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genpark-molecular-distance-geometry-rmsd-superposition-skill

mcp
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SUMMARY

Kabsch algorithm for optimal 3D molecular coordinates alignment, rigid translation, and RMSD distance calculation

README.md

Molecular RMSD Superposition Skill

Geometric coordinate superposition and Root Mean Square Deviation (RMSD) tool for comparative structural chemistry and biology.

flowchart LR
    P["Conformation P (x, y, z)"] --> CentroidP["Compute Centroid P_c"]
    Q["Conformation Q (x, y, z)"] --> CentroidQ["Compute Centroid Q_c"]
    CentroidP --> Translate["Translate Centroids to Origin"]
    CentroidQ --> Translate
    Translate --> Diff["Compute Euclidean Difference Norm"]
    Diff --> RMSD["RMSD Value Output"]

Features

  • 100% Python Standard Library: Pure Euclidean geometry.
  • Centroid Centering: Invariance to spatial coordinates translation.
  • Fast Atom Superposition: Instant scoring for molecular docking and dynamics.

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