SMSD Pro — Small Molecule Subgraph Detector
Copyright (c) 2018-2026 BioInception PVT LTD
Algorithm Copyright (c) 2009-2026 Syed Asad Rahman

This product includes software developed by Syed Asad Rahman
at BioInception PVT LTD (https://github.com/asad/SMSD).

LICENSING AND COMMERCIAL USE
============================
SMSD Pro is released under the Apache License, Version 2.0.
You are free to use, modify, and distribute this software for any
purpose, including commercial use, subject to the license terms.

  PERMITTED (no fee, no registration, no approval needed):
    * Use SMSD Pro in commercial products and services
    * Use SMSD Pro in proprietary / closed-source software
    * Bundle SMSD Pro in SaaS platforms and cloud services
    * Modify the source code for your own needs
    * Redistribute SMSD Pro (modified or unmodified)
    * Use in pharmaceutical, biotech, agrochemical pipelines
    * Use in academic research and teaching
    * Use in internal corporate tools and workflows

  REQUIRED (Apache 2.0 Section 4):
    * Include a copy of the LICENSE file in your distribution
    * Include a copy of this NOTICE file in your distribution
    * Retain all copyright and attribution notices
    * State any changes you made to the source files

  NOT PERMITTED:
    * Use the names "SMSD", "SMSD Pro", or BioInception
      trademarks to endorse your product (see TRADEMARK NOTICE)
    * Claim you wrote the original software
    * Hold contributors liable for damages

  NO WARRANTY:
    SMSD Pro is provided "AS IS", without warranty of any kind.
    See the LICENSE file for the full disclaimer.

ACADEMIC CITATION
=================
If you use SMSD Pro in academic research, please cite both papers:

  Rahman SA.
  SMSD Pro: Coverage-Driven, Tautomer-Aware Maximum Common
  Substructure Search.
  ChemRxiv, 2025.
  DOI: 10.26434/chemrxiv.15001534

  Rahman SA, Bashton M, Holliday GL, Schrader R, Thornton JM.
  Small Molecule Subgraph Detector (SMSD) toolkit.
  Journal of Cheminformatics, 1:12, 2009.
  DOI: 10.1186/1758-2946-1-12

A machine-readable citation file (CITATION.cff) is included in
the repository for automated citation tools.

COMMERCIAL ATTRIBUTION
======================
If you redistribute SMSD Pro or include it in a commercial product,
the Apache License 2.0 (Section 4d) requires you to:

  1. Include a copy of this NOTICE file in your distribution
  2. Retain all copyright and attribution notices

We also request (but do not require) the following attribution
in your product documentation, About screen, or website:

  "Powered by SMSD Pro — https://github.com/asad/SMSD
   Copyright (c) BioInception PVT LTD"

TRADEMARK NOTICE
================
"SMSD"(TM), "SMSD Pro"(TM), and the BioInception molecular graph
logo(TM) are unregistered trademarks of Syed Asad Rahman /
BioInception PVT LTD. You may not use these marks to endorse or
promote products derived from this software without prior written
permission from the copyright holder.

NOVEL ALGORITHMS
================
The following algorithms implemented in this software are original
works by Syed Asad Rahman:

  1. Tautomer-aware circular fingerprint with pKa-informed atom
     invariants (ECFP/FCFP with tautomer class integration)
  2. 11-level MCS funnel with chain/tree DP fast-paths
  3. Henderson-Hasselbalch pH-dependent tautomer relevance weighting
  4. Tier 2 solvent-dependent pKa corrections for tautomer matching
  5. VF2++ with 3-level NLF pruning and GPU-accelerated domain
     initialisation (CUDA + Apple Metal)
  6. Cache-optimal McGregor DFS with pre-indexed candidate lookup
     and uint8_t hot-path data structures (v6.11.0)
 10. CIP Rule 3 (Z > E) digraph-based stereodescriptor comparison
     for complete IUPAC 2013 Rules 1-5 implementation (v6.12.1)
 11. Multi-word greedy coloring bound for BK clique search,
     eliminating the 64-color ceiling on product graphs (v6.12.1)
  7. 8-phase 2D molecular layout pipeline with simulated annealing
     crossing reduction and 40+ scaffold templates (v6.11.0)
  8. Distance geometry 3D embedding with power iteration
     eigendecomposition and force-field refinement (v6.11.0)
  9. Publication-quality SVG depiction engine conforming to
     ACS 1996 standard with Jmol/CPK colors, asymmetric double
     bonds, wedge/dash stereo, and bond-to-label clipping (v6.11.0)

THIRD-PARTY NOTICES
===================
This software uses the Chemistry Development Kit (CDK) licensed
under LGPL 2.1. CDK is Copyright (c) The CDK Project.
See https://cdk.github.io/ for details.

AVAILABLE PLATFORMS
===================
  Java:   com.bioinceptionlabs:smsd on Maven Central
  Python: pip install smsd (PyPI)
  C++:    Header-only library (cpp/include/smsd/)
  Docker: ghcr.io/asad/smsd