utils.coordinates

Functions

get_center_of_mass_coordinates(positions, ...)	Calculates center of mass coordinates of a given number of atoms or molecules.
get_centroid_coordinates(positions, indices)	Calculates centroid coordinates of a given number of atoms or molecules.

utils.coordinates.get_centroid_coordinates(positions: openmm.unit.quantity.Quantity, indices: List[int]) → openmm.unit.quantity.Quantity

Calculates centroid coordinates of a given number of atoms or molecules.

Args:

positions (unit.Quantity): positions of all atoms in the system indices (List[int]): indices of the atoms you want the centroid from.

Returns:

unit.Quantity: Centroid coordinates of the specified atoms

utils.coordinates.get_center_of_mass_coordinates(positions: openmm.unit.quantity.Quantity, indices: openmm.unit.quantity.Quantity, masses: openmm.openmm.System) → openmm.unit.quantity.Quantity

Calculates center of mass coordinates of a given number of atoms or molecules.

Args:

positions (unit.Quantity): positions of all atoms in the system indices (List[int]): indices of the atoms you want the centroid from. masses (mm.openmm.System): openmm System that contains all the atom masses.

Returns:

unit.Quantity: center of mass coordinates of the specified atoms