Command Line Interface

Usage

xyz2graph [-h] [-o OUTPUT] [-b] [--debug] [-r REMOVE] xyz_file

Options

xyz_file
Input XYZ file path containing molecular coordinates (required).

-o, --output
Custom output path for the HTML visualization. Defaults to input filename with .html extension.

-b, --browser
Launch visualization directly in default web browser instead of saving to file.

-r, --remove
Remove specific atoms using comma-separated indices or element symbols (e.g., "1,2,H,O,5" removes atoms at positions 1,2,5 and all H,O atoms). Element symbols must be properly capitalized.

--debug
Enable verbose logging for troubleshooting and development.

-h, --help
Display command-line options and usage information.

Examples

# Basic usage - saves visualization as HTML in the same directory
xyz2graph molecule.xyz

# Save visualization with a specific name
xyz2graph molecule.xyz -o viz.html

# Open directly in browser without saving
xyz2graph molecule.xyz -b

# Remove hydrogens and oxygens from visualization
xyz2graph molecule.xyz -r "H,O"

# Remove specific atoms by index and element
xyz2graph molecule.xyz -r "1,2,H,O,5"