chemparseplot.parse.projection

Reaction valley (s, d) projection utilities.

Extracts the 2D RMSD-plane rotation into reusable functions. The projection maps (rmsd_a, rmsd_b) coordinates into progress s (along the path) and deviation d (perpendicular).

For NEB paths, reference A is the reactant and B is the product. For single-ended methods, A is the initial structure and B is the final (saddle or minimum).

Implements the method from :cite:goswami2026valley.

.. versionadded:: 1.5.0

Module Contents

Classes

ProjectionBasis

Orthonormal basis for the (s, d) reaction valley projection.

Functions

compute_projection_basis	Compute the projection basis from first/last points of the arrays.
project_to_sd	Project (rmsd_a, rmsd_b) into (s, d) reaction valley coordinates.
inverse_sd_to_ab	Map (s, d) grid coordinates back to (a, b) RMSD space.

API

class chemparseplot.parse.projection.ProjectionBasis

Orthonormal basis for the (s, d) reaction valley projection.

Attributes

a_start, b_start RMSD values of the first point (origin of the rotated frame). u_a, u_b Unit vector along the path direction in (a, b) space. v_a, v_b Unit vector perpendicular to the path (v = rotate(u, +90deg)). path_norm Euclidean length of the path vector in (a, b) space.

a_start: float

None

b_start: float

None

u_a: float

None

u_b: float

None

v_a: float

None

v_b: float

None

path_norm: float

None

chemparseplot.parse.projection.compute_projection_basis(rmsd_a: numpy.ndarray, rmsd_b: numpy.ndarray) → chemparseplot.parse.projection.ProjectionBasis

Compute the projection basis from first/last points of the arrays.

Parameters

rmsd_a, rmsd_b RMSD distance arrays (to reference A and B respectively). The first element defines the origin; the last defines the path direction.

Returns

ProjectionBasis Frozen dataclass with the orthonormal basis vectors.

Raises

ValueError If the path has zero length (first and last points coincide in RMSD space).

chemparseplot.parse.projection.project_to_sd(rmsd_a: numpy.ndarray, rmsd_b: numpy.ndarray, basis: chemparseplot.parse.projection.ProjectionBasis) → tuple[numpy.ndarray, numpy.ndarray]

Project (rmsd_a, rmsd_b) into (s, d) reaction valley coordinates.

Parameters

rmsd_a, rmsd_b RMSD arrays to project. basis Pre-computed projection basis.

Returns

s, d Progress and deviation arrays.

chemparseplot.parse.projection.inverse_sd_to_ab(s: numpy.ndarray, d: numpy.ndarray, basis: chemparseplot.parse.projection.ProjectionBasis) → tuple[numpy.ndarray, numpy.ndarray]

Map (s, d) grid coordinates back to (a, b) RMSD space.

Used for evaluating the RBF surface on a projected grid.

Parameters

s, d Progress and deviation arrays (can be meshgrid raveled). basis Pre-computed projection basis.

Returns

rmsd_a, rmsd_b Coordinates in the original RMSD plane.