geom-x 2.1.0

Include RDKit for molecular manipulation.

GEOM – Geometry File Management

GEOM is a tool for creating, modifying, and analyzing XYZ geometry files. It provides geometry transformations, nanoparticle generation, and graphene structure creation for computational research, with both a command-line interface and a native desktop GUI.

View the Documentation

Features

• GEOM Structure Studio: native desktop GUI for interactive nanoparticle and graphene generation, 3D visualization, and structure manipulation.
• RDKit tools: molecular visualization, file conversion, force field optimization, and conformers generation.
• AI Assistant for nanoparticle and graphene creation
• Geometry Transformations: Translation, rotation, merging, and specular (mirror) transformations.
• Nanoparticle Generation: Sphere, rod, core-shell, tip, pyramid, cone, icosahedron, and more.
• Graphene Structures: Ribbons, disks, rings, and triangles.
• Advanced Options: Alloying, dimer formation, and bowtie configurations.
• Minimum Distance Calculation between XYZ geometries.
• Geometrical Center Computation.

Installation

GEOM can be installed in two ways:

• pip (PyPI): best for quick installs, CI, and lightweight usage.
• conda (recommended for full scientific setups): full ecosystem with all extras and the desktop app.

On PyPI, the package name is geom-x (the import/module name is still geom).

Option A — pip (PyPI)

Create/activate an environment first, then:

pip install geom-x

Quick sanity check:

python -c "import geom; print('geom imported OK')"
geom -h

Option B — conda

./install.sh

This script will:

• Check if Miniconda or Anaconda is installed. If not, it will prompt you to install Miniconda.
• Set up a conda environment named geom_env with all dependencies.
• Configure shell aliases for running GEOM.
• Build the GEOM Structure Studio desktop app (macOS and Linux/WSL).

Quick Start

Load the GEOM environment:

geom_load

See all available options:

geom -h

Example commands:

• RDKit conformers generation

geom -rdkit -i tyrosine.mol -confs

• RDKit file conversion

geom -rdkit -i tyrosine.mol -o tyrosine.pdb

• Rotate geometry 90 degrees around the Y-axis:

geom -r1 90 geom.xyz origin_CM_yes +y

• Generate a nanoparticle sphere:

geom -create -sphere Ag 30

• Generate a graphene ribbon:

geom -create -graphene rib 50 20

GEOM Structure Studio

GEOM includes a native desktop GUI — GEOM Structure Studio — for interactive nanoparticle and graphene creation, 3D visualization, and structure manipulation.

Launch

• Terminal — load the environment with geom_load, then run geomapp.
• macOS — open ~/Applications/GEOM.app directly from Finder or Spotlight.
• Linux / WSL — open GEOM from your desktop application launcher (the installer registers a .desktop entry).

What you can do

• Generator — create nanoparticles (sphere, rod, tip, pyramid, cone, icosahedron, and more) and graphene structures (disk, ribbon, ring, triangle) with interactive parameter controls. Supports alloy, dimer, bowtie, and core-shell configurations.
• Viewer — load XYZ, PDB, or SMILES structures via file picker or drag-and-drop. Interactive 3D view with VdW/CPK rendering, atom selection expressions (x > 0 and name C), and adjustable sphere size, bond width, and resolution.
• Manipulator — translate, rotate, mirror (enantiomer), and center structures. Pair mode sets a controlled distance between two loaded structures along any axis.

Starting the AI Assistant

GEOM includes an AI-powered assistant that understands natural language, translates it into valid GEOM CLI commands, and executes them automatically.

This assistant is built using Microsoft's AutoGen framework, which enables a multi-agent system to interface with OpenAI's language models and run commands dynamically.

1. Export your OpenAI API key

export OPENAI_API_KEY=your-api-key-here

Obtain an API key at https://platform.openai.com/account/api-keys

2. Start the assistant

ai_geom

The assistant will automatically create and execute the corresponding GEOM command for you.

Running Tests

Tests run automatically during installation. To run them manually:

./geom/tests/run_all_tests.sh

License

GEOM is licensed under the GNU General Public License v3.0.

Funding

This project has been supported by the FARE 2020 program — "Framework per l'attrazione e il rafforzamento delle eccellenze per la ricerca in Italia."

Publications

GEOM has been used in the following research paper(s):

• Giovannini, T.; Grobas Illobre, P.; Lafiosca, P.; Nicoli, L.; Bonatti, L.; Corni, S.; Cappelli, C. plasmonX: an Open-Source Code for Nanoplasmonics. Comput. Phys. Commun. 2026, 110035. https://doi.org/10.1016/j.cpc.2026.110035

Contact

For issues or contributions:

• Email: [e-mail]
• Github issues: https://github.com/pgrobasillobre/geom/issues