API map¶

Lookup for the C++ identifiers in src/include/internal. Generated pages under api/ are the Doxygen comments from those headers, converted by doxyrest, the same path as rgpot. This is not a dump of pydseams.yoda and it is not a tutorial.

Fronts¶

Four fronts, one engine (libyodaLib). Flags live on seams CLI. Formats live on data formats.

Front	Package	First call
CLI	this repo (`seams`)	`seams read FILE`, `seams chill-plus FILE`, `seams cages FILE`
Python Frame	PydSEAMSlib	`pydseams.Frame` from `pydseams.read(...)`
Lua	yodaStruct	`require("dseams")`
Compiled Python	PydSEAMSlib	`pydseams.yoda` (`_core` and `cyoda` are aliases)

Doxyrest wiring¶

pixi run -e docs doxybuild runs from docs/source:

doxygen Doxyfile_seams.cfg – INPUT is ../../src/include/internal (EXTRACT_ALL=YES, private members off). src/include/external and tests/ are excluded.
doxyrest -c doxyrest-config.lua – reads xml/index.xml, writes =api/index.rst~ with title API Reference.

The book includes that tree as api/index (Reference toctree), not as a second hand list of functions. The generated pages are the API; the header table below is only a map onto those pages.

A sibling doxyYoda HTML tree of the same headers is at /api-cpp/ (pixi run -e docs doxyhtml). That landing page points back here.

C++ (doxygen)

API Reference

Headers¶

Every file under src/include/internal.

Header	Namespace	Role
`mol_sys.hpp`	`molSys`	`Point`, `PointCloud`, bond and ice enums
`seams_input.hpp`	`sinp`	LAMMPS / XYZ / chemfiles / readcon readers. `readLammpsTrjO` keeps every atom of one type and flags `inSlice`; `readLammpsTrjreduced` drops atoms outside the slice. Same slice arguments, different keep.
`seams_output.hpp`	`sout`	dump, cage, ring, and cluster writers
`neighbours.hpp`	`nneigh`	cutoff, k-nearest, skin neighbour lists
`bop.hpp`	`chill`, `sph`	CHILL, CHILL+, `q6`, Steinhardt `ql`
`franzblau.hpp`	`primitive`	Franzblau primitive rings
`ring.hpp`	`ring`	ring helpers and `strucType`
`topo_bulk.hpp`	`ring`, `prism3`	HC / DDC search, bulk polygons
`topo_one_dim.hpp`	`ring`	ice-nanotube prisms
`topo_two_dim.hpp`	`ring`	monolayer polygons
`cage.hpp`	`cage`	`Cage`, `cageType`, `iceType`, `Signature`
`cage_affiliation.hpp`	`ring`	claim-free HC / DDC flags; `seededCageAffiliation` and `ringAdjacentCompletion`
`cage_canon.hpp`	`cage`	nauty canonical certificates
`cage_enum.hpp`	`cage`	`findBySignature`, closed polyhedra from a ring-size census
`bulkTUM.hpp`	`tum3`	topological unit matching
`bond.hpp`	`bond`	geometric hydrogen bonds
`absOrientation.hpp`	`absor`	Horn absolute orientation
`pntCorrespondence.hpp`	`pntToPnt`	reference / target point sets
`shapeMatch.hpp`	`match`	prism shape-matching
`cluster.hpp`	`clump`	Stillinger ice clusters
`order_parameter.hpp`	`topoparam`	height% and coverage area
`rdf.hpp`	`rdf`	partial 3D `g_IJ(r)` and site-site CN
`rdf2d.hpp`	`rdf2`	in-plane radial distribution
`density.hpp`	`site`	type- or kind-resolved \(\rho\) along one axis
`selection.hpp`	`gen`, `ring`	type and slice selections
`generic.hpp`	`gen`	periodic distance, angles, medians
`structure_desc.hpp`	`chill`	SOAP, template overlay, linear classifier
`voronoi_qlm.hpp`	`chill`	Voronoi-weighted Steinhardt
`ira_sofi.hpp`	`ira`	IRA match and SOFI point groups
`sphericart_ylm.hpp`	`seams::sphericart_ylm`	batched Cartesian `Y_lm`
`steinhardt_device.hpp`	`seams::steinhardt`	host / MPI / offload Steinhardt kernel
`simd_distance.hpp`	`seams`	Highway periodic distance

pydseams.yoda and dseams.core register the C++ spellings from these headers. The generated pages are api/index.