API reference

Napoleon autodoc of the Python helpers. Human lookup of Frame, IceCounts, CageScore, read(), and ASE is the Python surface page.

The public constructors live on the pydseams package: from_ase(), from_arrays(), from_xyz(), from_chemfiles(), from_con(), to_solvis(). to_ase() is the inverse of from_ase().

The compiled extension is nanobind pydseams.yoda. _core and cyoda are aliases of yoda. Trajectory is an alias of Frame.

Classification (chill_plus(), cages()) does not write files. Prism, monolayer, and RDF helpers do.

d-SEAMS Python front end.

pydseams is the package. The compiled nanobind module is pydseams.yoda. Helpers (Frame, read(), ASE, solvis) sit on that surface. _core and cyoda are aliases of yoda. Trajectory is an alias of Frame.

Load a frame and ask for ice:

import pydseams as ds
frame = ds.read("water.lammpstrj")
print(frame.chill_plus())
print(frame.cages())

ASE Atoms work the same way:

frame = ds.from_ase(atoms)          # default: oxygen
atoms = frame.to_ase()

pydseams.Trajectory

alias of Frame

pydseams.from_ase(atoms, select='O', cutoff=3.5, bonded='auto')

Build a Frame from an ASE Atoms.

Parameters:

• atoms (ase.Atoms) – Configuration with an orthorhombic cell.

• select (str or int, optional) – Chemical symbol or atomic number of the species to analyse. Default "O". None keeps every atom.

• cutoff (float, optional) – Neighbour cutoff in Angstroms. Default 3.5.

• bonded ({"auto", "hbond", "cutoff"}, optional) – Graph for rings. "auto" uses hydrogen bonds when the Atoms contain H, otherwise the cutoff neighbour list.

Returns:

Analysable oxygen (or selected-species) configuration.

Return type:

Frame

Raises:

• ImportError – If ASE is not installed (pip install 'pydseams[ase]').

• TypeError – If atoms is not an ASE Atoms.

• ValueError – If the cell is not orthorhombic, or select matches no atom.

pydseams.from_arrays(positions, cell, numbers=None, cutoff=3.5, bonded='cutoff')

Build a Frame from coordinates and box lengths.

Parameters:

• positions (sequence of (x, y, z)) – Cartesian coordinates, shape (N, 3).

• cell (sequence of float) – Three orthorhombic box lengths [lx, ly, lz].

• numbers (sequence of int, optional) – Per-atom type codes stored as c_type. Default 1 for every particle.

• cutoff (float, optional) – Neighbour cutoff in Angstroms. Default 3.5.

• bonded ({"auto", "hbond", "cutoff"}, optional) – Graph for rings. Default "cutoff" because this constructor does not attach a hydrogen cloud.

Return type:

Frame

Raises:

ValueError – If positions is empty or cell is not three lengths.

pydseams.from_chemfiles(path, frame=1, **kwargs)

Build a Frame through chemfiles.

Parameters:

• path (path-like) – Trajectory chemfiles can read (PDB, GRO, DCD, …).

• frame (int, optional) – 1-indexed frame. Default 1.

• **kwargs – Forwarded to Frame.from_chemfiles() (cutoff, bonded, atom_type, type_filter).

Return type:

Frame

Raises:

RuntimeError – If this build of seams-core did not link chemfiles.

pydseams.from_con(path, frame=1, **kwargs)

Build a Frame from an eOn .con file.

Parameters:

• path (path-like) – eOn .con trajectory.

• frame (int, optional) – 1-indexed frame. Default 1.

• **kwargs – Forwarded to Frame.from_con() (cutoff, bonded, atom_type).

Return type:

Frame

Raises:

RuntimeError – If this build of seams-core did not link readcon-core.

pydseams.from_xyz(path, **kwargs)

Build a Frame from an XYZ file.

Parameters:

• path (path-like) – XYZ structure.

• **kwargs – Forwarded to Frame.from_xyz() (cutoff, bonded, atom_type).

