AlgoMol Core Library

C++ library for fast molecular graph representation and equivalence detection with Python bindings

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Overview

AlgoMol Core provides a robust framework for molecular modeling with specific focus on:

Installation

Requirements

  • C++17 compatible compiler (GCC 7+, Clang 5+, MSVC 2019+)
  • CMake 3.15 or newer
  • Python 3.9+ (for Python bindings)
  • pybind11 (for Python bindings)

Python Package (Recommended)

The easiest way to get started:

pip install algomol

Usage Examples

Python API

import algomol

# Create a molecule
molecule = algomol.MolGraph("ethane")

# Add atoms
molecule.add_atom(1, 6)  # Carbon (atomic number 6)
molecule.add_atom(2, 6)  # Carbon
molecule.add_atom(3, 1)  # Hydrogen (atomic number 1)
molecule.add_atom(4, 1)  # Hydrogen
molecule.add_atom(5, 1)  # Hydrogen
molecule.add_atom(6, 1)  # Hydrogen
molecule.add_atom(7, 1)  # Hydrogen
molecule.add_atom(8, 1)  # Hydrogen

# Add bonds
molecule.add_bond(1, 2, algomol.BondType.SINGLE)
molecule.add_bond(1, 3, algomol.BondType.SINGLE)
molecule.add_bond(1, 4, algomol.BondType.SINGLE)
molecule.add_bond(1, 5, algomol.BondType.SINGLE)
molecule.add_bond(2, 6, algomol.BondType.SINGLE)
molecule.add_bond(2, 7, algomol.BondType.SINGLE)
molecule.add_bond(2, 8, algomol.BondType.SINGLE)

# Initialize the molecule
molecule.init_mol()

# Generate equivalence classes
molecule.generate_equivalence_classes(algomol.QueryTypeFlag.TOPOLOGICAL)

# Get equivalence classes
classes = molecule.get_equivalence_classes(algomol.QueryTypeFlag.TOPOLOGICAL)

C++ API

#include "AlgoMol/molecules.hpp"

int main() {
    // Create a molecule
    auto molecule = std::make_shared<AlgoMol::molecules::MolGraph>("ethane");
    
    // Add atoms
    molecule->addAtom(1, AlgoMol::elements::_CARBON);
    molecule->addAtom(2, AlgoMol::elements::_CARBON);
    molecule->addAtom(3, AlgoMol::elements::_HYDROGEN);
    molecule->addAtom(4, AlgoMol::elements::_HYDROGEN);
    molecule->addAtom(5, AlgoMol::elements::_HYDROGEN);
    molecule->addAtom(6, AlgoMol::elements::_HYDROGEN);
    molecule->addAtom(7, AlgoMol::elements::_HYDROGEN);
    molecule->addAtom(8, AlgoMol::elements::_HYDROGEN);
    
    // Add bonds
    molecule->addBond(1, 2, AlgoMol::bonds::BondType::SINGLE);
    molecule->addBond(1, 3, AlgoMol::bonds::BondType::SINGLE);
    molecule->addBond(1, 4, AlgoMol::bonds::BondType::SINGLE);
    molecule->addBond(1, 5, AlgoMol::bonds::BondType::SINGLE);
    molecule->addBond(2, 6, AlgoMol::bonds::BondType::SINGLE);
    molecule->addBond(2, 7, AlgoMol::bonds::BondType::SINGLE);
    molecule->addBond(2, 8, AlgoMol::bonds::BondType::SINGLE);
    
    // Initialize the molecule
    molecule->init();
    
    // Generate equivalence classes
    molecule->generateEquivalenceClasses(AlgoMol::molecules::QueryTypeFlag::TOPOLOGICAL);
    
    // Get equivalence classes
    auto classes = molecule->getEquivalenceClasses(AlgoMol::molecules::QueryTypeFlag::TOPOLOGICAL);
}

Get Started

Ready to integrate AlgoMol Core into your project? Install the library and explore the examples to see how it can accelerate your molecular modeling workflows.

Install from PyPI

For questions and support, please contact: dev@algomol.com

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