Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format
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Mar 16, 2026 - Python
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kabsch
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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.
dft overlay molecule computational-chemistry superposition molecules coordinates xyz-reader kabsch-algorithm xyz-files kabsch inorganic-chemistry coordination-chemistry molecule-visualization molecule-viewer
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May 3, 2024 - Python
Calculate and apply the optimal transformation matrix that minimizes the RMSD (root mean squared deviation) between two paired sets of points.
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Mar 13, 2019 - JavaScript
Kabsch algorithm for optimally aligning two paired sets of points
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Jun 22, 2026 - Julia
A simple library to compute rigid transformation matrix between two point sets.
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Apr 22, 2022 - TypeScript
Differentiable, gradient-safe Kabsch (SVD) and Horn (quaternion) point-cloud alignment across NumPy, PyTorch, JAX, TensorFlow, and MLX.
computer-vision robotics tensorflow numpy protein-structure molecular-dynamics pytorch autograd computational-chemistry quaternion svd mlx rmsd point-cloud-registration differentiable jax kabsch umeyama structural-alignment rigid-body-transformation
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Jul 20, 2026 - Python
RNA structural alignment via multi-strategy TM-score optimization. Finds higher-scoring superpositions than USalign on 66% of pairs.
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Mar 26, 2026 - Python
batchwise Kabsch test with Jimmy Charnley's calculate_rmsd (https://github.com/charnley/rmsd) on multiple CPUs
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Mar 28, 2019 - Python
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