An open library for the analysis of molecular dynamics trajectories
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Sep 25, 2026 - Python
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rmsd
Here are 26 public repositories matching this topic...
Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format
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Sep 26, 2026 - Python
📐 Symmetry-corrected RMSD in Python
computational-biology computational-chemistry drug-discovery docking symmetry rmsd cadd molecular-docking computer-aided-drug-design
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Aug 3, 2026 - Python
Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure
machine-learning topology neural-network hpc pdb protein-structure dataset ab-initio amino-acids denovo protein-design rmsd denovo-design
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Mar 7, 2025 - Python
register 3D point clouds using rotation, translation, and scale transformations.
point-cloud registration cryo-em 3d rmsd cryoem point-cloud-registration structure-comparison scale-transformations
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Aug 20, 2025 - Python
Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar structures.
clustering python-script molecular-dynamics openbabel trajectory rmsd distance-matrix monte-carlo-trajectory
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Sep 28, 2026 - Python
PocketMaster is a flexible and automated tool for analyzing, clustering, and visualizing protein binding sites. It allows you to quickly compare structures, explore functional regions of proteins, and generate clear results, even when working with hundreds or thousands of models.
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Feb 22, 2026 - Python
Molecular Crystal Simulation Library (mcse) is an open-source Python package for manipulating and analyzing molecular crystal structures
python machine-learning dft analysis crystallography generation polymorphism molecular rmsd polymorph molecular-crystals crystals
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May 30, 2022 - Python
aligns arbitrarily ordered isomers
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Jun 19, 2026 - Python
High-throughput docking pose validation: symmetry-corrected RMSD and lightweight PoseBusters-style distance/clash filters.
cheminformatics pytorch drug-discovery rdkit rmsd molecular-docking protein-ligand posebusters pose-validation symmetry-correction
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Feb 19, 2026 - Python
Kabsch algorithm for optimal 3D molecular coordinates alignment, rigid translation, and RMSD distance calculation
mcp protein-structure computational-chemistry rmsd python-standard-library kabsch-algorithm coordinate-geometry agent-skills structural-alignment molecular-geometry 3d-superposition
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Sep 28, 2026 - Python
Kabsch algorithm for optimal 3D molecular coordinates alignment, rigid translation, and RMSD distance calculation
mcp protein-structure computational-chemistry rmsd python-standard-library kabsch-algorithm coordinate-geometry agent-skills structural-alignment molecular-geometry 3d-superposition
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Sep 28, 2026 - Python
A program that compares a protein structure prediction to a solved structure and evaluates the prediction's accuracy using RMSD.
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Jun 25, 2024 - Python
Project for analysis of protein structures in .pdb file format. It calculates some structure parameters and can compare two structures by calculating the RMSD.
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Feb 16, 2021 - Python
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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Aug 17, 2026 - Python
Python web app that compare, calculate and plot the mathematical differences between 2 sets of atomic coordinates
bioinformatics chemistry computational-chemistry xyz rmsd kabsch-algorithm geometry-optimization rmsd-algorithms
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Feb 7, 2023 - Python
Superimpose a set of protein structures and report a RSMD matrix, in CSV and Mega-compatible formats, using Pymol as a module
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Jul 6, 2020 - Python
Calculates the per-residue atomic distance between two proteins
bioinformatics structural-biology protein-structure matplotlib rmsd euclidean-distances pdbe bioinformatics-tool gemmi
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Jan 5, 2024 - Python
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