Return type:

Frame

Raises:

RuntimeError – If this build of seams-core has no readXYZ.

pydseams.to_solvis(frame, expand_box=True)

Wrap a Frame as a solvis.System.

Parameters:

• frame (Frame) – Configuration to view. Converted through Frame.to_ase().

• expand_box (bool, optional) – Passed to solvis.system.System. Default True.

Return type:

solvis.system.System

Raises:

ImportError – If solvis is not installed (pip install 'pydseams[solvis]').

Frame

User-facing one-frame handle.

Load a LAMMPS dump, an ASE Atoms, or raw arrays, then call Frame.chill_plus() or Frame.cages(). Classification does not write files. Rings use the bonded graph (hydrogen bonds when hydrogens are available, otherwise the cutoff neighbour list).

class pydseams.frame.IceCounts

Bases: dict

CHILL / CHILL+ histogram of ice labels on one frame.

Keys are the AtomStateType names written by the classifier (cubic, hexagonal, water, interfacial, clathrate, interClathrate, unclassified, reCubic, reHex). Missing keys read as 0 via attribute access, so counts.cubic and counts['cubic'] are equivalent.

Notes

repr omits zero-count labels.

class pydseams.frame.CageScore(hc, ddc)

Bases: object

Per-atom hexagonal-cage (HC) and double-diamond-cage (DDC) flags.

A molecule in an HC is ice Ih; a molecule in a DDC is ice Ic. Membership is a boolean per analysed atom.

Parameters:

• hc (sequence of bool) – True when the atom belongs to at least one hexagonal cage.

• ddc (sequence of bool) – True when the atom belongs to at least one double-diamond cage.

hc

Per-atom HC membership.

Type:

list of bool

ddc

Per-atom DDC membership.

Type:

list of bool

property n_ih

Number of atoms flagged HC (ice Ih).

property n_ic

Number of atoms flagged DDC (ice Ic).

property n_water

Number of atoms in neither cage.

class pydseams.frame.Frame(filename=None, frame=1, atom_type=None, cutoff=3.5, bonded='auto', region=None, *, cloud=None, h_cloud=None, symbols=None)

Bases: object

One configuration: neighbours, rings, CHILL(+), and cage membership.

Load a LAMMPS dump, an ASE Atoms, or raw arrays, then call chill_plus() or cages(). Classification does not write files. Prefer pydseams.io.read(), from_ase(), or from_arrays() over constructing this class by filename.

Parameters:

• filename (path-like, optional) – LAMMPS dump. Types 1 and 2 are treated as hydrogen and oxygen unless atom_type is set.

• frame (int, optional) – 1-indexed frame. Default 1.

• atom_type (int or None, optional) – Species to analyse. None picks oxygen (type 2) if that type is present, otherwise type 1 (mW-style single-site dumps).

• cutoff (float, optional) – Neighbour cutoff in Angstroms. Default 3.5.

• bonded ({"auto", "hbond", "cutoff"}, optional) – Graph for rings. "auto" uses hydrogen bonds when hydrogens are available, otherwise the cutoff neighbour list.

• region (((xlo, ylo, zlo), (xhi, yhi, zhi)) or None, optional) – Optional rectangular slice passed to pydseams.yoda.readLammpsTrjreduced().

Raises:

• ValueError – If bonded is not one of auto, hbond, cutoff, or if a LAMMPS dump has no atoms of type 1 or 2.

• TypeError – If neither a filename nor a pre-built cloud is supplied.

Notes

Keyword-only cloud, h_cloud, and symbols are the constructor plumbing used by from_ase() and from_arrays().

classmethod from_file(filename, frame=1, atom_type=None, cutoff=3.5, bonded='auto', region=None)

Load a LAMMPS dump through pydseams.yoda.readLammpsTrjreduced().

Parameters:

• filename (path-like) – LAMMPS dump (.lammpstrj, .dump, .lammps).

• frame (int, optional) – 1-indexed frame. Default 1.

