rgpycrumbs.geom.ira

Exceptions

IncomparableStructuresError

Custom exception raised for incompatible atomistic structures.

Classes

IRAComp

Result of an IRA comparison (rotation, translation, permutation, Hausdorff distance).

Functions

_perform_ira_match(atm1, atm2[, k_factor])	Performs IRA matching. Internal function.
is_ira_pair(atm1, atm2[, hd_tol, k_factor])	Checks if two atomistic structures are an IRA pair.
do_ira(atm1, atm2[, k_factor])	Performs IRA matching on two atomistic structures.
calculate_rmsd(atm1, atm2[, k_factor])	Calculates RMSD using do_ira.

Module Contents

class rgpycrumbs.geom.ira.IRAComp

Result of an IRA comparison (rotation, translation, permutation, Hausdorff distance).

Added in version 1.0.0.

rot: numpy.array

trans: numpy.array

perm: numpy.array

hd: float

exception rgpycrumbs.geom.ira.IncomparableStructuresError

Bases: ValueError

Custom exception raised for incompatible atomistic structures.

Added in version 1.0.0.

rgpycrumbs.geom.ira._perform_ira_match(atm1, atm2, k_factor=2.8)

Performs IRA matching. Internal function.

rgpycrumbs.geom.ira.is_ira_pair(atm1, atm2, hd_tol=1, k_factor=2.8)

Checks if two atomistic structures are an IRA pair.

Added in version 1.0.0.

rgpycrumbs.geom.ira.do_ira(atm1, atm2, k_factor=2.8)

Performs IRA matching on two atomistic structures.

Added in version 1.0.0.

rgpycrumbs.geom.ira.calculate_rmsd(atm1, atm2, k_factor=2.8)

Calculates RMSD using do_ira.

Added in version 1.0.0.