  Molecular lines hold valuable information on the physical and chemical
composition of disks around young stars, the likely progenitors of planetary
systems. This invited contribution discusses techniques to calculate the
molecular emission (and absorption) line spectrum based on models for the
physical and chemical structure of protoplanetary disks. Four examples of
recent research illutrate these techniques in practice: matching resolved
molecular-line emission from the disk around LkCa15 with theoertical models for
the chemistry; evaluating the two-dimensional transfer of ultraviolet radiation
into the disk, and the effect on the HCN/CN ratio; far-infrared CO line
emission from a superheated disk surface layer; and inward motions in the disk
around L1489 IRS.
