Deferred Structural Elucidation Analysis for Molecular Simulations: the topological ice score (hexagonal and double-diamond cages on primitive rings), CHILL and CHILL+, topology keys and key libraries, ions and guests, for LAMMPS, GROMACS and ASE trajectories.
| component | what it is | get it |
|---|---|---|
| seams-core | the C++ engine and the seams command line |
releases, book |
| PydSEAMSlib | Python: Frame API, features for deeptime and PyEMMA, MDAnalysis and OVITO adapters |
pip install pydseamslib, docs |
| yodaStruct | Lua and Fennel: require("dseams") |
docs |
| dseams-plumed | the DSEAMS_CAGES PLUMED action: cage counts, ion classes, key libraries, filled cages on the fly |
pixi run build |
| linkcell | periodic linked-cell k-nearest neighbour search | crates.io |
| dseams2_repro | the reproducibility package of the d-SEAMS 2 paper: locked revisions, workflow, reference results | Snakemake |
| wiki | worked examples for every front end | |
| dseams.info | the suite map |
Cite the d-SEAMS paper (Goswami, Goswami and Singh, J. Chem. Inf. Model. 2020) and the release tag you used; every repository carries a CITATION.cff.
