Although molecule files can be input and output at the command line to perform file conversion, they are more commonly specified within the input file to specify such things as the ligand input coordinates, the receptor site point and atom coordinates, and the ligand output coordinates for each scoring function. When each file name is read in from the input file, it is checked to make sure it has one of the recognized file extensions (*.mol2, *.pdb, *.xpdb, *.sph, *.ptr), so that dock can identify the proper the file format.
Dock can be run as part of a UNIX pipe of commands, in which molecule coordinates are passed between a series of commands. To configure a dock run to operate within a UNIX pipe, dock must be instructed to read molecule coordinates from the standard input stream and/or write coordinates to the standard output stream. To do this, the streams must not be in use for interactive processing (ie. dock output must be directed to an output file with the -o command line flag). Within the input file, dock can be instructed to use the standard streams for coordinates by using stdin.ext when specifying the input file name and stdout.ext for the output file name. The *.ext file extension must be one of the coordinate file extensions recognized by dock so that the proper file format can be used.