A light-weight, versatile XYZ tile server, built with Flask and Rasterio 🌍

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

Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.

Convert XYZ data to bond lengths & angles, calculate contacts, planes and dihedral angles and print tables

Manage your XYZ Hub or HERE Data Hub spaces from Python.

Scripts to convert between PDB to Tinker XYZ files, without using the existing TINKER programs for conversion.

A small python script to create animation from multiply xyz files

fast image color space conversion via numpy vectorization

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

Script to smooth xyz and cube file trajectories. Applies spline interpolation to the trajectory

Align atomic coordinates in xyz files. Align one or more atoms to x-, y- and z-axes. Set origin to a selected atom or a centroid of selected atoms. Rotate atomic coordinates about arbitrary angles. Translate atomic coordinates.

3d xyz graphing using threejs

A command line tool that creates a novel proton indicator from a coordinate file (.xyz) to highlight proton movement in acid/base chemical reactions.

Generate a molecular junction (electrode-molecule-electrode) with FCC111 gold electrodes.

Simple scripts to generate a NetCDF file from an xyz .txt file.

Transfer XYZ file into POSCAR/CONTCAR file with re-center feature. Useful for single molecule calculation in VASP.

Project Sophire's official repo forked as a playground

This repository contains the working files used in the work "Hot Electron Cooling in Silicon Nanoclusters via Landau-Zener Non-Adiabatic Molecular Dynamics: Size Dependence and Role of Surface Termination"

Python web app that compare, calculate and plot the mathematical differences between 2 sets of atomic coordinates

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