NCDK: The Chemistry Development Kit ported to C#

NCDK is .NET port of the Chemistry Development Project (CDK). Functionality is provided for many areas in cheminformatics.

NCDK is covered under LGPL v2.1. The modules are free and open-source and is easily integrated with other open-source or in-house projects.

The current release is based on CDK 2019-11-27 snapshot.

Getting Started

Most of codes are written in C#. You can learn NCDK from CDK documents, NCDKTests and NCDKDisplayTests project.

• NCDK -- Core module of NCDK.
• NCDK.Display -- Depiction module of NCDK. It is based on WPF.
• NCDK.RDF --- RDF functions.
• NCDK.Legacy --- Legacy modules.
• NCDK.Tests -- Unit tests for NCDK.
• NCDK.DisplayTests -- Unit tests for NCDK.Display.
• NCDK.RDFTests --- Unit test for NCDK.RDF.
• NCDK.LegacyTests --- Unit test for NCDK.Legacy.
• MolViewer -- MOL file viewer, which can depict SMILES. It includes WPF control to show molecular/reaction.
• Documentation -- Sandcastle Help File Builder project.

Chem object contains utility methods for quick access to frequently used functions. The methods' name are called after RDKit. They should work within C# interactive.

    using System;
    using System.IO;
    using System.IO.Compression;
    using System.Linq;

    class Chem_Example
    {
        static void Main(string[] args)
        {
            var toluene = Chem.MolFromSmiles("Cc1ccccc1");
            var mol1 = Chem.MolFromFile("Data/input.mol");
            var stringWithMolData = new StreamReader("Data/input.mol").ReadToEnd();
            var mol2 = Chem.MolFromMolBlock(stringWithMolData);

            using (var suppl = Chem.SDMolSupplier("Data/5ht3ligs.sdf"))
            {
                Console.WriteLine(suppl.Count);
                foreach (var mol in suppl)
                {
                    if (mol == null)
                        continue;
                    Console.WriteLine(mol.Atoms.Count);
                }
                Console.WriteLine(suppl[0].Atoms.Count);
            }

            using (var fsuppl = Chem.ForwardSDMolSupplier(new FileStream("Data/5ht3ligs.sdf", FileMode.Open)))
            {
                foreach (var mol in fsuppl)
                {
                    if (mol == null)
                        continue;
                    Console.WriteLine(mol.Atoms.Count);
                }
            }

            using (var gzsuppl = Chem.ForwardSDMolSupplier(
                new GZipStream(
                    new FileStream("Data/actives_5ht3.sdf.gz", FileMode.Open), 
                    CompressionMode.Decompress)))
            {
                Console.WriteLine(gzsuppl.Count(x => x != null));
            }
        }
    }

Build from Command Line

Windows: Open Developer Command Prompt for VS 2017, and launch BuildAll.bat.

Linux (.NET Core): To build NCDK.dll, launch dotnet build --framework netstandard2.0 in NCDK directory.

Test from Command Line

Windows: Launch vstest.console.exe NCDK.Tests\bin\Release\netcoreapp2.1\NCDK.Tests.dll and vstest.console.exe NCDK.DisplayTests\bin\Release\NCDK.DisplayTests.dll.

Linux: Launch dotnet build to build assemblies and copy libinchi.so.#.## to output directory of NCDK.Tests, and make a link of libinchi.so to the libinchi.so.#.##. And then, launch dotnet test in NCDK.Tests directory to test it.

NuGet Packages

• NCDK -- for .NET Standard 2.0 and .NET Framework 4.6.1. InChI features work only on Intel-based Windows or Intel-based Linux system.
• NCDK.Display -- for .NET Framework 4.6.1.

Copyright (c) 2016-2019 Kazuya Ujihara