algomol 0.0.3.post4

A Python/C++ library for fast detection of chemical equivalent (or magnetic equivalent) atoms in molecules, useful for assigning/computing peaks in NMR spectroscopy.

AlgoMol Core Library

AlgoMol Core is a C++ library for fast molecular graph representation and equivalence detection with Python bindings.

Overview

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

• Chemical and topological equivalence detection
• VSEPR geometry modeling of molecular structures

For more information, visit our official website at algomol.com.

Features

• Equivalence Classes: Generate equivalence classes based on topological or geometrical properties
• Stereochemistry Support: Correctly handles cis/trans isomerism and other stereochemical features
• VSEPR Geometry: Assign and manage molecular geometries based on VSEPR
• Python Bindings: Use the library directly from Python with full API support

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

AlgoMol is also available as a Python package:

pip install algomol

Usage

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);
}

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)

API Reference

Core Classes

• MolGraph: Main class for molecular graph representation
• Atom<Element>: Templated class for atoms of different elements
• Bond<BondType>: Templated class for different bond types
• Geometry<GeometryType>: Templated class for VSEPR geometries

Key Functions

• addAtom(): Add an atom to a molecule
• addBond(): Add a bond between atoms
• init(): Initialize a molecule after adding atoms and bonds
• generateEquivalenceClasses(): Compute equivalence classes
• isTopologyEquivalent(): Check if two atoms are topologically equivalent
• isChemicallyEquivalent(): Check if two atoms are chemically equivalent
• setCisAtoms(): Set cis stereochemistry
• setOrientations(): Set atom orientations

License

AlgoMol Core is proprietary software, owned exclusively by AlgoMol LLC. All rights reserved. This software and its source code are confidential and cannot be redistributed, modified, or used without explicit written permission from AlgoMol LLC. This is NOT open source software.

Copyright © AlgoMol LLC. Unauthorized use, reproduction, or distribution is strictly prohibited.

Contact

For questions and support, please contact: [e-mail]

Visit our official website at algomol.com for more information.