Fix GH issue 203 - uncaught exception in OpenMP#204
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…cessing buildQueryBatchParallel ran addQueryToBatch inside an OpenMP parallel region. The validation error for fragment (disconnected) queries escaped the region and called std::terminate whenever more than one preprocessing thread was used, so the error only surfaced as a RuntimeError on the single-threaded path. Capture the first exception with OpenMPExceptionRegistry and rethrow once the region joins.
# Conflicts: # src/substruct/molecules.cpp
evasnow1992
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Jun 11, 2026
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Thank you for fixing this. The current changes look good to me. We may, however, have similar issues elsewhere in molecules.cpp, such as around lines 2078–2086. It might be worth doing a quick scan with follow-up PRs if any related cases are found.
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We needed to catch and rethrow outside the openmp loop. Fixes #203