def get_gyration_radius(struct: Structure) -> float:
"""
Calculate radius of gyration protein
https://en.wikipedia.org/wiki/Radius_of_gyration
:param struct: structure of protein
:return: radius of gyration
"""
mass_center = get_mass_center(struct)
coords = [a.get_coord() for a in struct.get_atoms()]
masses = [_get_atom_mass(a) for a in struct.get_atoms()]
mr2_sum = 0
for r, m in zip(coords, masses):
mr2_sum += m * (math.dist(r, mass_center))**2
return math.sqrt(mr2_sum / sum(masses))
def get_molecular_mass(struct: Structure) -> float:
"""
Calculate molecular mass of protein structure
:param struct: structure of protein
:return: molecular mass
"""
mass = 0
for atom in struct.get_atoms():
mass += _get_atom_mass(atom)
return mass
def get_mass_center(struct: Structure) -> tuple:
"""
Calculate mass center of protein structure
:param struct: structure of protein
:return: coordinates of mass center
"""
x_sum, y_sum, z_sum = 0, 0, 0
mass = get_molecular_mass(struct)
for atom in struct.get_atoms():
atom_mass = _get_atom_mass(atom)
x_sum += atom.get_coord()[0] * atom_mass
y_sum += atom.get_coord()[1] * atom_mass
z_sum += atom.get_coord()[2] * atom_mass
return x_sum / mass, y_sum / mass, z_sum / mass
def get_geometric_center(struct: Structure) -> tuple:
"""
Calculate center of protein structure by arithmetic mean of all atoms coordinates
:param struct: structure of protein
:return: coordinates of center
"""
x_sum, y_sum, z_sum = 0, 0, 0
n = 0
for atom in struct.get_atoms():
n += 1
x_sum += atom.get_coord()[0]
y_sum += atom.get_coord()[1]
z_sum += atom.get_coord()[2]
return x_sum / n, y_sum / n, z_sum / n
