def _calculate_O_coordinates(position_CA, position_C, position_N, residue):
""" Calculate coordinates for the O atom.
@param position_CA: Coordinates of the CA atom
@type position_CA: Vector
@param position_C: Coordinates of the C atom
@type position_C: Vector
@param position_N: Coordinates of the N atom
@type position_N: Vector
@param residue: Amino acid.
@type residue: str
@rtype: Vector
@return: The calculated O position
"""
angle_O_C_N = ANGLE_O_C_N[residue] * pi / 180
bond_length_C_N = BOND_LENGTH_C_N[residue]
D = Vector(
BOND_LENGTH_C_O * cos(angle_O_C_N), BOND_LENGTH_C_O * sin(angle_O_C_N), 0)
bc = (position_N - position_C) / bond_length_C_N
n = ((position_C - position_CA) ** bc).normalized()
nbc = bc ** n
basis_change = numpy.array((bc, nbc, n)).transpose()
return D.left_multiply(basis_change) + position_C
def _place_backbone_atoms(coords, angles, cis, aa_seq):
""" Place atoms that are in the backbone.
@param coords: Array where the coordinates are to be saved.
@type coords: numpy.array
@param angles: Angles.
@type angles: list(float)
@param cis: Conformation of the peptide bonds.
@type cis: list(int)
@param aa_seq: Amino acid sequence.
@type aa_seq: list(int)
"""
for i in xrange(len(aa_seq)):
current_res = index_to_three(aa_seq[i])
current_atom = 'N'
prev_atom = 'C'
prev_prev_atom = 'CA'
for j in xrange(backbone_atoms):
index = i * atoms_per_residue + j
if i == 0 and current_atom == 'N':
coords[:,index] = 0
elif i == 0 and current_atom == 'CA':
coords[:,index] = 0
coords[X][index] = get_bond_length(
current_atom, prev_atom, current_res)
else:
v1 = _create_vector(coords, index, j, 1)
v2 = _create_vector(coords, index, j, 2)
if i == 0 and current_atom == 'C':
v3 = Vector(0, -1.0, 0)
else:
v3 = _create_vector(coords, index, j, 3)
angle = get_bond_angle(
prev_prev_atom, prev_atom, current_atom, current_res)
dihedral = _calculate_dihedral(prev_atom, angles, cis, i)
bond_length = get_bond_length(prev_atom, current_atom, current_res)
bond_length_prev = get_bond_length(
prev_prev_atom, prev_atom, current_res)
D = Vector(
bond_length * cos(pi - angle),
bond_length * cos(pi - dihedral) * sin(pi - angle),
bond_length * sin(pi - dihedral) * sin(pi - angle),
)
bc = (v1 - v2) / bond_length_prev
n = ((v1 - v3) ** bc).normalized()
nbc = bc ** n
basis_change = numpy.array((bc, nbc, n)).transpose()
D = D.left_multiply(basis_change) + v1
coords[:,index] = D
prev_prev_atom = prev_atom
prev_atom = current_atom
current_atom = ATOMS[(ATOMS.index(current_atom) + 1) % backbone_atoms]