rmsd

An open library for the analysis of molecular dynamics trajectories

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

📐 Symmetry-corrected RMSD in Python

Preforms De novo protein design using machine learning and PyRosetta to generate a novel protein structure

register 3D point clouds using rotation, translation, and scale transformations.

Python script that receives a molecular dynamics or Monte Carlo trajectory and performs agglomerative clustering to classify similar structures.

header-only C++ library for registering 3D point clouds using rotation, translation, and scale transformations

VMD plugin to calculate and visualize clusters of conformations for a trajectory

PCA and normal mode analysis of proteins

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.

Molecular Crystal Simulation Library (mcse) is an open-source Python package for manipulating and analyzing molecular crystal structures

Tool to calculate the root mean square deviation between molecular structures

aligns arbitrarily ordered isomers

利用xvg生成的csv文件进行画图的脚本

Command line recipes for the working chemoinformatician

A protein fragments picker

High-throughput docking pose validation: symmetry-corrected RMSD and lightweight PoseBusters-style distance/clash filters.

Pairwise structural comparison of .xyz by a Kabsch test with adjustable weights. For versions prior to v1.0.0, note the project «aRMSD-minimalWindowsSupport», too.

Kabsch algorithm for optimally aligning two paired sets of points

MODE-TASK plugin for PyMOL