0, 29.02], floattype)
result = sasmath.dihedral_angle(a, b, c, d)
expected = 89.502
self.assertAlmostEqual(result, expected, 3)
def test_tiny(self):
a = numpy.array([util.TINY, 3.0, 0.0], floattype)
b = numpy.array([6.0, util.TINY, 2.0], floattype)
c = numpy.array([2.0, 3.2, util.TINY], floattype)
d = numpy.array([2.1, 1.0, 29.02], floattype)
result = sasmath.dihedral_angle(a, b, c, d)
expected = 66.032
self.assertAlmostEqual(result, expected, 3)
def test_arb_2(self):
a = numpy.array([1.0168308, -1.35572028, -1.35362422], floattype)
b = numpy.array([-0.69958848, 1.66901076, 0.49978462], floattype)
c = numpy.array([12.0168308, 12.35572028, 1.35362422], floattype)
d = numpy.array([-20.69958848, 16.66901076, 20.49978462], floattype)
c = numpy.array([0.3, 0.0, -1.2], floattype)
result = sasmath.dihedral_angle(a, b, c, d)
expected = 85.786
self.assertAlmostEqual(result, expected, 3)
def calculate_initial_torsion_variables(other_self, main_pivots_masks):
mol = other_self.mol
frame = 0
torsion_angles = []
for mask in main_pivots_masks:
error, coor = mol.get_coor_using_mask(frame,mask)
if len(error) > 0:
log.error('ERROR: '+str(error))
else:
c = coor[0]
torsion_angles.append(sasmath.dihedral_angle(c[0],c[1],c[2],c[3]))
#print torsion_angles[-1]
return
def measure(other_self, group_molecule, group_number, pivot_number):
mvars = other_self.mvars
pvars = mvars.pvars
log = other_self.log
pgui = other_self.run_utils.print_gui
main_pivots_mask = pvars.main_pivots_masks[group_number][pivot_number]
coor = group_molecule.coor()
log.debug('in measure')
##pgui('Indices of selected main_pivots_mask = '+str(numpy.nonzero(main_pivots_mask)[0]))
ind=numpy.nonzero(main_pivots_mask*numpy.arange(1,len(main_pivots_mask)+1))[0]
this_frame_coor = coor[0,:,:]
lcoor=numpy.take(this_frame_coor[:,:],ind,0)
angle=sasmath.dihedral_angle(lcoor[0,:],lcoor[1,:],lcoor[2,:],lcoor[3,:])
return angle
def measure(coor, indices, an, this_mask, q0, first_last_resid, molecule_type,
drude=False):
ind = numpy.nonzero(this_mask * numpy.arange(1, len(this_mask) + 1))[0]
this_frame_coor = coor[0, :, :]
lcoor = numpy.take(this_frame_coor[:, :], ind, 0)
error = []
if(molecule_type == 'protein'):
if(an == 'phi'):
angle = sasmath.dihedral_angle(lcoor[0, :], lcoor[1, :],
lcoor[2, :], lcoor[3, :])
elif(an == 'psi'):
if(q0 == first_last_resid[0]):
angle = sasmath.dihedral_angle(lcoor[0, :], lcoor[1, :],
lcoor[2, :], lcoor[3, :])
else:
angle = sasmath.dihedral_angle(lcoor[1, :], lcoor[2, :],
lcoor[3, :], lcoor[4, :])
else:
angle = 0.0
message = 'error (in rotate.measure): %s angle not in phi/psi' % an
error.append(message)
assert not error, error
elif(molecule_type == 'rna'):
if(an == 'alpha'):
angle = sasmath.dihedral_angle(lcoor[0, :], lcoor[1, :],
lcoor[2, :], lcoor[3, :])
elif(an == 'beta'):
if(q0 == first_last_resid[0]):
angle = sasmath.dihedral_angle(lcoor[0, :], lcoor[1, :],
lcoor[2, :], lcoor[3, :])
else:
angle = sasmath.dihedral_angle(lcoor[1, :], lcoor[2, :],
lcoor[3, :], lcoor[4, :])
elif(an == 'gamma'):
if(q0 == first_last_resid[0]):
angle = sasmath.dihedral_angle(lcoor[1, :], lcoor[2, :],
lcoor[3, :], lcoor[4, :])
else:
angle = sasmath.dihedral_angle(lcoor[2, :], lcoor[3, :],
lcoor[4, :], lcoor[5, :])
elif(an == 'delta'):
if(q0 == first_last_resid[0]):
angle = sasmath.dihedral_angle(lcoor[2, :], lcoor[3, :],
lcoor[4, :], lcoor[5, :])
else:
