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Has clock transition something to do with the flip flop set up time values?
yes and no, but that is a different issue.
How clock transition value effect the set up time of a flip flop? How the set up time of a flip flop is calculated? In the library file, there is no set up time or hold time value of a flip flop specified. How the tool calculates the set up and hold time of a flip flop? On what all factors do the set up and hold time values depend?
If I remember correctly, there is a table in .lib file showing that relationship.