biotsr 1.0.0__tar.gz

biotsr-1.0.0/CHANGELOG.md

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+# Changelog
+
+All notable user-visible changes to BioTSR. Versions follow
+[PEP 440](https://peps.python.org/pep-0440/); the release process is in
+[docs/RELEASING.md](https://github.com/TSRMethod/BioTSR/blob/main/docs/RELEASING.md).
+
+## [1.0.0]
+
+The first release of BioTSR, the unified software implementation of the
+Triangular Spatial Relationship (TSR) methodology: one Python package, one
+command line and one shared scientific core — the TSR Engine — in place of a
+family of independent historical TSR programs. Every method runs under one
+standard profile, the accepted TSR science as set by the TSR Research Group,
+and writes one self-describing output format.
+
+### Platforms
+
+- **CPython 3.9, 3.10, 3.11, 3.12 and 3.13, on Linux and macOS.** The full
+  default test suite runs on every one of them on Linux (x86-64) and on macOS
+  (arm64); the slow reference cases over large structures run on macOS arm64.
+  Keys, frequencies and fingerprints are identical on both systems.
+- **Windows is not supported**: it is neither tested nor validated.
+- Input is PDB format; mmCIF is not read.
+
+### Installation
+
+- **From GitHub:** `pip install "biotsr @ git+https://github.com/TSRMethod/BioTSR@v1.0.0"`,
+  or the wheel and source distribution attached to the
+  [1.0.0 release](https://github.com/TSRMethod/BioTSR/releases/tag/v1.0.0); from a
+  clone, `pip install .`.
+- **From PyPI:** `pip install biotsr`, available when
+  <https://pypi.org/project/biotsr/> lists version 1.0.0.
+- One runtime dependency, joblib, runs batch rows in parallel; the calculation
+  itself uses the standard library only. The optional `plot` extra
+  (matplotlib) draws the clustered heat map.
+
+### What 1.0.0 provides
+
+- **Twenty methods in three families:** protein Cα; atomic — amino-acid,
+  ligand, carbohydrate, nucleotide/DNA/RNA, and residue or atom selections;
+  and five cross (two-sided) methods — drug–protein, carbohydrate–protein,
+  nucleotide–protein, protein–protein all-atom and protein–protein Cα. The
+  [capability matrix](https://github.com/TSRMethod/BioTSR/blob/main/docs/CAPABILITY_MATRIX.md)
+  says what each supports.
+- **One TSR Engine** — geometry, canonical vertex ordering, angle and distance
+  binning, labelling and integer key encoding shared by every method — with
+  composable modifiers: amino-acid grouping and SSE-TSR (18 secondary-structure
+  categories) on the Cα methods, mirror signing and size filtering.
+- **Labels.** Cα points are labelled by residue — the 20 regular amino acids
+  and eleven modified residues — at radix 30, collision-free; atoms are
+  labelled by their PDB element field at radix 112, from one packaged,
+  validated element table.
+- **Strict, recorded input rules.** Atom names and elements are read from their
+  full PDB fields, nothing is guessed, and a selection with an unknown residue
+  (`UNK`), an atom without an element, an atom written twice or an unreadable
+  residue number is refused with the records named.
+- **Two identities on every result** — a `KeySpace` fingerprint (what the keys
+  mean) and a `SamplingProfile` fingerprint (how the triangles were drawn).
+  Results whose keys are defined differently are refused, never combined;
+  results processed under other settings, and partial results, are compared
+  only when acknowledged (`--allow-mixed-processing`, `--allow-partial`).
+- **Native output** — `PREFIX.keys`, `PREFIX.triplets`, `PREFIX.meta.json` and
+  a completion record `PREFIX.run.json` written last — read back by
+  `biotsr.load_result` with both fingerprints restored.
+- **Datasets.** `biotsr batch` over manifests and wide dataset sheets, with
+  `--dry-run`, verified resuming (`--if-exists skip`), parallel rows
+  (`--jobs`), a per-request `batch_summary.csv`, and opt-in, verified download
+  of PDB entries (`biotsr fetch`, `--download-missing`).
+- **Analysis** over results of any method family: feature matrices, common
+  keys, five similarity measures, the average-linkage tree, dendrogram and
+  ordered heat map, and flat clusters by an explicit rule.
+- **Licensed under the Apache License 2.0.** Third-party material keeps its
+  own terms; its notices are in
+  [`NOTICE`](https://github.com/TSRMethod/BioTSR/blob/main/NOTICE).
+
+### Known limitations
+
+The [known limitations](https://github.com/TSRMethod/BioTSR/blob/main/docs/KNOWN_LIMITATIONS.md)
+state each one precisely. In short: only the standard science is computed —
+the historical programs' outputs are not reproduced; only model 1 of a PDB
+file is read, with alternate locations blank or `A`; a `TER` record without a
+chain identifier ends no chain; atomic methods read three modified amino acids
+written as `HETATM` (TPO, SEP, PTR) and name the others; triplet files are
+compared byte for byte only on macOS arm64, where their reference geometry was
+produced; and similarity and clustering are available from Python, not from
+the command line.
+
+### Results from the pre-release builds
+
+1.0.0 reads and compares the results of the last pre-release build as its own.
+It refuses — it does not silently combine — older results whose keys mean
+something else: Cα results from builds that labelled residues at radix 20, and
+atomic results from builds that labelled atoms by name, must be computed
+again, and outputs in the earlier per-sample directory layout are not read.
+What changed from one pre-release build to the next is recorded in
+[docs/PRE_RELEASE_CHANGES.md](https://github.com/TSRMethod/BioTSR/blob/main/docs/PRE_RELEASE_CHANGES.md).
+
+Besides its version and release metadata, 1.0.0 corrects one thing in the last
+pre-release build: when a download run (`biotsr fetch`, `--download-missing`)
+is interrupted, an identifier that was still queued is reported `not_started`,
+as documented. The worker that the cancellation freed could take it up first,
+and it was then reported `interrupted` although nothing was requested for it.
+
+[1.0.0]: https://github.com/TSRMethod/BioTSR/releases/tag/v1.0.0

