Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format

Python 3 script for overlaying or superimposing two or more molecules. The overlayed / superimposed molecules can be displayed and the modified coordinates can be saved as xyz files. Coloring by atom or molecule is possible.

Calculate and apply the optimal transformation matrix that minimizes the RMSD (root mean squared deviation) between two paired sets of points.

Pairwise structural comparison of .xyz, a fork of aRMSD to work without PyInstaller in Linux. Note the project «aRMSD-minimalWindowsSupport», too.

Kabsch algorithm for optimally aligning two paired sets of points

A simple library to compute rigid transformation matrix between two point sets.

A collection of the Kabsch (SVD-based) and Horn (Quaternion-based) optimal structural alignment algorithms, implemented in Python (NumPy, PyTorch, JAX, TensorFlow, MLX).

RNA structural alignment via multi-strategy TM-score optimization. Finds higher-scoring superpositions than USalign on 66% of pairs.

batchwise Kabsch test with Jimmy Charnley's calculate_rmsd (https://github.com/charnley/rmsd) on multiple CPUs

Clustering based on RMSD