autofragment.core.geometry

Geometric utilities for isolated molecular fragments.

This module provides functions for: - Computing centroids - Computing RMSD between structures - Kabsch alignment

These helpers operate on isolated Molecule objects. Convert from ChemicalSystem explicitly when working with full systems.

Functions

compute_centroid(coords)	Compute the centroid of a set of coordinates.
compute_centroids(molecules)	Compute centroids for a list of isolated molecules.
compute_rmsd(coords1, coords2)	Compute the root-mean-square deviation between two coordinate sets.
hybrid_distance(mol1, mol2[, alpha])	Compute a hybrid distance combining centroid distance and RMSD.
kabsch_align(reference, target)	Apply Kabsch alignment to target molecules based on centroids.
kabsch_rotation(P, Q)	Compute the optimal rotation matrix to align P onto Q using Kabsch algorithm.
molecule_rmsd(mol1, mol2)	Compute RMSD between two molecules.