angle = sasmath.dihedral_angle(lcoor[3, :], lcoor[4, :],
lcoor[5, :], lcoor[6, :])
elif(an == 'epsilon'):
if(q0 == first_last_resid[0]):
angle = sasmath.dihedral_angle(lcoor[3, :], lcoor[4, :],
lcoor[5, :], lcoor[6, :])
else:
angle = sasmath.dihedral_angle(lcoor[4, :], lcoor[5, :],
lcoor[6, :], lcoor[7, :])
elif(an == 'eta'):
if(q0 == first_last_resid[0]):
angle = sasmath.dihedral_angle(lcoor[4, :], lcoor[5, :],
lcoor[6, :], lcoor[7, :])
else:
angle = sasmath.dihedral_angle(lcoor[5, :], lcoor[6, :],
lcoor[7, :], lcoor[8, :])
else:
angle = 0.0
message = ('error (in rotate.measure): %s angle not in '
'alpha/beta/gamma/delta/epsilon/eta' % an)
error.append(message)
assert not error, error
elif(molecule_type == 'dna'):
if(first_last_resid[0] == first_last_resid[1]):
print 'WARNING: only given one DNA base for calculating angles'
print 'WARNING: change input or revise code'
print 'WARNING: cowardly refusing to calculate angle, returni'
return 0
# order of drude atoms differ from charmm27 (not sure about charmm36)
if drude:
i = {"O3'-1": 0, "P": 1, "O5'": 2, "C5'": 3, "chi3": 4,
"chi4": 5,"C4'": 6, "O4'": 7, "C1'": 8, "C3'": 9,
"O3'": 10, "P+1": 11, "O5'+1": 12}
else:
i = {"O3'-1": 0, "P": 1, "O5'": 2, "C5'": 3, "C4'": 4,
"O4'": 5,"C1'": 6, "chi3": 7, "chi4": 8, "C3'": 9,
"O3'": 10, "P+1": 11, "O5'+1": 12}
if q0 == first_last_resid[0]:
if len(lcoor) == 12:
# missing the O3'-1 atom
first_last_coor = numpy.zeros((13, 3))
first_last_coor[1:] = lcoor
elif len(lcoor) == 11:
# missing the O3'-1 and P atoms
first_last_coor = numpy.zeros((13, 3))
first_last_coor[2:] = lcoor
else:
# not sure
assert False, ('ERROR: cannot calculate dihedral angles from '
'%d atoms, not clear which atoms are which) \n'
'Please review atoms in PDB and input resids')
if(an == 'alpha'):
angle = numpy.nan
return angle
elif(an == 'beta' and len(lcoor) == 11):
angle = numpy.nan
return angle
else:
lcoor = numpy.copy(first_last_coor)
if(an == 'alpha'):
angle = sasmath.dihedral_angle(
lcoor[i["O3'-1"], :], lcoor[i["P"], :],
lcoor[i["O5'"], :], lcoor[i["C5'"], :])
elif(an == 'beta'):
angle = sasmath.dihedral_angle(
lcoor[i["P"], :], lcoor[i["O5'"], :],
lcoor[i["C5'"], :], lcoor[i["C4'"], :])
elif(an == 'gamma'):
angle = sasmath.dihedral_angle(
lcoor[i["O5'"], :], lcoor[i["C5'"], :],
lcoor[i["C4'"], :], lcoor[i["C3'"], :])
elif(an == 'delta'):
angle = sasmath.dihedral_angle(
lcoor[i["C5'"], :], lcoor[i["C4'"], :],
lcoor[i["C3'"], :], lcoor[i["O3'"], :])
elif(an == 'epsilon'):
if(q0 == first_last_resid[1]):
assert len(lcoor) == 11, ('ERROR: expected 11 atoms for last '
'resid but received %d' % len(lcoor))
angle = numpy.nan
else:
angle = sasmath.dihedral_angle(
lcoor[i["C4'"], :], lcoor[i["C3'"], :],
lcoor[i["O3'"], :], lcoor[i["P+1"], :])
elif(an == 'zeta'):
if(q0 == first_last_resid[1]):
assert len(lcoor) == 11, ('ERROR: expected 11 atoms for last '
'resid but received %d' % len(lcoor))
angle = numpy.nan
else:
angle = sasmath.dihedral_angle(
lcoor[i["C3'"], :], lcoor[i["O3'"], :],
lcoor[i["P+1"], :], lcoor[i["O5'+1"], :])
elif(an == 'chi'):
angle = sasmath.dihedral_angle(
lcoor[i["O4'"], :], lcoor[i["C1'"], :],
lcoor[i["chi3"], :], lcoor[i["chi4"], :])
else:
angle = numpy.nan
message = ('error (in rotate.measure): %s angle not in '
'alpha/beta/gamma/delta/epsilon/zeta/chi' % an)
error.append(message)
assert not error, error
return angle
