Utilize equations as inputs to Energy+

edit

If your setpoint temperatures are only dependent on outside temperature, then you can pre-process the weather file and create a static schedule for EnergyPlus.

But if your setpoint temperatures need to vary based on other conditions such that they need to be calculated dynamically for each time step, then you can use EnergyPlus's Energy Management System (EMS) to implement custom equations/logic. For example, you can create an EMS program where you actuate (override) a Schedule Value. The EnergyPlus documentation has an example of doing just this.