leonarski_f
bcb71136ab
Metal sites were held only by the 1.9 A metal contact of the repulsions; REFMAC restrains the metal LINKs of the coordinate file (its documentation), which was the one geometry term the 0-cycle comparison did not share (one 2.8 A set: bond rmsd 0.018 against REFMAC's 0.042). - monomers/metals.cif: the Monomer Library's own statistics of metal sites (metals.json, LGPL data as the rest of monomers/), cut by update_monomers.py to the metal ions of its compound list and O, N, S donors: mean distance, spread and number of sites per metal, donor element and coordination number. - AddMetalLinks (before prepare_topology): every LINK / struct_conn record between a metal ion and an O, N or S that no link of the dictionary describes (its ZN-CYS, ZN-HIS, FE-CYS, FE-HIS are taken as they are) gets a link of one bond at EmbeddedMetalDistance for the two elements and the ion's coordination - the number of its donor records, symmetry mates included - from the rows resting on at least 20 sites (the coordination's own row, else the neighbours interpolated), sigma their spread (>= 0.02 A); a His or Cys donor loses the proton the bond replaces (DEL-HD1 / DEL-HE2 / CYSmod1, as the library's links do). Records only, no distance search; records to a symmetry mate count for the coordination but are not restrained (bonds to symmetry mates are not, anywhere). - The metal bonds are a restraint set of their own (RefinementTopology::metal_bonds), evaluated with the geometry and reported apart (GeometryStatistics::rmsd_metal, REFINE_RMSD_METAL_BONDS, REFINE_SCORE_RMSD_METAL_BONDS / _BONDS_ALL): their sigma is the spread of real sites, so they sit further from ideal than covalent bonds, and the weight ladder's 0.02 A bound stays a bound on the covalent ones. refine_parity.py compares REFMAC's bond rmsd (links included) with the combined one, and takes --gpu. Score-only geometry against REFMAC 5.8 0-cycle, all bonds (count): 2.8 A Zn/Fe set 0.0402 (4934) vs 0.042 (4935), was 0.0178; a Zn-Cys set 0.0186 (7102) vs 0.019 (7102); a Ca set 0.0297 vs 0.026 (REFMAC also refines the sugars and uses one Ca-O distance); a Mg set 0.0114 vs 0.017 (REFMAC restrains 8 symmetry links and puts Mg-O at 1.99 A, the library's statistics at 2.07). R of the scored model unchanged (+0.0001 on the first from the removed His/Cys protons). Refined R-free with the links vs without: +0.0016, -0.0002, +0.0005, +0.0004. Test: RefinementRestraints_metal_links (Zn-Cys4 by the dictionary's link, Mg(H2O)6 by the new ones, both back at their distances). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 0fcffc5c71e03e184cff18f07524473462a57b68)
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Third-party software notices
Jungfraujoch is licensed under GPL-3.0 (see LICENSE); the FPGA design is
licensed under CERN-OHL-S-2.0 (see fpga/LICENSE). It builds on a number of
third-party components, acknowledged below as required by their licenses.
This file is the human-readable manifest. The verbatim license texts live in the
licenses/ directory (regenerate with bash licenses/COLLECT.sh). The frontend's
bundled JavaScript dependencies are listed separately in
frontend/dist/THIRD_PARTY_LICENSES.txt, generated at build time (npm run licenses).
All licenses below are GPL-3.0-compatible, with one exception: the NVIDIA CUDA Toolkit is used under its own EULA (see the notes at the end of this file).
Fetched at build time and statically linked into the C++ binaries
These are downloaded by CMake (FetchContent / ExternalProject) during the first configure and
linked into the Jungfraujoch executables.
| Component | Version | Copyright | License (SPDX) | License text |
|---|---|---|---|---|
| spdlog | 1.17.0 | Gabi Melman | MIT | spdlog.txt |
| Zstandard | 1.5.7 | Meta Platforms, Inc. | BSD-3-Clause | zstd.txt |
| HDF5 | 2.2.0 | The HDF Group; UIUC | BSD-3-Clause-style + Apache-2.0 | hdf5.txt |
| slsDetectorPackage | 8.0.2 / 9.2.0 | PSI | LGPL-3.0-or-later | LGPL, GPL |
| cpp-httplib | 0.56.0 | Yuji Hirose | MIT | cpp-httplib.txt |
| libzmq (ZeroMQ) | 4.3.5 | iMatix and contributors | MPL-2.0 | libzmq.txt |
| libtiff | 4.7.2 | Sam Leffler; SGI | libtiff (BSD-like) | libtiff.txt |
| FFTW | 3.3.10 | Matteo Frigo; MIT | GPL-2.0-or-later | fftw.txt |
| Ceres Solver | (pinned) | Google Inc. and contributors | BSD-3-Clause | ceres-solver.txt |
| Abseil | 20250127 (required by Ceres) | Google Inc. | Apache-2.0 | abseil.txt |
| libjpeg-turbo | 3.2.0 | D. R. Commander and others; IJG | IJG + BSD-3-Clause + Zlib | libjpeg-turbo.txt |
| Mbed TLS (with TF-PSA-Crypto) | 4.2.0 | The Mbed TLS Contributors | Apache-2.0 OR GPL-2.0-or-later (used under Apache-2.0) | mbedtls.txt, tf-psa-crypto.txt |
| Catch2 | 3.16.0 | Catch2 Authors | BSL-1.0 | catch2.txt |
| zlib-ng | 2.3.3 | Jean-loup Gailly and Mark Adler; the zlib-ng contributors | Zlib | zlib.txt |
| Eigen | 3.4.1 | Benoit Jacob, Gael Guennebaud and contributors | MPL-2.0 (+ BSD parts) | eigen.txt, README |
Mbed TLS is fetched and statically linked only for viewer builds (JFJOCH_VIEWER_BUILD /
JFJOCH_VIEWER_ONLY), where it is the TLS backend of jfjoch_viewer's cpp-httplib client; the
broker and writer never link it.
