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TRACE Analysis

TRACE is Clavis’s general hydrogen-bond topology path for finding hydrate cages with canonical or unusual face signatures.

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How It Works

  1. Build a PBC-aware hydrogen-bond graph from O–O distance and donor-angle criteria.
  2. Enumerate and geometrically validate 4-, 5-, and 6-membered rings.
  3. Assemble closed polyhedra from shared ring edges.
  4. Classify complete and incomplete candidates by topology and face signature.
The current default thresholds are 0.36 nm for O–O distance and 35° for the donor-angle criterion. These are TRACE settings; HTR and GRADE have different contracts.

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Cage and Quality Labels

TRACE can return canonical cages such as 5^12, 5^12·6^2, and 5^12·6^4, as well as arbitrary signatures such as 4^3·5^6·6^3. An arbitrary signature is valid TRACE output. It must not be presented as native GRADE output.

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Running TRACE

  1. Upload a supported structure or trajectory containing cage-forming waters.
  2. Open ANALYZE, select TRACE, and run the selected frame or sampled range.
  3. Inspect per-type counts and SEC/nSEC/IC totals before interpreting occupancy.
Normal GRO, large streamed GRO, mapped LAMMPS, and native XTC/TRR trajectories support algorithm-owned TRACE range results. Each row records algorithm, zero-based frameIndex, and one-based display frame. Native ranges decode the selected frame indices before running the same algorithm dispatcher. The bundled example_H2O regression now matches native TRACE exactly: SEC 10, nSEC 0, IC 12. The port follows the native 4–10-member ring walk and two-pass cup state machine. New fixtures still require independent reference comparison; this one golden does not validate unrelated inputs automatically.

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Reference

Hsu, Y.-C. & Lin, S.-T. TRACE. Journal of Chemical Theory and Computation. DOI: 10.1021/acs.jctc.5c01459