leonarski_f
e406eb17ea
- New docs/CPU_DATA_ANALYSIS_REFINEMENT.md (§15): the ML amplitude target and its FFT gradient, scale/robust fit/fine solvent mask, D and the variance (work/free), the embedded Monomer Library subset and topology, geometry/metal/KL-B restraints, the minimiser, the weight trials, refined maps, blobs, GPU/CPU, and a "Not yet" list; with its own References. Linked from TECHNICAL.md and CPU_DATA_ANALYSIS.md; §14 no longer says the structure is never refined. - RUGNUX_REPORT.md: a Refinement (REFINE_*) section - every REFINE_ and REFINE_SCORE_ key, the --mode refine input keys and the _blobs.json fields. - RUGNUX_MODEL_AND_REFERENCE.md: "What it does not do yet"; RUGNUX_ADVANCED.md: --model mentions the refinement, --no-refine as in the usage, a --mode refine options table; GPU_DATA_ANALYSIS.md: the refinement's CUDA engines and the missing Metal path. - ACKNOWLEDGEMENT.md: Brunger, Karplus & Petsko 1989 (gradient-balanced starting weight), Nocedal 1980 (two-loop recursion), Charbonnier et al. 1997 (pseudo-Huber), Jiang & Brunger 1994 (flat solvent mask), Kullback & Leibler 1951; all DOIs checked against Crossref. - In-source credit lines: the weight balancing (replacing a "Brunger (1992)-style" line that named the R-free paper), Nocedal 1980, Charbonnier 1997, Jiang & Brunger 1994, Emsley et al. 2010 at FindDensityBlobs, Read 1986 at the refined maps. Comments only. - docs/THIRD_PARTY_NOTICES.md regenerated from the root file with update_version.sh's own step (it lacked the CCP4 Monomer Library row). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 09375dba351bae0cc73e9a6f0f79455dc92b3a10)
1005 B
1005 B
Technical reference
The pages that describe how things work rather than how to use them: the algorithms behind the analysis, the file formats and streams, the programming interfaces, the hardware and the FPGA design. Nothing here is needed to run Rugnux or the viewer; all of it is needed to build on them.
:caption: Data analysis
:maxdepth: 1
CPU_DATA_ANALYSIS
CPU_DATA_ANALYSIS_IMAGE
CPU_DATA_ANALYSIS_INDEXING
CPU_DATA_ANALYSIS_INTEGRATION
CPU_DATA_ANALYSIS_DECISIONS
CPU_DATA_ANALYSIS_REFINEMENT
GPU_DATA_ANALYSIS
DETECTOR_GEOMETRY
RUGNUX_BENCHMARKING
EXTERNAL_TEST_DATA
EXTERNAL_TEST_DATA_STILLS
:caption: Formats and interfaces
:maxdepth: 1
HDF5
PIXEL_MASK
IMAGE_STREAM
CBOR
OPENAPI
OPENAPI_SPECS
:caption: Hardware and FPGA
:maxdepth: 1
HARDWARE
SOFTWARE
DETECTORS
FPGA
FPGA_DESIGN
FPGA_DATA_ANALYSIS
FPGA_NETWORK
FPGA_PCIE_DRIVER
FPGA_SETTINGS
FPGA_LICENSE
:caption: Development
:maxdepth: 1
TESTS
VERSIONING
SECURITY