• atom_type (int or None, optional) – Species to keep. None tries type 2 (oxygen) then type 1.

• cutoff (float, optional) – Neighbour cutoff in Angstroms. Default 3.5.

• bonded ({"auto", "hbond", "cutoff"}, optional) – Graph for rings.

• region (((xlo, ylo, zlo), (xhi, yhi, zhi)) or None, optional) – Optional rectangular slice.

Return type:

Frame

classmethod from_arrays(positions, cell, numbers=None, cutoff=3.5, bonded='cutoff', box_low=None)

Build a frame from (N, 3) positions and three box lengths.

Parameters:

• positions (sequence of (x, y, z)) – Cartesian coordinates.

• cell (sequence of float) – Orthorhombic box lengths [lx, ly, lz].

• numbers (sequence of int, optional) – Per-atom type codes stored as c_type. Default 1.

• cutoff (float, optional) – Neighbour cutoff in Angstroms. Default 3.5.

• bonded ({"auto", "hbond", "cutoff"}, optional) – Graph for rings. Default "cutoff".

• box_low (sequence of float, optional) – Box origin. Default (0, 0, 0).

Return type:

Frame

Raises:

ValueError – If positions is empty or cell is not three lengths.

classmethod from_xyz(filename, cutoff=3.5, bonded='cutoff', atom_type=None)

Load an XYZ file through pydseams.yoda.readXYZ().

Parameters:

• filename (path-like) – XYZ structure.

• cutoff (float, optional) – Neighbour cutoff in Angstroms. Default 3.5.

• bonded ({"auto", "hbond", "cutoff"}, optional) – Graph for rings. Default "cutoff".

• atom_type (int or None, optional) – Species to analyse. None uses the first particle’s c_type.

Return type:

Frame

Raises:

RuntimeError – If this build has no readXYZ.

classmethod from_chemfiles(filename, frame=1, type_filter=-1, cutoff=3.5, bonded='cutoff', atom_type=None)

Load PDB/GRO/DCD (or any chemfiles format) when chemfiles is linked.

Parameters:

• filename (path-like) – Trajectory chemfiles can read.

• frame (int, optional) – 1-indexed frame. Default 1.

• type_filter (int, optional) – Chemfiles type filter. -1 keeps every type.

• cutoff (float, optional) – Neighbour cutoff in Angstroms. Default 3.5.

• bonded ({"auto", "hbond", "cutoff"}, optional) – Graph for rings. Default "cutoff".

• atom_type (int or None, optional) – Species to analyse. None uses the first particle’s c_type.

Return type:

Frame

Raises:

RuntimeError – If chemfiles is not linked in this build of seams-core.

classmethod from_con(filename, frame=1, cutoff=3.5, bonded='cutoff', atom_type=None)

Load an eOn .con file when readcon-core is linked.

Parameters:

• filename (path-like) – eOn .con trajectory.

• frame (int, optional) – 1-indexed frame. Default 1.

• cutoff (float, optional) – Neighbour cutoff in Angstroms. Default 3.5.

• bonded ({"auto", "hbond", "cutoff"}, optional) – Graph for rings. Default "cutoff".

• atom_type (int or None, optional) – Species to analyse. None uses the first particle’s c_type.

Return type:

Frame

Raises:

RuntimeError – If readcon-core is not linked in this build of seams-core.

classmethod from_ase(atoms, select='O', cutoff=3.5, bonded='auto')

Load an ASE Atoms. select is a symbol, atomic number, or None.

Parameters:

• atoms (ase.Atoms) – Configuration with an orthorhombic cell.

• select (str or int, optional) – Chemical symbol or atomic number of the species to analyse. Default "O". None keeps every atom.

• cutoff (float, optional) – Neighbour cutoff in Angstroms. Default 3.5.

• bonded ({"auto", "hbond", "cutoff"}, optional) – Graph for rings. "auto" uses hydrogen bonds when the Atoms contain H.

Return type:

Frame

to_ase()

ASE Atoms for this frame.

