If you are within range (accounting for enemy jammer and stealth), you have active sensors on and you have BFCs with weapons assigned you can target enemy ships.
Any weapon can be used as PD (with more or much less effectiveness depending on the weapon, turret speed, BFC speed and range and the reload rate), you just need to assign a PD behaviour to a BFC (right part of the combat tab of the naval organization window when you have a ship selected).
Since PD weapons are just normal weapons with assigned PD behaviours you can just assign an enemy target to a PD BFC and order the BFC to open fire as normal.