stko.KabschRmsdCalculator

class stko.KabschRmsdCalculator(initial_molecule)[source]

Bases: object

Calculates the root mean square distance between molecules.

This calculator uses the rmsd package with the default settings and no reordering.

See also

rmsd https://github.com/charnley/rmsd

This calculator will only work if the two molecules are the same and have the same atom ordering.

Parameters:: initial_molecule (Molecule) – The stk.Molecule to calculate RMSD from.

Examples

import stk
import stko
import numpy as np

bb1 = stk.BuildingBlock('C1CCCCC1')
calculator = stko.KabschRmsdCalculator(bb1)
results = calculator.get_results(stko.UFF().optimize(bb1))
rmsd  = results.get_rmsd()

Methods

`calculate`
`get_results`	Calculate the RMSD between mol and the initial molecule.

calculate(mol)[source]

Parameters:: mol (Molecule)
Return type:: float

get_results(mol)[source]

Calculate the RMSD between mol and the initial molecule.

Parameters:: mol (Molecule) – The stk.Molecule to calculate RMSD to.
Returns:: The RMSD between the molecules.
Return type:: RmsdResults