Module validation 

Validation checks matching RDKit’s embedding validation pipeline. Part of the retry-on-failure loop in embedPoints().

Structs

TetrahedralCenter

Tetrahedral center — any sp3 atom with 4 neighbors (not necessarily chiral)

Constants

MAX_MINIMIZED_E_PER_ATOM

Functions

check_chiral_centers

Check chiral center volumes have correct sign. Matches RDKit’s checkChiralCenters — intentionally permissive (allows 20% undershoot if sign matches). Uses f64 coords matching RDKit’s Point3D.

check_double_bond_geometry

Double bond geometry check: reject if substituent-double_bond_atom-other is nearly linear. Matches RDKit’s doubleBondGeometryChecks with doubleBondEnds filtering. Uses f64 coords matching RDKit’s Point3D.

check_planarity

Planarity check: compute OOP (improper torsion) energy for SP2 centers. Reject if energy > n_impropers * tolerance. Matches RDKit’s planarity check in minimizeWithExpTorsions.

check_tetrahedral_centers

Check all tetrahedral centers for minimum volume and center-in-volume. Matches RDKit’s checkTetrahedralCenters. Uses f64 coords matching RDKit’s Point3D.

find_sssr_pub

Find the Smallest Set of Smallest Rings (SSSR) using Horton’s algorithm. Returns a list of rings, each ring being a vector of atom indices.

identify_tetrahedral_centers

Identify tetrahedral centers for volume checks. Matches RDKit’s findChiralSets logic for tetrahedralCarbons:

perturb_if_planar

Check if coordinates are quasi-planar (2D) and perturb the z-axis if so. Returns true if coordinates were perturbed (caller should re-minimise).