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28 changes: 14 additions & 14 deletions pikachu/drawing/drawing.py
Original file line number Diff line number Diff line change
Expand Up @@ -3259,10 +3259,10 @@ def resolve_primary_overlaps(self) -> None:
"""
Resolve overlaps when a ring has two outgoing edges
"""
overlaps: list[dict[str, Union[Atom, list[int], list[Atom]]]] = []
overlaps: List[Dict[str, Union[Atom, List[int], List[Atom]]]] = []

# Keep track of which atoms are resolved
resolved_atoms: dict[Atom, bool] = {}
resolved_atoms: Dict[Atom, bool] = {}

for atom in self.structure.graph:
if atom.draw.is_drawn:
Expand Down Expand Up @@ -3477,7 +3477,7 @@ def get_non_ring_neighbours(atom: Atom) -> List[Atom]:
as atom

"""
non_ring_neighbours: list[Atom] = []
non_ring_neighbours: List[Atom] = []

for neighbour in atom.drawn_neighbours:
nr_overlapping_rings = len(set(atom.draw.rings).intersection(set(neighbour.draw.rings)))
Expand Down Expand Up @@ -3626,7 +3626,7 @@ def create_ring(self, ring: Ring, center: Optional[Vector] = None, start_atom: O
if center is None:
center = Vector(0, 0)

ordered_neighbour_ids: list[int] = ring.get_ordered_neighbours(self.ring_overlaps)
ordered_neighbour_ids: List[int] = ring.get_ordered_neighbours(self.ring_overlaps)
starting_angle: float = 0

if start_atom:
Expand Down Expand Up @@ -3869,7 +3869,7 @@ def define_rings(self) -> None:
break

ring: Ring = self.id_to_ring[ring_id]
involved_ring_ids: Union[list[int], set[int]] = []
involved_ring_ids: Union[List[int], Set[int]] = []
self.get_bridged_ring_subrings(ring.id, involved_ring_ids)
involved_ring_ids = set(involved_ring_ids)

Expand Down Expand Up @@ -3902,8 +3902,8 @@ def hide_hydrogens(self) -> None:
Mark explicit hydrogens as drawn and implicit hydrogens as not drawn. Store these hydrogens in the adjacent,
drawn atoms.
"""
hidden: list[Atom] = []
exposed: list[Atom] = []
hidden: List[Atom] = []
exposed: List[Atom] = []

self.structure.refresh_structure()

Expand Down Expand Up @@ -3941,7 +3941,7 @@ def hide_hydrogens(self) -> None:

self.drawn_atoms = self.structure.get_drawn_atoms()

def get_bridged_rings(self) -> list[Ring]:
def get_bridged_rings(self) -> List[Ring]:
"""
Returns a list of bridged ring systems

Expand All @@ -3951,14 +3951,14 @@ def get_bridged_rings(self) -> list[Ring]:
contain at least two rings which share an overlap of 2 or more bonds

"""
bridged_rings: list[Ring] = []
bridged_rings: List[Ring] = []
for ring in self.rings:
if ring.bridged:
bridged_rings.append(ring)

return bridged_rings

def get_bridged_ring_subrings(self, ring_id: int, involved_ring_ids: list[int]) -> None:
def get_bridged_ring_subrings(self, ring_id: int, involved_ring_ids: List[int]) -> None:
"""
Edit list of ring IDs until it contains all rings that are involved in a bridged ring system with the original
ring
Expand All @@ -3977,7 +3977,7 @@ def get_bridged_ring_subrings(self, ring_id: int, involved_ring_ids: list[int])
rings_connected_by_bridge(self.ring_overlaps, ring_id, neighbour_id):
self.get_bridged_ring_subrings(neighbour_id, involved_ring_ids)

def create_bridged_ring(self, involved_ring_ids: set[int]) -> None:
def create_bridged_ring(self, involved_ring_ids: Set[int]) -> None:
"""
Create and store a bridged ring system from a list of involved ring identifiers

Expand All @@ -3987,10 +3987,10 @@ def create_bridged_ring(self, involved_ring_ids: set[int]) -> None:
ring system
"""
# Keeps track of all atoms involved in the ring system
atoms: set[Atom] = set()
atoms: Set[Atom] = set()

# Keeps track of all rings that neighbour the bridged ring system
neighbours: set[int] = set()
neighbours: Set[int] = set()

for ring_id in involved_ring_ids:
ring: Ring = self.id_to_ring[ring_id]
Expand All @@ -4003,7 +4003,7 @@ def create_bridged_ring(self, involved_ring_ids: set[int]) -> None:
neighbours.add(neighbour_id)

leftovers = set()
ring_members: set[Atom] = set()
ring_members: Set[Atom] = set()

for atom in atoms:
intersect = involved_ring_ids & set(atom.draw.rings)
Expand Down