biotsr-1.0.0/CITATION.cff

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+# Citation metadata for BioTSR (Citation File Format 1.2.0).
+#
+# The authors, in the order the maintainers set. No DOI is recorded because none
+# has been registered; when the release is archived (docs/RELEASING.md,
+# section 10), its DOI is added here and to the README.
+cff-version: 1.2.0
+message: "If you use BioTSR in your research, please cite it using the metadata from this file."
+type: software
+title: "BioTSR"
+abstract: >-
+  BioTSR is the unified software implementation of the Triangular Spatial
+  Relationship (TSR) methodology. It computes TSR keys -- integers encoding the
+  shape and vertex labels of triangles drawn over a 3D structure -- for protein
+  C-alpha, atomic, ligand, carbohydrate, nucleotide and cross (two-sided) method
+  families on one shared scientific core, each under its standard profile.
+authors:
+  - given-names: "Poorya"
+    family-names: "Khajouie"
+  - given-names: "Krishna"
+    family-names: "Rauniyar"
+  - given-names: "Vijay V."
+    family-names: "Raghavan"
+  - given-names: "Wu"
+    family-names: "Xu"
+version: "1.0.0"
+license: Apache-2.0
+repository-code: "https://github.com/TSRMethod/BioTSR"
+url: "https://tsrmethod.github.io/"
+keywords:
+  - "Triangular Spatial Relationship"
+  - "TSR"
+  - "protein structure"
+  - "structural bioinformatics"
+  - "PDB"

biotsr-1.0.0/LICENSE

@@ -0,0 +1,202 @@
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biotsr-1.0.0/MANIFEST.in

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+# What the source distribution carries, stated explicitly rather than left to
+# setuptools' defaults.  The sdist is the package plus what is needed to build,
+# test and cite it -- including tests/data/structures/, the small set of
+# unmodified PDB entries the computational tests run on.  The frozen reference
+# outputs, the historical programs and the documentation stay in the repository
+# (docs/RELEASING.md).
+include README.md CHANGELOG.md CITATION.cff pyproject.toml
+# LICENSE and NOTICE are added by setuptools itself (its default license-file
+# patterns) to both the sdist and the wheel.
+graft src/biotsr
+graft tests
+prune validation
+prune legacy
+prune docs
+prune .github
+global-exclude __pycache__ *.py[cod] .DS_Store ._*
+# Spreadsheets and private dataset tables never ship, even if one is left in the
+# working tree (release_artifacts.py also refuses any member that is not a
+# tracked file).
+global-exclude *.xls *.xlsx *.xlsm *.ods *.numbers sample_details*.csv column_means*

biotsr-1.0.0/NOTICE

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+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/".
+
+------------------------------------------------------------------------------
+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.
+
+------------------------------------------------------------------------------
+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.
+
+------------------------------------------------------------------------------
+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,
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+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.
+
+------------------------------------------------------------------------------
+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).
+
+------------------------------------------------------------------------------
+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).