Returns:

Orthorhombic cell, pbc=True. After chill_plus() (or chill()), arrays['ice_type'] holds the labels. After cages(), arrays['hc'] and arrays['ddc'] hold the cage flags.

Return type:

ase.Atoms

to_solvis(expand_box=True)

solvis.System for this frame.

Parameters:

expand_box (bool, optional) – Passed to solvis.system.System. Default True.

Return type:

solvis.system.System

Notes

Optional extra: pip install 'pydseams[solvis]'.

property n_atoms

Number of particles in the analysed cloud (cloud.nop).

property box

Orthorhombic box lengths [lx, ly, lz].

property positions

List of (x, y, z) coordinates for the analysed particles.

property neighbor_list

Cutoff neighbour list from pydseams.yoda.neighListO().

Built once per loaded frame and cached. Rows are atom IDs of neighbours within cutoff for atom_type.

property hbonds

Hydrogen-bond neighbour list.

Uses pydseams.yoda.populateHbondsWithInputClouds() when an ASE hydrogen cloud is attached, otherwise pydseams.yoda.populateHbonds() on the LAMMPS dump.

Raises:

ValueError – If no hydrogens are available (arrays-only frame, or bonded='hbond' without H).

load_frame(frame)

Reload a later (or earlier) frame from the same trajectory file.

Parameters:

frame (int) – 1-indexed frame to read.

Raises:

ValueError – If this Frame was built from arrays or ASE and has no trajectory path.

Notes

Clears cached neighbours, hydrogen bonds, rings, and cages.

property bonds_by_index

Index-based bonded graph used for rings.

Hydrogen-bond list when bonded is "hbond", otherwise the cutoff neighbour list. Converted with pydseams.yoda.neighbourListByIndex().

property rings

Primitive rings up to size 6 on bonds_by_index.

Computed by pydseams.yoda.RingUpdater and cached.

property rings_recomputed_sources

Sources recomputed by the last RingUpdater pass.

chill_plus()

CHILL+ labels for every analysed atom. Does not write a file.

Calls pydseams.yoda.getCorrelPlus() then pydseams.yoda.getIceTypePlusNoPrint() on neighbor_list. Mutates cloud.pts[].iceType.

Returns:

Histogram of CHILL+ labels on this frame.

Return type:

IceCounts

chill()

CHILL labels for every analysed atom. Does not write a file.

Calls pydseams.yoda.getCorrel() then pydseams.yoda.getIceTypeNoPrint() on neighbor_list. Mutates cloud.pts[].iceType.

Returns:

Histogram of CHILL labels on this frame.

Return type:

IceCounts

classify_chill_plus()

Alias of chill_plus().

classify_chill()

Alias of chill().

cages(seeded=True, k=4, candidate_cutoff=None)

Ice score: HC = Ih, DDC = Ic, neither = water.

Parameters:

• seeded (bool, optional) – True (default) is the hysteresis construction: mutual four-nearest seeds, union-graph completion (seeded_affiliation()). False is cutoff-graph affiliation on this frame’s six-rings (cage_affiliation()).

• k (int, optional) – Neighbours kept in the seeded k-nearest graphs. Default 4.

• candidate_cutoff (float or None, optional) – Candidate-list cutoff for the k-nearest graphs. None uses cutoff + 1.5.

Returns:

Per-atom HC/DDC flags. Cached as _cages for to_ase().

Return type:

CageScore

cage_affiliation()

Order-free per-ring HC/DDC flags on this frame’s six-rings.

Uses pydseams.yoda.AffiliationUpdater on the cutoff-or-hbond six-rings.

Returns:

six_rings (list of 6-cycles), hc and ddc (per-ring bools), and reclassified (updater delta).

Return type:

dict

seeded_affiliation(k=4, candidate_cutoff=None)

Seeded (hysteresis) per-atom cage flags.

Strict-graph seeds from a mutual k-nearest list, permissive completion on the union k-nearest list. Delegates to pydseams.yoda.seededCageAffiliation().

