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Feat/184 intarna eval - #252

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feat/184-intarna-eval
Oct 2, 2026
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Adds --rri and the IntaRNAeval personality to evaluate predefined RNA–RNA interactions through the existing energy models and output handlers. For example, IntaRNAeval -t GGGG -q CCCC --rri='1||||&1||||:2||&2||' reports the energies of both supplied structures without searching for replacements.

The new PredictorEvalOnly validates colon-separated hybridDB input, including shifted indices, bounds, pairing balance and complementarity. Evaluation requires one query and target, ignores prediction and output-filter constraints with INFO messages, and retains energy/accessibility settings. Distinct structures are reported in input order, including positive energies; duplicate structures count once. Direct reporting preserves different internal pairings with identical energies and boundaries. Partition functions and trackers describe only the supplied structures. Unavailable energies under the chosen accessibility/energy model fail with a diagnostic.

Includes API/CLI regression tests, installation of the personality through the existing mechanism, README/CLI documentation and both ChangeLog entries.

Validation on Linux with GCC 14 and the bundled Kokkos mdspan backend:

  • Release and debug make tests -j2: 73,801 assertions in 50 API cases and all three CLI suites pass in each build.
  • Regression coverage includes malformed inputs, single/GU pairs, shifted indices, ignored constraints, equal-energy structures, duplicates, tracker coordinates, partition resets and ViennaRNA prediction/evaluation energy round trips with/without dangling ends.
  • make install: installed IntaRNAeval command works; every installed public header compiles independently; an external evaluation consumer compiles, links and runs using pkg-config and the documented Easylogging++ initialization/flags.
  • make dist: includes the new predictor and regression tests.
  • git diff --check passes.

Fixes #184.

@martin-raden
martin-raden merged commit afede02 into master Oct 2, 2026
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martin-raden deleted the feat/184-intarna-eval branch October 2, 2026 09:15
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IntaRNAeval (C++)

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