To predicate X of Y is to say that Y is X or that Y is an X. This terminology comes from syllogistic logic, where they tend to be loose about the distinction between a property, a class, and an individual, so in this definition, X could be any of those three.
- If X is the property of being mortal and Y is Socrates then "Socrates is mortal" predicates mortality of Socrates.
- If X is the class of philosophers and Y is Socrates then "Socrates is a philosopher" predicates being a philosopher of Socrates.
- If X is the individual Phosphorus and Y is the individual Hesperus, then "Hesperus is Phosphorus" predicates of Hesperus that it is the same thing as Phosphorus.
To predicate a composite of one of its parts would be to take a composite object like a car and a part such as the hood and say, for example, "the hood is the car". So, what Aquinas is saying, roughly, is that no composite individual is identical with one of its parts.
There may be some subtlety in that passage that I don't understand, because he doesn't directly say that no composite individual is identical with its parts, what he says is more like "one can't form a true sentence that says a composite individual is identical with one of its parts." Whether this is significant, I don't know. I'm not familiar enough with Aquinas.
In modern logic, this conflation of properties, classes, and individuals is no longer done. There is a careful distinction between an object instantiating a property, an object being a member of a class, and an object being identical with another object.