Parameters:

• k (int, optional) – Neighbours kept in each k-nearest graph. Default 4.

• candidate_cutoff (float or None, optional) – Candidate-list cutoff. None uses cutoff + 1.5.

Return type:

CageScore

find_prisms(output_dir='output/', max_depth=6, shape_matching=False)

Identify prism blocks and write engine output under output_dir.

Parameters:

• output_dir (path-like, optional) – Directory passed to pydseams.yoda.prismAnalysis(). Default "output/".

• max_depth (int, optional) – Largest ring size considered. Default 6.

• shape_matching (bool, optional) – Enable TUM shape matching inside the prism search.

Notes

This path writes files. chill_plus() and cages() do not.

monolayer_rings(output_dir, sheet_area, max_depth=4)

Classify quasi-2D polygon rings and read coverage back.

Parameters:

• output_dir (path-like) – Directory for pydseams.yoda.polygonRingAnalysis().

• sheet_area (float) – Sheet area passed to the engine.

• max_depth (int, optional) – Largest ring size. Default 4.

Returns:

{ring_size: {"count": int, "coverage_xy": float}} parsed from topoMonolayer/coverageAreaXY.dat.

Return type:

dict

rdf_2d(output_dir, cutoff=12.0, binwidth=0.05)

2D radial distribution function for identical atom types.

Parameters:

• output_dir (path-like) – Directory for pydseams.yoda.rdf2Danalysis_AA().

• cutoff (float, optional) – RDF cutoff in Angstroms. Default 12.0.

• binwidth (float, optional) – Histogram width. Default 0.05.

Returns:

r, g – Bin centres and g(r) parsed from topoMonolayer/rdf.dat.

Return type:

list of float

steinhardt(order_l=6)

Local and neighbour-averaged Steinhardt parameters.

Parameters:

order_l (int, optional) – Degree l (3, 4, or 6). Default 6.

Returns:

ql and ql_bar lists from pydseams.yoda.steinhardtQl().

Return type:

dict

steinhardt_voronoi(order_l=6, cutoff=None)

Voronoi facet-area weighted Steinhardt parameters.

Parameters:

• order_l (int, optional) – Degree l. Default 6.

• cutoff (float or None, optional) – Candidate cutoff for the Voronoi pass. None uses cutoff.

Returns:

ql and ql_bar lists from pydseams.yoda.steinhardtQlVoronoi().

Return type:

dict

classify_templates(k_neigh=12)

IRA/Horn overlay onto FCC, HCP, BCC, and SC neighbour shells.

Parameters:

k_neigh (int, optional) – Neighbours in each template shell. Default 12.

Returns:

Each hit has name, rmsd, and kind.

Return type:

list of dict

soap(iatom=None, n_max=3, l_max=6, rcut=None)

SOAP power spectrum of one particle, or of every particle.

Parameters:

• iatom (int or None, optional) – Particle index. None (default) computes every particle via pydseams.yoda.soapSpectrumAll().

• n_max (int, optional) – Radial basis size. Default 3.

• l_max (int, optional) – Angular momentum cutoff. Default 6.

• rcut (float or None, optional) – SOAP cutoff. None uses cutoff.

Returns:

One spectrum, or one spectrum per particle.

Return type:

list of float or list of list of float

voronoi_features(cutoff=None)

Per-atom [q4, q6, q8] from one Voronoi-weighted pass.

Parameters:

cutoff (float or None, optional) – Candidate cutoff. None uses cutoff.

Returns:

One [q4, q6, q8] row per particle from pydseams.yoda.voronoiFeatures().

Return type:

list of list of float

fit_classifier(X, y, labels=None)

Fit a pydseams.yoda.LinearClassifier on feature rows.

Parameters:

• X (sequence of sequence of float) – Feature matrix.

• y (sequence of int) – Integer class labels.

• labels (sequence of str, optional) – Human-readable class names stored on the classifier.

