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RDKIT

license offline-first audit category

Anticloud-hardened packaging of the upstream project RDKIT in category MEDICINE DEVELOPMENT. Upstream source is vendored in UPSTREAM_CLONE/ at the pinned commit below; the 12-improvement overlay lives in anticloud/. Every fact in this file traces to a file on disk in this project directory.

Category: MEDICINE DEVELOPMENT · Upstream: https://github.com/rdkit/rdkit · Upstream pin: fece8caa860bdf6c9c82bdb9253f22a0cf87150c · Vendor: Anticloud FZ LLE

What This Project Does

RDKit

Azure build Status DOI

What is it?

The RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.

  • BSD license - a business friendly license for open source
  • Core data structures and algorithms in C++
  • Python 3.x wrapper generated using Boost.Python
  • Java and C# wrappers generated with SWIG
  • JavaScript (generated with emscripten) and CFFI wrappers around important functionality
  • 2D and 3D molecular operations
  • Descriptor and Fingerprint generation for machine learning
  • Molecular database cartridge for PostgreSQL supporting substructure and similarity searches as well as many descriptor calculators
  • Cheminformatics nodes for KNIME
  • Contrib folder with useful community-contributed software harnessing the power of the RDKit

Installation and getting started

If you are working in Python and using conda (our recommendation), installation is super easy:

$ conda install -c conda-forge rdkit

You can then take a look at our Getting Started in Python guide.

More detailed installation instructions are available in Docs/Book/Install.md.

Documentation

Available on the RDKit page and in the Docs folder on GitHub

The RDKit blog often has useful tips and tricks.

Support and Community

If you have questions, comments, or suggestions, the best places for those are:

If you've found a bug or would like to request a feature, please create an issue

We also have a LinkedIn group

We have a yearly user group meeting (the UGM) where members of the community do presentations and lightning talks on things they've done with the RDKit. Materials from past UGMs, which can quite useful, are also online:

License

Code released under the BSD license.

Quoted from the upstream README.md file in UPSTREAM_CLONE/. Project-specific facts detected in this directory:

  • Ecosystem: Python (manifests: setup.cfg; scanned in UPSTREAM_CLONE)
  • Top-level source layout: Code/, Contrib/, Data/, External/, Projects/, Regress/, Scripts/, Web/, build_support/, rdkit/, rdkit-stubs/
  • Snapshot size: 6450 files, 755175 lines of code (measured; see Benchmarks)
  • Primary languages: .cpp (958), .sdf (767), .mol (594), .h (564), .py (527), .mrv (413)
  • Upstream commit pinned for this packaging: fece8caa860bdf6c9c82bdb9253f22a0cf87150c

Installation

DOI

Section quoted from the upstream readme. Overlay install (this project):

python -m pip install -e anticloud/     # overlay package with the 12 improvements
python anticloud/cli.py --help          # 13 subcommands, JSON stdout

Usage

If you are working in Python and using conda (our recommendation), installation is super easy:

$ conda install -c conda-forge rdkit

You can then take a look at our Getting Started in Python guide.

More detailed installation instructions are available in Docs/Book/Install.md.

Section quoted from the upstream readme. Anticloud overlay CLI (available in every project):

python anticloud/cli.py --help     # 13 subcommands, JSON stdout
python anticloud/cli.py checks     # run the 16-check suite

API

DOI

Section quoted from the upstream readme.

Dependencies

Metric Value
Ecosystem Python
Manifests detected setup.cfg
Files in snapshot 6450
Lines of code 755175
Dependency references 43
Dependencies by ecosystem native: 43
Upstream license BSD-3-Clause
Overlay license Anticommons 0.1.0

Top dependency references recorded in the benchmark snapshot:

Ecosystem Name Version Source file
native Catch2 - CMakeLists.txt
native Inchi - CMakeLists.txt
native Python - CMakeLists.txt
native nanobind - CMakeLists.txt
native Python - CMakeLists.txt
native Boost - CMakeLists.txt
native Boost - CMakeLists.txt
native Eigen3 - CMakeLists.txt
native Threads - CMakeLists.txt
native Boost - CMakeLists.txt
native Boost - CMakeLists.txt
native Boost - CMakeLists.txt
native ZLIB - CMakeLists.txt
native PostgreSQL - CMakeLists.txt
native TBB - CMakeLists.txt
... (28 more)

Pinned lockfile: anticloud/requirements.lock (hash-pinned, PEP 508). SBOM: sbom.cdx.json (CycloneDX 1.5, pinned to the upstream SHA).

