propka.calculations

Calculations

Mathematical helper functions.

Module Attributes

MAX_DISTANCE

Maximum distance used to bound calculations of smallest distance

Functions

distance(atom1, atom2)

Calculate the distance between two atoms.

get_smallest_distance(atoms1, atoms2)

Calculate the smallest distance between two groups of atoms.

squared_distance(atom1, atom2)

Calculate the squared distance between two atoms.
propka.calculations.MAX_DISTANCE = 1000000.0

Maximum distance used to bound calculations of smallest distance

propka.calculations.distance(atom1: _XYZ, atom2: _XYZ) → float[source]

Calculate the distance between two atoms.

Parameters:

  • atom1 – first atom for distance calculation

  • atom2 – second atom for distance calculation

Returns:

distance

propka.calculations.get_smallest_distance(atoms1: Iterable[_BoundXYZ_1], atoms2: Iterable[_BoundXYZ_2]) → Tuple[_BoundXYZ_1 | None, float, _BoundXYZ_2 | None][source]

Calculate the smallest distance between two groups of atoms.

Parameters:

  • atoms1 – atom group 1

  • atoms2 – atom group 2

Returns:

smallest distance between groups

propka.calculations.squared_distance(atom1: _XYZ, atom2: _XYZ) → float[source]

Calculate the squared distance between two atoms.

Parameters:

  • atom1 – first atom for distance calculation

  • atom2 – second atom for distance calculation

Returns:

distance squared