CDKSwiftNativePort

CDKSwiftNativePort is a Swift Package that encapsulates CDK-derived chemistry functionality in native Swift.

It provides:

• molecule data model and graph utilities
• import/export for multiple chemistry formats
• SMILES and InChI parsing/generation paths
• CDK-style 2D layout + depiction scene generation
• molecular property and descriptor calculation (including XLogP and Rule-of-Five helpers)

Design Goals

• Keep CDK-derived chemistry logic in one reusable package.
• Keep package boundaries clean: no dependency on app-level code (Spotlight, Quick Look, app bundle identifiers, window/UI app state).
• Preserve CDK-inspired organization while staying idiomatic in Swift.

Platform and Toolchain

• Swift tools: 5.9
• Platform: macOS 14+ (as declared in Package.swift)

Installation (SwiftPM)

In Xcode, add a package dependency:

https://github.com/<your-org-or-user>/CDKSwiftNativePort.git

or in Package.swift:

.package(url: "https://github.com/<your-org-or-user>/CDKSwiftNativePort.git", from: "1.0.0")

Quick Start

import CDKSwiftNativePort

let input = "CC(=O)OC1=CC=CC=C1C(=O)O"
let molecules = try CDKSMILESReader.read(text: input)
guard let first = molecules.first else { fatalError("No molecule") }

// 2D layout
let laidOut = Depiction2DGenerator.generate(for: first)

// Identifiers
let ids = CDKMoleculeIdentifierService.compute(for: laidOut)
print(ids.smiles)
print(ids.inchi)

// Properties
let props = CDKMoleculePropertyService.compute(for: laidOut)
print(props.formula, props.molecularWeight, props.ruleOfFive.statusText)

// Export SVG
let svg = CDKDepictionGenerator.toSVG(molecule: laidOut)

Import and Export APIs

• Generic importer: CDKFileImporter
• Generic exporter: CDKFileExporter

Supported families include:

• MDL Molfile / SDFile (.mol, .sdf, .sd)
• SMILES / isomeric SMILES
• InChI
• MOL2, PDB, XYZ, CML
• RXN / RDF
• SVG depiction export

API Documentation

• High-level API reference: Documentation/API.md
• Architecture notes: Documentation/ARCHITECTURE.md
• Contribution guide: CONTRIBUTING.md
• Security policy: SECURITY.md
• Publishing/release process: PUBLISHING.md
• Changelog: CHANGELOG.md

Quality Gates

• Run tests:

swift test

• The suite includes package-boundary checks that prevent app-specific coupling from leaking into package source code.

Repository Standards

This repository includes:

• CI workflow (.github/workflows/ci.yml)
• Pull request template (.github/pull_request_template.md)
• Issue templates (.github/ISSUE_TEMPLATE/)
• Changelog-based release notes (CHANGELOG.md)

CDK Attribution and License

This package contains CDK-derived work.

• Upstream project: https://github.com/cdk/cdk
• Reference parity target used in this porting effort: CDK 2.11

Licensing:

• Package license: LGPL-2.1-or-later (see LICENSE)
• Additional attribution notes: NOTICE.md