Unless the bike was in an accident i wouldn't suspect any part of the frame..
To align the wheels on a bike, you can use two long straight pieces of wood.. lay them on the ground aside and against the rear tire.. the front tire should be centered between the two pieces of wood.
The bike has a chain drive? Sight down the top of the chain.. the chain and front sprocket should be in a straight line.. Or remove the chain and putt a straight edge flat againt the rear sprocket. The front (drive) sprocket should line up perfectly..
I don't own a Tomos and wouldn't know exactly why this rear wheel wouldn't have enough room to move.. perhaps the chain is stretched and the wheel's axle is too far back on the swingarm.. have you changed sprockets? Did you change the chain's length?
Explain the situation on the rear.. where does the axle hit and what prevents it from being adjusted more straight.. Maybe someone else has a suggestion.