Parameter Table

keyword	variable name	allowed values	default
check_degeneracy	check_degeneracy	yes,br>no	no
degeneracy_wobble	wobble	0 - 2	0
degenerate_save_interval	keepmult	integer	0
check_degenerate_children	checkmult	yes no	no

Parameter Descriptions

check_degeneracy

indicates whether to discard geometrically similar orientations. This functionality is further described in the Degeneracy Checking section.

degeneracy_wobble

dictates how stringent degeneracy checking will be. This parameter is inversely related to run-time. Higher degeneracy_wobble values permit looser degeneracy checking, resulting in more degenerate orientations and fewer orientations minimized. degeneracy_wobble of 0 is usually too stringent and run-times can become inflated. degeneracy_wobble of 2 often provides fast results of good quality.

degenerate_save_interval

specifies the number of times an orientation must be found in any given family before minimizing and attempting to save another member of the same family. So, if a particular binding mode is found 100 times and degenerate_save_interval is 25, DOCK will minimize and evaluate four additional members of this family in hopes of finding a better scoring representative. This parameter provides a method for retaining additional members of popular families and smoothing the bias of sphere locations. Recommended values are in the range 10 to 25.

check_degenerate_children

indicates whether to check for degeneracy against orientations which were saved as multiples of a family due to the degenerate_save_interval parameter. Recommended value is no.