> ## Documentation Index
> Fetch the complete documentation index at: https://docs.claviscage.app/llms.txt
> Use this file to discover all available pages before exploring further.

# Method Queue

> Published methods planned for ClavisCage, in the order they will be added

# Method Queue

The order follows one principle: a method that can be checked against an open implementation (T2) comes before one that can only be built from its paper. Requests that come with a fixture and its expected output move up. See [Adding a Method](https://docs.claviscage.app/contributing/methods.md) for the tiers and rules.

## Next: methods with an open reference (T2)

| # | Method | Paper | Reference to check against | Licence of reference |
| - | - | - | - | - |
| 1 | CHILL+ to T2 (already shipped at T1) | Nguyen & Molinero 2015, doi 10.1021/jp510289t | OVITO's Chill+ modifier, including its gas-hydrate class | `ovito` pip module, MIT |
| 2 | Polyhedral template matching (PTM) | Larsen et al. 2016, doi 10.1088/0965-0393/24/5/055007 | `pmla` reference code; OVITO | MIT |
| 3 | Ring statistics (King / Franzblau shortest-path rings) | King 1967, doi 10.1038/2131112a0; Franzblau 1991, doi 10.1103/PhysRevB.44.4925 | matscipy ring statistics | LGPL-2.1 |
| 4 | Topological cage building blocks (`genice2-cage`) | Matsumoto et al. 2007, doi 10.1063/1.2772627 | genice-cage plugin of GenIce2 | MIT |
| 5 | Unsupervised hydrate classification (DBSCAN on F3/F4 features, with a cavity finder) | Cai, Striolo & Salvalaglio, J. Phys. Chem. C 130 (2026) 3074 | the authors' repository `mme-ucl/clathrate_hydrate_classification` | GPL-3.0 |

## Then: paper-only methods (T1 with crystal fixtures)

| # | Method | Paper | Why it waits |
| - | - | - | - |
| 6 | Local structure index (LSI) | Shiratani & Sasai 1996, doi 10.1063/1.471475 | No open reference; the definition is short, so the spec gaps are few. |
| 7 | Jacobson cage order parameters | Jacobson et al., doi 10.1021/ja1051445; doi 10.1021/jp107269q; doi 10.1063/1.3613667 | Written for the coarse-grained mW model; carrying it over to atomistic water needs its spec gaps listed first. |
| 8 | MCG-1 and other MCG variants | Barnes et al. 2014, doi 10.1063/1.4871898 | MCG-3 is shipped. The variants differ only in the neighbour count, so they mostly need fixtures. |

## Deferred

| Method | Paper | Reason |
| - | - | - |
| ICA / FSICA | Guo et al. 2008, doi 10.1063/1.2919558; Guo et al. 2011, doi 10.1039/c1cp20070d | No public code, and the cage-search details the papers leave open exceed the two-gap limit. |
| ICO | Hao et al. 2021, doi 10.1021/acs.jpcb.0c08964 | No public code, and its spec gaps are not yet listed. |

## Machine-learning methods: after the benchmark

No released model classifies hydrate cages in a form that can run in the browser.

* GCIceNet (doi 10.1039/D0CP03456H) ships MIT code but no weights.
* DeepIce has weights but no licence, so it cannot be redistributed.

The plan is to train a small model on labels produced by the verified methods above, using the [benchmark](https://docs.claviscage.app/analysis/benchmark.md) crystals and deposited trajectories, and ship its weights in the repository with their training data named. It will carry its own level, "ML · trained here", and will not be presented as a published method.


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