def get_proximal_atoms(self, center_atom, neighbour_atom_type,
max_neighbour_distance):
"""
Get atoms inside a particular radii's sphere
(exception) Atoms belonging to water residues are excluded
"""
results = []
for line in self.lines:
if line[12:16].strip(
)[0] == neighbour_atom_type and line[17:20].strip() != "HOH":
atom = Protein.parse_line_atom_details(line)
if Atom.distance(center_atom, atom) <= max_neighbour_distance:
results.append(atom)
return results
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
and (90 <= degrees(
Atom.get_bond_angles(hydrogen, se, oxygen)) <= 130)
and Atom.distance(se, oxygen) >= 1.0):
distances3.append(Atom.distance(se, oxygen))
angles3.append(
degrees(Atom.get_bond_angles(hydrogen, se, oxygen)))
excluded_h_bond.append(
