Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.
macOS desktop app and Quick Look extension for molecular previews: Mol* 3D, xyzrender SVG, and RDKit grids.
Convert XYZ data to bond lengths & angles, calculate contacts, planes and dihedral angles and print tables
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.
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.
A small python script to create animation from multiply xyz files
How to plot a 3D surface with python by interpolation
These are important tools written for working with ORCA (a computational chemistry open source package) in a super-computing environment. They include multiple job submission scripts (BASH), multiple job cancellation (BASH), job setup with different geometries (in python), data extraction (BASH), final optimized geometry extraction (BASH) and
Automatic Schoenflies point-group determination from a .xyz file: numerically detects all symmetry elements (rotations, reflections, inversion, improper rotations), then generates the full character table for any axial group on the fly — with HTML/LaTeX export, idealized-structure building, and an optional 3-D viewer.
Computes CShM (shape measures) and other geometric indices from crystallographic information files (CIFs), which may contain single or multiple entries, or from COD (Crystallography Open Database) entries.
The comparison between two structures is based on the cartesian coords.
Script to smooth xyz and cube file trajectories. Applies spline interpolation to the trajectory
A versatile Python tool for converting LAMMPS dump files to XYZ format and sampling molecular dynamics trajectories with precise frame control.
Fast and memory-efficient converter for the Materials Project Trajectory (MPtrj) dataset to extended XYZ format with element-based filtering.
A command-line tool for computing radial distribution functions (RDFs) from molecular dynamics trajectories in XYZ format, powered by OVITO.
Serverless browser application for CIF reporting, average calculations, geometry-parameter analysis, interatomic distance analysis, disorder-model summarisation, ORTEP-style plotting and XYZ export.
Fortran code that convert xyz-file to POSCAR file for VASP calculation
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