MetricShell(sel1, sel2, numshells=4, shellwidth=3, pbc=True, gap=None, truncate=None)¶
Calculates 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.
numshells (int, optional) – Number of shells to use around atoms of sel1
shellwidth (int, optional) – The width of each concentric shell in Angstroms
pbc (bool, optional) – Set to false to disable distance calculations using periodic distances
gap (int, optional) – Not functional yet
truncate (float, optional) – Set all distances larger than truncate to truncate
Produces a deep copy of the object
Returns the description of each projected dimension.
Molecule object) – A Molecule object which will be used to calculate the descriptions of the projected dimensions.
map – A DataFrame containing the descriptions of each dimension