b_flag = 0
connected_atoms = protein.get_connected_atoms(se)
proximal_oxygen = protein.get_proximal_atoms(se, "O", 7.0)
proximal_nitrogen = protein.get_proximal_atoms(se, "N", 7.0)
for oxygen in proximal_oxygen:
if oxygen.occupancy != 1.00:
continue
connected_hydrogen = []
connected_hydrogen.extend(protein.get_connected_hydrogens(oxygen))
for hydrogen in connected_hydrogen:
try:
for anti_antecedent in connected_atoms:
bond_angle = Atom.get_bond_angles(
se, hydrogen, anti_antecedent)
if bond_angle < numpy.pi / 2:
raise ContinueLabelled
except ContinueLabelled:
continue
if Atom.distance(hydrogen, oxygen) <= 1.1 and Atom.distance(
se, oxygen) >= 1.0:
bond_angle = Atom.get_bond_angles(hydrogen, se, oxygen)
if bond_angle >= numpy.pi / 19:
distances1.append(Atom.distance(se, oxygen))
angles1.append(degrees(bond_angle))
if (Atom.distance(hydrogen, oxygen) <= 1.1
and Atom.distance(se, oxygen) <= 4.0
