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Getting Started

Welcome to MolPy! This section will help you get up and running quickly. Whether you're new to molecular modeling or an experienced researcher, we'll guide you through the essentials.

Learning Path

We recommend following these guides in order:

  • 1️⃣ Installation

    Get MolPy installed and verify your setup. Learn about dependencies, optional packages, and development installation.

  • 2️⃣ Quickstart

    Build your first molecular system in minutes. This hands-on tutorial covers the core workflow from parsing to export.

  • 3️⃣ Core Concepts

    Understand MolPy's fundamental data structures: Atomistic, Frame, Block, and Box. Learn how topology and coordinates work together.

  • 4️⃣ Naming Conventions

    Learn the standardized field names used throughout MolPy for coordinates, atomic properties, and connectivity data.

  • ❓ FAQ

    Common questions and answers. Troubleshooting tips and comparisons with other tools.

What You'll Learn

Installation

  • Installing MolPy via pip
  • Setting up a development environment
  • Understanding dependencies and optional packages
  • Verifying your installation

Quickstart

  • Parsing chemical notation (SMILES, BigSMILES)
  • Building simple molecular structures
  • Working with topology and coordinates
  • Exporting to common formats (LAMMPS, PDB)

Core Concepts

  • Atomistic: The fundamental molecular structure representation
  • Frame: Tabular data structure for coordinates and properties
  • Block: Hierarchical composition of multiple structures
  • Box: Periodic boundary conditions
  • Topology: Bonds, angles, dihedrals, and their relationships

Next Steps

Once you've completed the Getting Started guides, explore:

Tutorials

Deep dive into specific topics with runnable Jupyter notebooks in the Tutorials section.

User Guide

Follow complete workflows for real-world tasks in the User Guide: - Parsing chemistry notation - Building polymers step-by-step - Creating crosslinked networks - Working with polydisperse systems

API Reference

Browse detailed API documentation in the API Reference section.

Prerequisites

Before you begin, make sure you have:

  • Python 3.12+ installed
  • Basic familiarity with Python
  • (Optional) Experience with molecular modeling or chemistry

No prior knowledge of MolPy is required—we'll teach you everything you need!

Ready to Start?

Begin with Installation to get MolPy set up on your system.

Need Help?

Check the FAQ for answers to common questions, or open an issue on GitHub.

Want Examples?

Jump to the Quickstart for hands-on examples you can run immediately.

What Makes MolPy Different?

MolPy is designed with these principles in mind:

  • Type Safety: Strong typing throughout for better IDE support and fewer runtime errors
  • Composability: Build complex workflows by combining simple, reusable components
  • Explicit APIs: No hidden magic—every operation is clear and documented
  • Interoperability: Seamless integration with RDKit, LAMMPS, OpenMM, and more
  • AI-Friendly: Predictable APIs that work well with LLM code generation

Ready to get started? Let's begin with Installation!