leonarski_f
a218c0bec8
rugnux --mode refine --model model.cif -o out data.mtz The input is an MTZ or a structure-factor mmCIF, gzipped or not, by content (writer/RugnuxReflectionFile: parsing in the file layer, the library reads no file). Columns are found, not named: F/SIGF-like amplitudes (calculated amplitudes and map coefficients passed over), else intensities made into amplitudes by French-Wilson, else the mean of the anomalous pairs; the free set from a FreeR_flag-like column (0 the test set, or the minority value), else rugnux's own 5 % set. RunRefineOnly (rugnux/RugnuxRefine) runs RefineModel; the outputs are --refine's (_refined_model.cif, _refined_maps.mtz, _blobs.json) and a report with the REFINE_ keys, the input's REFINE_FRENCH_WILSON / REFINE_FREE_FLAGS, and every term of the start score under REFINE_SCORE_ (also in --refine's section). --refine-score-only scores the model as given; --refine-d-min cuts the resolution. tools/battery/refine_parity.py runs REFMAC 5.8 at 0 cycles and rugnux --refine-score-only on the same files and prints the terms side by side, with R by resolution from both programs' model amplitudes on the same reflections. Tests: [refine_only] - column choice (observed over map coefficients, intensities, 1-marks-free flags, no flags, no usable column), an MTZ read from its bytes, and the mode end to end on a synthetic cell (French-Wilson, generated flags, score-only, the report keys). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu (cherry picked from commit 63ee830c39c988588cffb8c9d4638a678815ec2c) (cherry picked from commit d7397311e6ce0d3bb37ac91e8973b6052e38589f)
27 lines
1.4 KiB
C++
27 lines
1.4 KiB
C++
// SPDX-FileCopyrightText: 2026 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#pragma once
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#include <string>
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#include "../image_analysis/structure_refinement/RugnuxModel.h"
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// The atomic model of a run from the bytes of its file: PDB or mmCIF, gzipped or not, the format taken from
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// the content, never from a name. `pae_json` is the AlphaFold DB's predicted-aligned-error JSON of a
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// prediction, empty where there is none; one that cannot be read is left out, as one never given. `name` is
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// what the report calls the model, and what gemmi names a PDB structure after. Throws where the bytes hold no
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// atomic model.
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RugnuxModel ParseRugnuxModel(const std::string &bytes, const std::string &name, const std::string &pae_json = {});
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// `bytes` inflated where they are a gzip stream (by the magic number), as they are otherwise.
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std::string GunzipIfCompressed(const std::string &bytes);
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// The model file at `path`, with the predicted aligned error the AlphaFold DB puts beside it where it is there
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// (PaePathFor). Named by `path`.
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RugnuxModel ReadRugnuxModelFile(const std::string &path);
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// The PAE file the AlphaFold DB puts beside a model: AF-<id>-F1-model_v<n>.cif ->
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// AF-<id>-F1-predicted_aligned_error_v<n>.json in the same directory; empty where the name does not follow it.
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std::string PaePathFor(const std::string &model_path);
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