CelleditPy — A Python Crystal Cell Editor

CelleditPy is a Python-based GUI application designed for crystallographers and computational chemists. It provides a visual, interactive environment to load molecular structures (from .mol or .cif files), define or adjust unit cell parameters, and reposition the molecule within the cell before saving the result as a .cif file.

This tool is built using PyQt6, PyVista, and ASE (Atomic Simulation Environment).

Features

• Load Structures: Load molecular structures from .mol and .cif files.
• Save as CIF: Save the final structure, including the unit cell, in .cif format.
• Interactive Cell Editing: Manually set or adjust unit cell parameters (a, b, c, alpha, beta, gamma).
• Auto-Fit Cell: Automatically calculate and apply the minimum cell dimensions (a, b, c) required to contain the molecule, while preserving the current cell angles.
• 3D Manipulation:
  • Translation: Move the molecule along Cartesian (XYZ) axes or fractional cell (ABC) axes.
  • Rotation: Rotate the molecule around Cartesian (XYZ) axes (centered on a selected atom) or cell (ABC) axes (centered on the axis itself).
• Molecule Fitting:
  • Fit Molecule to Axis: Align the molecule to a specific cell axis (a, b, or c) by defining the molecular direction using two or more atoms.
  • Fit in Cell (Auto-fit): Automatically detects atoms lying on a cell axis, fixes them, and rotates the rest of the molecule to best fit within the cell boundaries.
• Coordinate Wrapping: Wrap atomic coordinates to fit all atoms inside the defined unit cell (0.0 to 1.0 fractional coordinates).
• Visualization:
  • 3D visualization powered by PyVista.
  • Toggle the display of atom indices.
  • Reset the camera view.

Installation

Prerequisites:

• Python 3.8+
• The following libraries (and their dependencies) are required:
  • PyQt6
  • pyvista
  • pyvistaqt
  • ase
  • numpy
  • scipy

These dependencies will be installed automatically when installing the package.

Install from Source:

Install the package using pip. This will also install all required dependencies and register the command-line entry point. bash pip install celleditpy

Usage

After installation, you can run the application by simply typing the following command in your terminal:

celleditpy

This will launch the main application window.

License

This project is licensed under the GNU General Public License v3.0 (GPL-v3) License. See the LICENSE file for details.

Author

• HiroYokoyama