DNA Design Suite
Copyright (c) the DNA Design Suite contributors.

Licensed under the Apache License, Version 2.0. See LICENSE.

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Third-party attribution
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DNA Design Suite does not bundle, vendor, or redistribute any of the software named
below. Each is an optional backend that the user installs themselves, detected
at runtime behind the StructureEngine seam. The credits here are given because
the licences require credit from anyone who uses the software, and because the
work deserves it.

Recorded per AMD-013 (planning/00-scope/03-architecture-amendments.md), which
verified each licence against its primary source rather than its reputation.

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ViennaRNA Package
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Used as an optional structure-prediction backend for windowed local
accessibility, via the RNAplfold sliding-window partition function.

Credit is given, as its licence requires, to the authors of the ViennaRNA
Package and to the Institute for Theoretical Chemistry of the University of
Vienna.

The ViennaRNA Package's licence (COPYING / license.txt in its source
distribution) states:

    The programs, library and source code of the Vienna RNA Package are free
    software. They are distributed in the hope that they will be useful
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

    Permission is granted for research, educational, and commercial use
    and modification so long as 1) the package and any derived works are not
    redistributed for any fee, other than media costs, 2) proper credit is
    given to the authors and the Institute for Theoretical Chemistry of the
    University of Vienna.

    If you want to include this software in a commercial product, please contact
    the authors.

    Note that the file ./src/ViennaRNA/plotting/naview.c has its own copyright
    attached.

Two consequences DNA Design Suite holds itself to:

  * Condition 1 is satisfied by construction. DNA Design Suite is distributed free of
    charge and does not redistribute ViennaRNA at all - the user installs it -
    so no fee attaches to any copy of the package or to a derived work. If
    DNA Design Suite is ever distributed for a fee, this arrangement must be
    re-examined before that release ships.

  * The naview.c carve-out does not apply while DNA Design Suite only depends on
    ViennaRNA. It would apply immediately to anyone proposing to vendor
    ViennaRNA source into this repository, and such a proposal needs its own
    licence check before proceeding.

ViennaRNA's bundled thermodynamic parameter files (misc/*.par) carry no licence
header of their own. DNA Design Suite does not redistribute them either: ViennaRNA
loads its own tables. Any proposal to bundle or redistribute those files
directly reopens a question this project has not resolved and must not assume.

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LinearFold
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Supported as an optional structure-prediction backend on the same
user-installed, never-vendored terms.

Its licence requires the following citation, which is reproduced as its LICENSE
file gives it:

    Liang Huang, He Zhang, Dezhong Deng, Kai Zhao, Kaibo Liu, David Hendrix,
    and David Mathews (2019). LinearFold: Linear-Time Approximate RNA Folding
    by 5'-to-3' Dynamic Programming and Beam Search. Bioinformatics, Vol. 35,
    July 2019, Special Issue of ISMB 2019 Proceedings.

The LinearFold LICENSE file states:

    Permission is granted for research, educational, and commercial use
    and modification so long as 1) the package and any derived works are not
    redistributed for any fee, other than media costs, 2) proper credit is
    given to the authors.

A note on a correction, kept because the mistake is an easy one to repeat:
LinearFold's *paper* is CC BY-NC 4.0, and this project once recorded that as the
code's licence. The LICENSE file above governs the code, and it permits
commercial use. Code licence and paper licence are separate questions.

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LinearDesign - deliberately not used
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LinearDesign is not a dependency, is not called, and its method is not
implemented. This is a patent question rather than a licensing one: US
2022/0269951 A1 and EP 4 030 438 A1 (applicant Baidu USA LLC) claim, as a
required element of every independent claim, intersecting a context-free grammar
with a deterministic finite automaton over synonymous codon choices and
searching the result.

DNA Design Suite contains no context-free grammar. That exclusion is enforced by a
test rather than by intention alone - see
test_amd_013_no_grammar_intersection_reaches_the_search_layer.

See AMD-013 for the full analysis, including what it does not establish: grant
status was not confirmed, and claim scope outside the US and EP was not
examined. Release of structure-kernel functionality is gated on sign-off from a
faculty advisor, PI, or institutional technology-transfer contact.
