leonarski_fandClaude Opus 5.5
5028aac0ee
WritePlacedModel was handed the result of find_spacegroup_by_name unchecked, and PlacedModelStructure indexed every per-atom vector by atom_name's length. A malformed block from the wire could crash the writer. Now the per-atom vectors must all have atom_name's length and aniso must be empty or six per atom (PlacedModelStructure throws otherwise), and an unknown data space group is an error; WriteRugnuxResultFiles logs either and writes nothing for the model, as it already did for an MTZ table WriteMtz refuses. StreamWriter: "Received end message" is logged only with -v again, exactly as before this branch. The wall-clock times of the rugnux files are still logged where they are written, which only happens when the END carries them. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
34 lines
1.6 KiB
C++
34 lines
1.6 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 "gemmi/model.hpp"
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#include "../common/JFJochMessages.h"
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class Logger;
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// The files rugnux writes beside its merged output, made from the structured END-message blocks
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// (common/JFJochMessages.h), so that jfjoch_writer can write them with no analysis library. rugnux
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// writes its own MTZ files through the same function.
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// An MTZ file from its table. Throws where the table does not describe one: a column with another number
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// of rows than the first, a column or a batch naming a dataset the table does not have, a batch header that
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// is not 29 + 156 long, or a space group gemmi does not know.
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void WriteMtz(const MtzTable &table, const std::string &filename);
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// The model the block describes, for WritePlacedModel (writer/WriteModel.h). Throws where the block
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// describes none: a per-atom field with another number of entries than atom_name, or aniso neither empty
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// nor six per atom.
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gemmi::Structure PlacedModelStructure(const PlacedModelMessage &model);
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// The three files above, from whichever blocks `end` carries, at <file_prefix>.mtz, _maps.mtz and
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// _model.cif (WritePlacedModel adds _model.pdb where a PDB can hold the cell). Each is written under a
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// temporary name and renamed into place. An existing file is replaced only with `overwrite`; otherwise
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// it is kept and the new one is not written.
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void WriteRugnuxResultFiles(const EndMessage &end, const std::string &file_prefix, bool overwrite,
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Logger &logger);
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