moleculekit.projections.metricshell module#
- class moleculekit.projections.metricshell.MetricShell(sel1, sel2, periodic, numshells=4, shellwidth=3, pbc=None, gap=None, truncate=None)#
Bases:
ProjectionCalculates the density of atoms around other atoms.
The MetricShell class calculates the density of a set of interchangeable atoms in concentric spherical shells around some other atoms. Thus it can treat identical molecules (like water or ions) and calculate summary values like the changes in water density around atoms. It produces a n-by-s dimensional vector where n the number of atoms in the first selection and s the number of shells around each of the n atoms.
- Parameters:
sel1 (
str|ndarray) – Atom selection for the first set of atoms around which the shells will be calculated (a selection string, boolean mask, or integer index array). See more heresel2 (
str|ndarray) – Atom selection for the second set of atoms whose density will be calculated in shells around sel1 (a selection string, boolean mask, or integer index array). See more hereperiodic (
str) – See the documentation of MetricDistance class for options.numshells (
int) – Number of shells to use around atoms of sel1shellwidth (
int) – The width of each concentric shell in Angstromspbc (
bool|None) – Deprecated. Use the periodic option as described in MetricDistance.truncate (
float|None) – Set all distances larger than truncate to truncate