rgpycrumbs.geom.api.alignment¶

Attributes¶

ira_mod

Classes¶

`IRAMatchInputs`	Encapsulates the raw arrays required for an IRA graph match.
`IRAMatchResults`	Encapsulates the transformation outputs from the IRA algorithm.
`IRAConfig`	Configuration parameters for the Iterative Rotations and Alignment.
`AlignmentMethod`	Tracks which algorithm was successfully applied.
`AlignmentResult`	Container for alignment outputs.

Functions¶

`_apply_ira_alignment`(→ bool)	Performs the low-level IRA isomorphism and affine transformation.
`align_structure_robust`(→ AlignmentResult)	Aligns a mobile structure to a reference using IRA with an ASE fallback.

Module Contents¶

rgpycrumbs.geom.api.alignment.ira_mod[source]¶

class rgpycrumbs.geom.api.alignment.IRAMatchInputs[source]¶

Encapsulates the raw arrays required for an IRA graph match.

ref_count: int[source]¶

ref_numbers: numpy.ndarray[source]¶

ref_positions: numpy.ndarray[source]¶

mobile_count: int[source]¶

mobile_numbers: numpy.ndarray[source]¶

mobile_positions: numpy.ndarray[source]¶

kmax: float[source]¶

class rgpycrumbs.geom.api.alignment.IRAMatchResults[source]¶

Encapsulates the transformation outputs from the IRA algorithm.

rotation: numpy.ndarray[source]¶

translation: numpy.ndarray[source]¶

permutation: numpy.ndarray[source]¶

hausdorff_dist: float[source]¶

class rgpycrumbs.geom.api.alignment.IRAConfig[source]¶

Configuration parameters for the Iterative Rotations and Alignment.

enabled: bool = False[source]¶

kmax: float = 1.8[source]¶

class rgpycrumbs.geom.api.alignment.AlignmentMethod(*args, **kwds)[source]¶

Bases: enum.Enum

Tracks which algorithm was successfully applied.

ASE_PROCRUSTES[source]¶

IRA_PERMUTATION[source]¶

NONE[source]¶

class rgpycrumbs.geom.api.alignment.AlignmentResult[source]¶

Container for alignment outputs.

Parameters:

atoms – The aligned structure (modified in-place, but returned for chaining).
method – The specific algorithm that was used.

atoms: ase.Atoms[source]¶

method: AlignmentMethod[source]¶

property used_ira: bool[source]¶: Helper to maintain backward compatibility with boolean checks.

rgpycrumbs.geom.api.alignment._apply_ira_alignment(ref_atoms: ase.Atoms, mobile_atoms: ase.Atoms, config: IRAConfig) → bool[source]¶

Performs the low-level IRA isomorphism and affine transformation.

This function modifies mobile_atoms in-place. It returns True if the alignment succeeds, or False if an error occurs or IRA remains unavailable.

rgpycrumbs.geom.api.alignment.align_structure_robust(ref_atoms: ase.Atoms, mobile_atoms: ase.Atoms, ira_config: IRAConfig) → AlignmentResult[source]¶

Aligns a mobile structure to a reference using IRA with an ASE fallback.

This method minimizes the RMSD between the reference and mobile structures. It first attempts to solve the isomorphism problem (finding $P, R, t$) using IRA. If IRA fails or remains unavailable, it defaults to standard Procrustes superimposition (finding $R, t$) via ASE.

Parameters:

ref_atoms – The fixed reference configuration.
mobile_atoms – The configuration to align (modified in-place).
ira_config – Configuration object with state of IRA and the adjacency cutoff distance for IRA graph matching.

Returns:

An AlignmentResult.