leonarski_fandClaude Opus 5.5
4bf41983ed
The analysis read the --model file itself, four to five times per run (the model kind, every validation, molecular replacement, the stills reference intensities) and located the PAE sidecar from the file name. The library is to do no file I/O, so the model now arrives in memory: - RugnuxModel (image_analysis/structure_refinement/RugnuxModel.h): the gemmi structure as read, whether it is ModelCIF, the PAE matrix where a prediction came with one, and the name the report gives it. - ParseRugnuxModel / ReadRugnuxModelFile (writer/RugnuxModelFile.h, in JFJochRugnuxFiles): bytes in, gzip by magic, PDB/mmCIF by content, _ma_qa_metric detection as before; the file reader takes the PAE JSON from the same place PaePathFor named. - ProcessConfig::model replaces model_path; PrepareSearchModel, RunMolecularReplacement, ValidateAgainstModel and ModelReferenceIntensities take the model; result fields name it by model_name. - rugnux reads the model before the run starts and stops with an error where the file holds no model (it used to run and report the model as not validated). The viewer reads it when the job is set up. - The broker parses an uploaded model at once and answers 400 where it is not one; it keeps the parsed model in memory, with no temporary directory or file. It takes no PAE. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
24 lines
1.2 KiB
C++
24 lines
1.2 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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// 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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