Database schema:

CREATE TABLE atom (
	atom_id TEXT NOT NULL -- atom id, example: ['TR000_1', 'TR000_2'],
	molecule_id TEXT DEFAULT NULL -- molecule id, example: ['TR000', 'TR001'],
	element TEXT DEFAULT NULL -- example: ['c', 'cl'],
	PRIMARY KEY (atom_id), 
	CONSTRAINT fk_atom_molecule FOREIGN KEY(molecule_id) REFERENCES molecule (molecule_id)
)


CREATE TABLE bond (
	bond_id TEXT NOT NULL -- example: ['TR000_2_3', 'TR000_1_2'],
	molecule_id TEXT DEFAULT NULL -- example: ['TR000', 'TR001'],
	bond_type TEXT DEFAULT NULL -- example: ['=', '-'],
	PRIMARY KEY (bond_id), 
	CONSTRAINT fk_bond_molecule FOREIGN KEY(molecule_id) REFERENCES molecule (molecule_id)
)


CREATE TABLE connected (
	atom_id TEXT NOT NULL -- atom id, example: ['TR000_1', 'TR000_2'],
	atom_id2 TEXT NOT NULL -- atom id 2, example: ['TR000_1', 'TR000_2'],
	bond_id TEXT DEFAULT NULL -- bond id, example: ['TR000_2_3', 'TR000_1_2'],
	PRIMARY KEY (atom_id, atom_id2), 
	CONSTRAINT fk_connected_bond FOREIGN KEY(bond_id) REFERENCES bond (bond_id),
	CONSTRAINT fk_connected_atom FOREIGN KEY(atom_id2) REFERENCES atom (atom_id),
	CONSTRAINT fk_connected_atom FOREIGN KEY(atom_id) REFERENCES atom (atom_id)
)


CREATE TABLE molecule (
	molecule_id TEXT NOT NULL -- molecule id, example: ['TR000', 'TR001'],
	label TEXT DEFAULT NULL -- example: ['+', '-'],
	PRIMARY KEY (molecule_id)
)

Question: How many bonds which involved atom 12 does molecule TR009 have?
Evidence: TR009 is the molecule id;  involved atom 12 refers to atom_id = 'TR009_12' or atom_id2 = 'TR009_12'

SQL:
SELECT COUNT(T2.bond_id) FROM bond AS T1 INNER JOIN connected AS T2 ON T1.bond_id = T2.bond_id WHERE T1.molecule_id = 'TR009' AND T2.atom_id = T1.molecule_id || '_1' AND T2.atom_id2 = T1.molecule_id || '_2'