Compute cube based sterimol parameters — steRimol.cube • moleculaR

This function acts on Gaussian cube file NOTE - the function is meant to work in a single molecule data folder and does not allow the choice of a cube file to work with. This is by design and is due to the workflow approach of moleculaR.

Usage

steRimol.cube(
  cubefile,
  coordinates,
  only.sub = T,
  drop = NULL,
  plot = T,
  degrees = 90,
  isovalue = 0.036
)

Arguments

cubefile: a .cube file
coordinates: primary axis, a two atom character
only.sub: if TRUE (default) will account only for atoms directly bonded
drop: numeric value of an atom, from which onward atoms will be dropped from calculation
plot: if TRUE (default) will generate a 3D plot of molecule, with the density surface and sterimol arrows.
degrees: define the rotational scan, defaults to 90 (same as 360)
isovalue: what minimal density isovalue should be considered, defaults to 0.036

Value

sterimol values for a single molecule