While he was feuding with the New Lights, Clap was partnering with the Anglicans. Beginning in 1740, he worked with the Rev. Samuel Johnson of Stratford, Connecticut, to reform Yale. He brought math and science into Yale's curriculum, and undergraduate studies in divinity were replaced by Johnson's non-denominational moral philosophy. Clap published a Yale library catalog in 1743, with an index system based on his friend Samuel Johnson's map of learning, and drafted a new charter of the school, granted by the General Assembly in 1745, incorporating the institution as "The President and Fellows of Yale College in New Haven". Clap was sworn in as Yale's first President on June 1, 1745. His formulation of a new code of laws for Yale in Latin became, in 1745, the first book printed in New Haven.