Catch2 is used only to build the test binary (jfjoch_test) and is not part of any shipped
artifact; it is listed here for completeness.
zlib is supplied by zlib-ng built in its zlib-compatible mode (same zlib.h, same API and symbol
names), so it is the zlib that HDF5, libtiff, cpp-httplib and GEMMI all link. It is
built during the configure rather than added as a subproject; the licence is the zlib licence
either way. Eigen is header-only: only its headers reach the binaries, and no Eigen CMake runs.
Vendored directly in the repository
These live in the source tree (see the path) rather than being fetched; traccc and the Ceres-derived minimiser are the exceptions - code adapted into first-party files rather than a vendored directory, see the notes at the end of this file.
| Component | Path | Copyright | License (SPDX) | License text |
|---|---|---|---|---|
| nlohmann/json | include/nlohmann/ |
Niels Lohmann | MIT | nlohmann-json.txt |
| Macaron Base64 | include/base64/ |
tomykaira | MIT | base64-macaron.txt |
| TinyCBOR | frame_serialize/tinycbor/ |
Intel Corporation | MIT | tinycbor.txt |
| Bitshuffle | compression/bitshuffle/ |
Kiyoshi Masui | MIT | bitshuffle.txt |
| Bitshuffle (h-perf) | compression/bitshuffle_hperf/ |
Kal Conley | Apache-2.0 | bitshuffle-hperf.txt |
| LZ4 | compression/lz4/ |
Yann Collet | BSD-2-Clause | lz4.txt |
| HLS arbitrary-precision types | fpga/include/ |
Xilinx, Inc. | Apache-2.0 | xilinx-hls-headers.txt |
| fast-feedback-indexer (commit a94fd4f) | image_analysis/indexing/fast-feedback-indexer/ |
PSI | BSD-3-Clause | fast-feedback-indexer.txt |
| GEMMI | gemmi_gph/ |
Global Phasing Ltd. | MPL-2.0 | gemmi.txt |
| CCP4 Monomer Library (subset: restraint dictionary data) | image_analysis/structure_refinement/monomers/ |
CCP4 / the Monomer Library authors (Vagin et al.) | LGPL-3.0-only | ccp4-monomer-library.txt |
| PEGTL | gemmi_gph/gemmi/third_party/tao/ |
Dr. Colin Hirsch and Daniel Frey | MIT | pegtl.txt |
| sajson | gemmi_gph/gemmi/third_party/sajson.h |
Chad Austin | MIT | sajson.txt |
| fast_float | gemmi_gph/gemmi/third_party/fast_float.h |
The fast_float authors (Daniel Lemire et al.) | Apache-2.0 OR MIT OR BSL-1.0 | fast-float.txt |
| half | gemmi_gph/gemmi/third_party/half.hpp |
Christian Rau | MIT | half.txt |
| pocketfft | gemmi_gph/gemmi/third_party/pocketfft_hdronly.h |
Max-Planck-Society; Peter Bell; MIT (FFTW-derived parts) | BSD-3-Clause | pocketfft.txt |
| tinydir | gemmi_gph/gemmi/third_party/tinydir.h |
Cong Xu, Lautis Sun, Baudouin Feildel, Andargor | BSD-2-Clause | tinydir.txt |
| traccc (ACTS) | image_analysis/spot_finding/StrongPixelSet.cpp, SpotExtractorGPU.cu |
CERN, for the benefit of the ACTS project | MPL-2.0 | traccc.txt |
| fast-feedback-indexer (adapted) | image_analysis/indexing/FFBIDXIndexerCPU.cpp |
PSI | BSD-3-Clause | fast-feedback-indexer.txt |
| Ceres Solver (adapted) | image_analysis/geom_refinement/LMSolver.h, LMSolver.cpp |
Google Inc. | BSD-3-Clause | ceres-solver.txt |
| xbflash.qspi | tools/xbflash.qspi/ |
Xilinx / AMD | Apache-2.0 | xbflash-qspi.txt |
| wingetopt | tools/wingetopt/ |
Todd C. Miller; The NetBSD Foundation | ISC AND BSD-2-Clause | wingetopt.txt |
Data files in the repository
Not code and not linked into any binary: input files of the battery's timing benchmark
(tools/battery/timing.json), kept verbatim as downloaded.
