Question

I have 3 tables:

Molecule:
  id

Atom:
  id

MoleculeAtom: # Composite primary key
  molecule_id
  atom_id

My goal is to ensure that no combination of atoms which make up a molecule, are repeated. For example, the water molecule, I would store two rows in the MoleculeAtom table; 1 row for a hydrogen atom and 1 row for an oxygen atom. As you can see, I need to ensure that no other molecule has JUST hydrogen and oxygen, even though there may be other molecules which include hydrogen and oxygen.

At this point I have a query which identifies which molecules includes either hydrogen or oxygen, and only having 2 atoms in the MoleculeAtom table.

SELECT
  m.id, m.name, (SELECT count(*) from molecule_atom where molecule_id = m.id group by molecule_id) as atomCount
FROM
  molecule AS m
INNER JOIN
  molecule_atom AS ma ON ma.molecule_id = m.id
WHERE
  ma.atom_id IN (1,2)
HAVING atomCount = 2;

Which returns (demonstrative snippet):

+----+----------------------------+-----------+
| id | name                       | atomCount |
+----+----------------------------+-----------+
| 53 | Carbon Dioxide             |         2 |
| 56 | Carbon Monoxide            |         2 |
+----+----------------------------+-----------+

(I know, that both CO and CO2 have the same exact atoms, in differing quantities, but dis-regard that, as I am tracking the quantities as a another column in the same table.)

As of now I am pulling the above results and checking their atom_ids via PHP, which means I have to issue a separate query for each molecule, which seems inefficient, so I was looking to see if it’s possible to do this checking using strictly SQL.

Excuse any mistakes which may be chemical related, it’s been a long time since chem101.

Answer 1

As ypercube mentioned, MySQL doesn’t support assertions, so I ended writing a query to find all molecules having at least one of the atoms which belong to the new molecule I am trying to create, and having the same number of atoms. After querying for matches, the application steps through each molecule and determines if they have the same exact atoms as the new molecule. Query looks like this (assumes I am trying to create a new molecule with 2 atoms):

SELECT 
    m.id,
    m.name,
    (SELECT GROUP_CONCAT(ma.atom_id) FROM molecule_atom AS ma WHERE ma.molecule_id = m.id GROUP BY ma.molecule_id HAVING (SELECT COUNT(ma.atom_id)) = 2) AS atoms
FROM
    molecule AS m
INNER JOIN
    molecule_atom AS mas ON mas.molecule_id = m.id
WHERE 
    mas.atom_id IN (1,2)

Then in code (PHP) I do:

foreach ($molecules as $molecule) {

    if (isset($molecule['atoms'])) {

        $diff = array_diff($newAtomIds, explode(',', $molecule['atoms']));

        // If there is no diff, then we have a match
        if (count($diff) === 0) {
            return $molecule['name'];
        }
    }
}

Thanks for everyone’s response.