Distance Function Setup Parameter Block

Hydropathic Term

enumerated choices: {Off|exp(-nr)|(1/r**n)}

The Hydropathic Term of the Distance Function controls the mathematical form of the distance dependence for hydropathic interactions. (See Theory Chapter for more information.) Off disables the hydropathic term; exp(-nr) uses an exponential decay function to represent the distance dependence of hydropathy through space; (1/r**n) uses an inverse power function to represent the distance dependence of hydropathy through space. The value of n is set in a separate parameter.

n

integer number

The n parameter is the integer number in the (1/r**n) hydropathic term of the HINT distance function.

Steric Term

on/off

The Steric_Term of the Distance_Function is an adaptation of the Lennard-Jones function. For the most part it represents a penalty function to prevent the too-close approach of interacting atoms. In general, use the Steric_Term for Map and HintTable interaction calculations, but don't use it for Molecule and Complement Map calculations.

Steric/Hydro Scaler

real number

The Steric/Hydro Scaler is an empirical parameter designed to balance the two terms (Steric and Hydropathic) of the HINT Distance_Function. Experience has shown that a value of 50.0 for this parameter gives a HINT atom-atom interaction score that is about 2/3 hydropathic and 1/3 steric for an acid-base interaction at Van der Waals contact distance. The primary purpose, however, of the HINT Steric_Term is to flag invalid contact distances between interacting atoms.

Direction Vectors

enumerated choices: {None (Spherical)|Bond Axes (Geom.)|Hybridizd/Lone Pair}

The Direction Vectors parameter(s) provide a mechanism to more specifically direct hydropathy along either Bond Axis or Lone Pair vectors. This is especially important for polar/H-Bond interactions where directionality of interactions is expected to be important. Hydrophobic interactions are less likely to be directional.

Bond Axes (Geom.) directs the hydropathy along the axis of the bond (or average of bonds) to the selected atom.

Hybridizd/Lone Pair directs the hydropathy along vectors coinciding with the placement of lone pairs and pi orbitals on the selected atom. The magnitude of these vectors are weighted for the occupancy (lectrons) of the lone pair or pi orbital.

Vector Focus

real number

The Vector Focus parameter allows control over the focus of the directionality vectors, larger Vector Focus parameters cause a tighter focus of the probability function controlling interactions.