We predict how protoplanetary disks around low-mass young stars would appear in molecular lines observed with the ALMA interferometer. Our goal is to identify those molecules and transitions that can be used to probe and distinguish between chemical and physical disk structure and to define necessary requirements for ALMA observations. Disk models with and without vertical temperature gradient as well as with uniform abundances and those from a chemical network are considered. As an example, we show the channel maps of HCO$^+$(4-3) synthesized with a non-LTE line radiative transfer code and used as an input to the GILDAS ALMA simulator to produce noise-added realistic images. The channel maps reveal complex asymmetric patterns even for the model with uniform abundances and no vertical thermal gradient. We find that a spatial resolution of $0.2-0.5arcsec$ and 0.5--10 hours of integration time will be needed to disentangle large-scale temperature gradients and the chemical stratification in disks in lines of abundant molecules.
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