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-# StructureCloud/MacrocycleDB -- licence and provenance
-
-This repository re-hosts and re-derives data from **Macrocycle-DB** (School of Pharmacy, Jinan University) and the
-**wwPDB**. Read this file before using or redistributing anything here.
-
-## What is here, and whose it is
-
-| content | origin | licence |
-|---|---|---|
-| `preprocessed/pdb.pt`, `preprocessed/receptor.pt` -- atom coordinates, atom/residue identifiers, B-factors, occupancies, CCD bond graphs and charges, BIRD definitions, PDB sequences | wwPDB (PDB entries, Chemical Component Dictionary, BIRD), fetched 2026-09-30/10-01 | **CC0 1.0** (wwPDB usage policy) |
-| `raw/pdb_entries.tar`, `raw/wwpdb/*` | wwPDB, byte-identical | **CC0 1.0** |
-| the catalogue annotations attached to each sample (`mcd_id(s)`, `m_type`, `max_phase`, `smiles_mcd`, `inchikey_mcd`, the 48 `descriptors`, `largest_ring_size_mcd`, `n_bioactivities`, `listed_by_macrodb`) | Macrocycle-DB bulk downloads | **no licence stated** -- see below |
-| `preprocessed/ligprep.pt` (coordinates, bond blocks, LigPrep/Epik tags) | Macrocycle-DB `SDF.zip`, generated by the database authors with Schrodinger LigPrep/Epik (Suite 2023-4) | **no licence stated** |
-| `preprocessed/compounds.csv`, `raw/macrocycle-db/*` (All.csv, PDB.csv, Biological Activities.csv, Linker.csv, Target-*.csv, per-class CSVs, SDF.zip) | Macrocycle-DB bulk downloads, byte-identical (with HTTP headers) | **no licence stated** |
-| `sequence_derived`, match tiers, `ring_size_rdkit`, `is_head_to_tail`, drop/merge counters | computed by this build (`scripts/macrocycledb/` in github.com/TyJPerez/StructureCloud) | derived |
-| `raw/macrocycle_benchmark/{benchmark_index.csv, LICENSE, CITATION.cff, COMMIT}` | dptech-corp/MacroCycle-Benchmark (cross-check only; nothing imported into the dataset) | curation **CC BY 4.0**, PDB-derived data CC0 |
-| `raw/ringer/{amino_acids.csv, LICENSE, COMMIT}` | Genentech/ringer (residue table used by `sequence_derived`) | **MIT** |
-
-## The Macrocycle-DB licence situation -- recorded, not resolved
-
-Facts verified 2026-09-30/10-01 and quoted verbatim:
-
-- The database site (https://macro-db.dpbio.tech/, alias https://macro-db.cn/) carries **no data licence and no
-  terms of use**. Its footer reads: *"Copyright © 2024 School of Pharmacy, Jinan University. All Rights Reserved."*
-- Its `robots.txt` carries `Content-Signal: ai-train=no, search=yes, ai-input=yes` (and `Allow: /` for all agents).
-- The paper's Data Availability names only the URLs: *"Macrocycle-DB is accessible at https://macro-db.dpbio.tech/
-  and https://macro-db.cn/."* Its abstract calls the database *"freely accessible"*. The **article** is published
-  under CC BY-NC 4.0 (Oxford University Press); that licence covers the article text, not the data.
-- The paper's Methods state the content was aggregated (reference brackets removed): *"The data in Macrocycle-DB
-  were compiled from scientific literature, patents, and several established public databases, including ChEMBL,
-  DrugBank, ClinicalTrials.gov, the Protein Data Bank (PDB), PubChem, the Therapeutic Target Database (TTD), and
-  UniProt."* and *"When such data were not available in these databases, DrugFlow's literature extraction function
-  was employed to capture target and activity information."* Upstream licences as published by those resources:
-  ChEMBL **CC BY-SA 3.0**; DrugBank open data **CC BY-NC 4.0**; UniProt **CC BY 4.0**; PDB **CC0**; PubChem and
-  ClinicalTrials.gov are NLM/NCBI services (NLM places no restrictions on its own data; individual submitters'
-  records may carry their own terms); TTD and DrugFlow: not verified here.
-
-**Decision (repository owner, 2026-09-30):** publish all tiers, accepting the licence risk stated above. No
-dataset-card licence metadata is set. If you redistribute or build on the Macrocycle-DB-derived parts, you are
-responsible for your own assessment; attribute Jinan University and cite the paper below, and respect the
-upstream licences (notably ChEMBL's share-alike and DrugBank's non-commercial terms, which may attach to
-bioactivity and approval annotations). A permission request to the corresponding author is recommended.
-
-## Snapshot identity
-
-- Macrocycle-DB: no version exists; the HTTP `last-modified` stamps (Thu 03 Sep 2026 02:22:59 -- 02:23:10 GMT) and
-  sha256 of every file are in `raw/macrocycle-db/PROVENANCE.md`; `SDF.zip` is 377,463,927 B.
-- wwPDB: see `raw/wwpdb/SNAPSHOT.md` (CCD/BIRD last-modified Sat 26 Sep 2026; 2,846 entries fetched
-  2026-10-01T00:04:44Z .. 00:16:36Z; 260,724 entries in holdings).
-
-## Cite
-
-- Jiang M, Liu T, Hussain M, Luo Y, Zheng R, Hou T, Lu X, Zhou Y. *Macrocycle-DB: a comprehensive database for
-  macrocycle-based drug discovery.* Nucleic Acids Research 54(D1):D1469-D1476 (2026). doi:10.1093/nar/gkaf1107
-- wwPDB consortium. *Protein Data Bank: the single global archive for 3D macromolecular structure data.* Nucleic
-  Acids Research 47(D1):D520-D528 (2019). doi:10.1093/nar/gky949
-- Grambow CA, Weir H, Diamant NL, Scalia G, Biancalani T, Chuang KV. *Accurate and Efficient Structural Ensemble
-  Generation of Macrocyclic Peptides using Internal Coordinate Diffusion.* arXiv:2305.19800 (2023) -- the RINGER
-  residue table used for `sequence_derived`.