BioTSR
Copyright 2026 TSR Research Group

BioTSR is the unified software implementation of the Triangular Spatial
Relationship (TSR) methodology. It is licensed under the Apache License,
Version 2.0 (see LICENSE).

BioTSR includes, or is derived from, the third-party material listed below.
That material is not relicensed: each item remains under its own terms, and
its required notices are reproduced here. Provenance is recorded in
docs/LICENSING.md in the source repository
(https://github.com/TSRMethod/BioTSR/blob/main/docs/LICENSING.md). File paths
below are source-tree paths; in an installed package drop the leading "src/".

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1. TSR-Package -- MIT License

   Used for: the theta and distance bin tables (src/biotsr/binning/theta.py,
   src/biotsr/binning/distance.py) and the amino-acid label and group tables
   (src/biotsr/labels/schemes.py), whose values come from TSR-Package; the
   secondary-structure category rules (src/biotsr/sse/), reimplemented from
   TSR-Package's SSE_TSR.py; and, in the source distribution, one column of
   TSR-Package output used as test reference data
   (tests/data/reference/historical/).

MIT License

Copyright (c) 2024 Poorya Khajouie

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

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2. CarbohydratesTSR -- MIT License

   Used for: src/biotsr/labels/resources/element_labels_v1.csv, the element
   codes of the CarbohydratesTSR atom lexicon (each chemical element with the
   code the lexicon gives it; chlorine's from its CL rows).

MIT License

Copyright (c) 2026 Krishna Rauniyar

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

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3. SciPy -- BSD 3-Clause License

   Used for: src/biotsr/analysis/clustering.py follows the algorithms of
   SciPy's nn_chain, maxclust and dendrogram implementation; how far its
   results agree with particular SciPy releases is stated in
   docs/methods/ANALYSIS.md. No SciPy code is imported or bundled.

Copyright (c) 2001-2002 Enthought, Inc. 2003, SciPy Developers.

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" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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4. Historical TSR repositories by Krishna Rauniyar (attribution)

   The atom-count tables (src/biotsr/selection/completeness.py) and residue
   sets (src/biotsr/cross/sides.py) are transcribed from TSR_AMINOACID_PACKAGE,
   TSR_NUCLEOTIDE_PACKAGE, Nucleotide-Protein and CarbohydratesTSR. The first
   three repositories carry no licence text of their own (docs/LICENSING.md).

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5. Historical lineage (acknowledgement)

   TSR-Package shares code with hsp70_actin (Feng Chen), whose key-generation
   library credits Venkata Sarika Kondra; BioTSR's bin and label tables reach
   it through TSR-Package. BioTSR contains no hsp70_actin code. The lineage was
   considered by the ownership and provenance review
   (docs/LICENSING.md).