| Component | Path | Copyright | License (SPDX) | License text |
|---|---|---|---|---|
| AlphaFold Protein Structure Database predictions AF-P68082-F1, AF-P62894-F1, AF-P17090-F1, AF-P32322-F1 and AF-Q65MG6-F1 (v6), with their predicted aligned error | tools/battery/models/AF-* |
DeepMind Technologies Limited; EMBL-EBI | CC-BY-4.0 | alphafold-db.txt |
| wwPDB entries 4DC8, 4NWV, 9GJX, 9S02 and 9ZLO, deposited coordinates (mmCIF as the RCSB PDB serves them) | tools/battery/models/pdb/ |
the depositors; the wwPDB | CC0-1.0 | wwPDB usage policy |
The deposited entries are the reference models the benchmark's placements are checked against, and 4NWV's is also moved by a fixed transform at run time to make one start model.
Runtime libraries and SDKs (shipped in binaries, not in the source tree)
| Component | Used by | License | Notice |
|---|---|---|---|
| Qt 6 | jfjoch_viewer |
LGPL-3.0 | notice, LGPL-3.0 |
| NVIDIA CUDA Toolkit (cudart, cuFFT) | CUDA builds | NVIDIA CUDA EULA | notice, EULA |
Frontend (npm) dependencies
The React/TypeScript frontend (frontend/) bundles a large transitive tree of npm packages,
overwhelmingly MIT/ISC/BSD/Apache-2.0 licensed. Their full notices are generated automatically:
cd frontend && npm run licenses # writes dist/THIRD_PARTY_LICENSES.txt
The generated file is produced as part of the frontend build target and installed alongside the
served frontend, so the shipped web UI carries its own attribution.
Notes on weak-copyleft and attribution-sensitive components
- MPL-2.0 (Eigen, GEMMI, libzmq, traccc): file-level copyleft. GEMMI is vendored in
gemmi_gph/in trimmed form; libzmq and Eigen are fetched at build time (Eigen is header-only). The corresponding source is available from each project upstream. - GEMMI's own bundled third-party headers — PEGTL, sajson, fast_float, half, pocketfft and
tinydir, all under
gemmi_gph/gemmi/third_party/— are listed separately above rather than being absorbed into GEMMI's row: they are other authors' code under other licences (MIT, BSD and Apache/MIT/BSL), and GEMMI's MPL-2.0 does not speak for them. Their terms are carried in the headers themselves rather than inLICENSEfiles, so thelicenses/*.txtcopies are kept by hand; only PEGTL ships aLICENSE, whichCOLLECT.shcopies. - traccc is the one entry that is not a vendored directory. Its sparse connected-component
labelling enters two otherwise first-party files:
StrongPixelSet.cppadapts the SparseCCL source, andSpotExtractorGPU.cufollows the design of its GPU counterpart. MPL-2.0 is file-level, so both files name the origin at the top and are covered bylicenses/traccc.txt. See ACKNOWLEDGEMENT.md for the citation. - Ceres Solver is also fetched and linked (table above); separately,
LMSolver.h/.cppre-implement its trust-region Levenberg-Marquardt minimiser, projected line search, polynomial step choice and sphere manifold for the crystal refinement, following its source. Both files name the origin at the top and are covered bylicenses/ceres-solver.txt. - fast-feedback-indexer is also vendored and linked in CUDA builds (table above); separately,
FFBIDXIndexerCPU.cppports its CUDA kernels to the CPU. The file names the origin at the top and is covered bylicenses/fast-feedback-indexer.txt. - FFTW is GPL-2.0-or-later — compatible with, and absorbed by, this project's GPL-3.0 license.
- Apache-2.0 components: where upstream ships a
NOTICEfile, it is reproduced in the correspondinglicenses/text. - CCP4 Monomer Library (LGPL-3.0) is data, not code: the restraint dictionaries of the compounds
rugnux's refinement restrains, copied unmodified per compound into
image_analysis/structure_refinement/monomers/(links_and_mods.cifandener_lib.cifcut down to the entries those compounds use, and the library's metal-site distances ofmetals.jsonfor its ions asmetals.cif), with the library's ownCOPYING. The build embeds them in the binary as text, andmonomers/update_monomers.pyregenerates the subset from the upstream library, so the copy can be replaced by a user with a version of their own. - Qt (LGPL-3.0) and NVIDIA CUDA (EULA) carry redistribution conditions beyond a copyright
notice; see their dedicated notice files. The verbatim LGPL-3.0 and CUDA EULA texts are bundled
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licenses/Qt6-LGPL-3.0.txt,licenses/NVIDIA-CUDA-EULA.txt); the CUDA EULA is the one shipped with CUDA Toolkit 12.8 — replace it if you build against a different toolkit version.