RDKit Kotlin Example Template

This repository is a Kotlin example template for experimenting with RDKit — the open-source cheminformatics toolkit — on the JVM. It provides a simple setup to render 2D molecular depictions from SMILES strings and serves as a reference project for Kotlin developers integrating RDKit.

---

Table of Contents

• Overview
• Features
• Prerequisites
• Setup
• Usage
• Project Structure

---

Overview

This template project demonstrates:

• How to integrate RDKit Java bindings in a Kotlin project
• Rendering 2D chemical structures from SMILES
• Configuring basic drawing options like canvas size, scaling, and atom indices

It is intended as a starting point for Kotlin developers exploring cheminformatics workflows with RDKit on the JVM.

This project is based upon the Conan RDKit package, which can be used to create the Java SWIG bindings for RDKit. This means that the other native libraries for macOS and Linux can be built with that project. Currently, only the Windows build is provided in this repository, but it can be easily extended to include the other platforms.

---

Features

• Load and parse SMILES strings into RDKit molecular objects
• Generate 2D PNG images using MolDraw2DCairo
• Display atom indices for easier molecule inspection
• Pre-configured Gradle Kotlin DSL for JVM projects
• Cross-platform ready with java.library.path configuration

---

Prerequisites

• Java 21+
• Kotlin 2.2.20
• RDKit native libraries installed and accessible on the JVM library path

The project expects RDKit .so (Linux/macOS) or .dll (Windows) files to reside in the bin/ folder of the project.

---

Setup

1. Clone the repository:

git clone https://github.com/urban233/rdkit-kotlin-example-template.git
cd rdkit-kotlin-example-template

2. Build and run:

./gradlew run

---

Usage

The project provides a simple class DepictSmiles to generate 2D molecule depictions:

fun main() {
  // First, load the native library.
  System.loadLibrary("GraphMolWrap")
  val depict = DepictSmiles()
  depict.create2DPng("c1ccc(C)c(C)c1C")
}

This will generate a test.png in the project root with the 2D depiction of the molecule.

---

Project Structure

rdkit-kotlin-template/
├─ build.gradle.kts          # Gradle Kotlin DSL build file
├─ settings.gradle.kts
├─ src/
│  ├─ main/kotlin/
│     └─ DepictSmiles.kt
├─ bin/                      # RDKit native libraries are available here
├─ libs/                     # org.RDKit.jar is available here
└─ README.md

---