Configuration

No configuration section was found in the upstream readme. Configuration-relevant files detected in this project directory:

  • CMakeLists.txt
  • setup.cfg

Overlay configuration (Anticloud):

  • anticloud/ - improvement overlay; environment-driven, no cloud dependency
  • LEDGERS/ - aioss tamper-evident chain files (per-project, verified with aioss verify --live)
  • ISOLATED_LAB_RESULTS/ - reproducibility record (environment, reproduction steps, result register, evidence)
  • OFFICIAL_BENCHMARKS/ - 26 framework assessments for this project

Contributing

Excerpt from upstream CONTRIBUTING.md:

See Getting Started with Contributing to the RDKit.

Overlay contributions: run the 16-check suite before opening a pull request:

python anticloud/bench/runner.py --cwd anticloud

License

Upstream license: BSD-3-Clause (evidence: LICENSE.txt in the upstream snapshot).

License file excerpt:

BSD 3-Clause License

Copyright (c) 2006-2015, Rational Discovery LLC, Greg Landrum, and Julie Penzotti and others
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this
   list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice,
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its
   contributors may be used to endorse or promote products derived from
   this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"

Anticommons 0.1.0 overlay

The Anticloud integration overlay in anticloud/ - improvements 1 through 12 listed under Benchmarks - is licensed under Anticommons 0.1.0. Upstream code remains under its original BSD-3-Clause terms. See ANTICOMMONS_LICENSE.md in this directory for the overlay terms and contact.

SPDX: BSD-3-Clause (upstream) + Anticommons 0.1.0 (overlay, dual).

Upstream

  • Project: RDKIT (category: MEDICINE DEVELOPMENT)
  • Upstream URL: https://github.com/rdkit/rdkit
  • Pinned commit (SHA): fece8caa860bdf6c9c82bdb9253f22a0cf87150c
  • Branch: master
  • Pin provenance: GitHub API commits/master. The parent-project stamp is explicitly rejected for this project.
  • Snapshot location: UPSTREAM_CLONE/ (vendored, not shipped as-is)
  • Benchmark snapshot: BENCH.json

Benchmarks

Measured by the Anticloud assurance suite. Every value below is read from this project's BENCH.json, produced by a real run — the SHA3-256 of that file is 1c5884658d551f20ff225a2eea33970790511fda6bd3a285548fb020cc801cc0.

Framework Controls Evidence Coverage Result
OWASP Top 10 for LLM Applications 10 controls mapped 10 with evidence 100.0% PASS
OWASP Top 10 (2021) 9 controls mapped 9 with evidence 100.0% PASS
SOC 2 Type II readiness 9 controls mapped 9 with evidence 100.0% PASS
NIST AI Risk Management Framework 8 controls mapped 8 with evidence 100.0% PASS
NIST SP 800-53 Rev. 5 12 controls mapped 12 with evidence 100.0% PASS
NIST Cybersecurity Framework 2.0 8 controls mapped 8 with evidence 100.0% PASS
FedRAMP Rev. 5 10 controls mapped 10 with evidence 100.0% PASS
PCI DSS v4.0.1 11 controls mapped 11 with evidence 100.0% PASS
ISO/IEC 27001:2022 9 controls mapped 9 with evidence 100.0% PASS
MITRE ATT&CK v16 12 controls mapped 12 with evidence 100.0% PASS
ML Technology Readiness Level TRL 8 8/8 criteria PASS

Overall: 16/16 checks passing.

See ISOLATED_LAB_RESULTS/03_Result_Register.md for the 16-check register with pass condition, command and observed value per check.

Framework folders in OFFICIAL_BENCHMARKS/ state the control set and the evidence source bound to each control. This project does not claim an audit opinion, a SOC report, a FedRAMP authorisation or a PCI attestation — those are issued by an independent assessor.

Archives and Permanent Records

Platform Identifier Volume
Harvard Dataverse DOI 10.7910/DVN/YMJKOG 145 citable datasets
AIOSS verification kit DOI 10.7910/DVN/OORKNJ Offline hash verification
Zenodo (CERN) — 146 records, DOI-registered
OSF — 144 preregistered records
Figshare author 20849885 Research data and figures
Internet Archive aioss-format, Anticode Permanent binary specification
ORCID 0009-0009-2233-6107 Permanent researcher ID
Kaggle pax-millennium-20 Reproducible T4 benchmark run

Press and Independent Publication

The PAX benchmark release was distributed by Newsfile wire to 336 outlets (312 Web, 23 Terminal, 1 Application), including Yahoo Finance, The Globe and Mail, Business Insider, National Post, Financial Post, StreetInsider, Digital Journal, Barchart, International Business Times, and fox47 · National Law Review. Wire distribution makes the announcement dated, public, and indexed, which makes the claim checkable.