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rugnux: always write both MTZ and CIF; drop --scaling-output

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The merged reflections were written in one of mtz/cif/txt selected by
--scaling-output. Write both an MTZ and an mmCIF unconditionally instead - each
has its uses downstream (MTZ for the CCP4/phenix tools, mmCIF for deposition) -
and remove the format selector, the plain-text .hkl writer, and the now-unused
IntensityFormat enum / ScalingSettings::FileFormat plumbing.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This commit is contained in:
leonarski_f
2026-07-16 10:45:08 +02:00
co-authored by Claude Opus 4.8
parent ce12d69751
commit eae7ea90dc
7 changed files with 7 additions and 67 deletions
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image_analysis/WriteReflections.cpp
+4 -26
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@@ -334,21 +334,6 @@ void WriteMtzReflections(const std::vector<MergedReflection> &reflections,
mtz.write_to_file(filename);
}
void WriteHKLReflections(const std::vector<MergedReflection> &reflections,
const std::string &filename) {
std::ofstream hkl_file(filename);
if (!hkl_file)
throw JFJochException(JFJochExceptionCategory::FileWriteError, "Cannot open file " + filename + " for writing");
for (const auto &r: reflections)
hkl_file << r.h << " " << r.k << " " << r.l << " "
<< r.I << " " << r.sigma << " "
<< (r.rfree_flag ? 1 : 0) << " "
<< r.F << " " << r.sigmaF << std::endl;
hkl_file.close();
}
void WriteReflections(const std::vector<MergedReflection> &reflections,
const UnitCell &unitCell,
const DiffractionExperiment &experiment,
@@ -356,15 +341,8 @@ void WriteReflections(const std::vector<MergedReflection> &reflections,
const std::string &isa,
const TwinningAnalysisResult &twinning,
const std::string &filename) {
switch (experiment.GetScalingSettings().GetFileFormat()) {
case IntensityFormat::Text:
WriteHKLReflections(reflections, filename + ".hkl");
break;
case IntensityFormat::mmCIF:
WriteMmcifReflections(reflections, unitCell, experiment, statistics, isa, twinning, filename + ".cif");
break;
case IntensityFormat::MTZ:
WriteMtzReflections(reflections, unitCell, experiment, filename + ".mtz");
break;
}
// Always write both an MTZ and an mmCIF - each has its uses downstream (MTZ for the CCP4 /
// phenix reflection tools, mmCIF for deposition and as the self-describing native format).
WriteMtzReflections(reflections, unitCell, experiment, filename + ".mtz");
WriteMmcifReflections(reflections, unitCell, experiment, statistics, isa, twinning, filename + ".cif");
}