stko.RmsdMappedCalculator

class stko.RmsdMappedCalculator(initial_molecule, ignore_hydrogens=False)[source]

Bases: RmsdCalculator

Calculates the root mean square distance between molecules.

This calculator allows for different molecules but they should be aligned, see the example below. It will calculate the RMSD based on the nearest atom of the same class (element). Both molecules are moved to a centroid position of (0, 0, 0). The number of atoms is based on the mol input into calculate.

Warning: the RMSD depends on the order, i.e. it is not guaranteed to be the same when you switch the initial and test molecule.

Examples

import stk
import stko
import numpy as np

bb1 = stk.BuildingBlock('C1CCCCC1')
# Fake rotation of new molecule.
bb2 = stk.BuildingBlock('C1CCCCC1').with_rotation_about_axis(
    1.34, np.array((0, 0, 1)), np.array((0, 0, 0)),
)

# Get RMSD without alignment.
calculator = stko.RmsdMappedCalculator(bb1)
results = calculator.get_results(bb2)
rmsd  = results.get_rmsd()

# Align the molecules.
optimizer = stko.Aligner(bb1, (('C', 'C'), ))
aligned_bb2 = optimizer.optimize(bb2)

calculator = stko.RmsdMappedCalculator(bb1)
results = calculator.get_results(aligned_bb2)
rmsd  = results.get_rmsd()

Methods

calculate

get_results

Calculate the RMSD between mol and the initial molecule.
Parameters:

  • initial_molecule (Molecule)

  • ignore_hydrogens (bool)

calculate(mol)[source]
Parameters:

mol (Molecule)

Return type:

float

get_results(mol)

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