Returns:

Fitted classifier, also stored on the frame.

Return type:

pydseams.yoda.LinearClassifier

predict_class(x)

Predict a class for one feature row.

Parameters:

x (sequence of float) – Feature vector matching the last fit_classifier() fit.

Returns:

Predicted class index.

Return type:

int

Raises:

RuntimeError – If fit_classifier() has not been called.

I/O

Suffix dispatch onto the compiled I/O readers.

The compiled module stays thin. This helper picks LAMMPS, XYZ, chemfiles, or readcon from the path suffix and returns a Frame.

pydseams.io.read(path, frame=1, **kwargs)

Load one configuration. Format follows the file suffix.

Parameters:

• path (path-like) – Trajectory or structure file.

• frame (int, optional) – 1-indexed frame for multi-frame formats (LAMMPS, chemfiles, .con). Ignored for XYZ. Default 1.

• **kwargs – Forwarded to the matching Frame constructor (cutoff, bonded, atom_type, region, …).

Returns:

Analysable configuration.

Return type:

Frame

Notes

Suffix dispatch:

• .xyz – Frame.from_xyz()

• .con – Frame.from_con()

• .pdb, .gro, .dcd – Frame.from_chemfiles()

• otherwise – Frame.from_file() (LAMMPS dump)

.lammpstrj, .dump, and .lammps take the LAMMPS path. Builds without chemfiles or readcon raise RuntimeError when those suffixes are used.

pydseams.io.available_readers()

Report which compiled I/O readers this build linked.

Returns:

lammps is always True. xyz, chemfiles, and readcon are True when the matching pydseams.yoda symbol exists (readXYZ, readChemfiles, readCon).

Return type:

dict of str to bool

ASE helpers

Implementation of from_ase() and to_ase(). Optional extra: pip install 'pydseams[ase]'.

ASE Atoms in and out of a Frame.

Optional extra: pip install 'pydseams[ase]'. The compiled engine does not import ASE; this module is the adapter.

pydseams.aseio.frame_from_ase(cls, atoms, select='O', cutoff=3.5, bonded='auto')

Construct cls (a Frame) from ASE Atoms.

Parameters:

• cls (type) – Frame or a subclass.

• atoms (ase.Atoms) – Configuration with an orthorhombic cell.

• select (str or int, optional) – Chemical symbol or atomic number kept for analysis. Default "O". None keeps every atom.

• cutoff (float, optional) – Neighbour cutoff in Angstroms. Default 3.5.

• bonded ({"auto", "hbond", "cutoff"}, optional) – Graph for rings. "auto" becomes "hbond" when the Atoms contain hydrogen, otherwise "cutoff".

Returns:

Selected-species cloud plus an optional hydrogen cloud for hydrogen-bond analysis.

Return type:

Frame

Raises:

• ImportError – If ASE is not installed.

• TypeError – If atoms has no get_positions.

• ValueError – If the cell is not orthorhombic, or select matches no atom.

Notes

Hydrogens stay in a side cloud so the analysed species remain the CHILL / ring particles. Cell origin follows atoms.get_celldisp().

pydseams.aseio.frame_to_ase(frame)

Build an ASE Atoms from a Frame.

Parameters:

frame (Frame) – Configuration to export.

Returns:

Orthorhombic cell, pbc=True. Symbols come from the ASE import when present; LAMMPS-only frames fall back to O.

Return type:

ase.Atoms

Notes

After chill_plus() (or chill()), atoms.arrays['ice_type'] holds the per-atom labels. After cages(), atoms.arrays['hc'] and atoms.arrays['ddc'] hold the cage flags. atoms.info['dseams_n_atoms'] is the analysed particle count.

solvis

Implementation of to_solvis() and to_solvis(). Optional extra: pip install 'pydseams[solvis]'.

Optional solvis (PyVista) view of a Frame.

solvis takes an ASE Atoms. This helper is the same pattern as metatomic’s ASE adapter: the C++ core does not know about the viewer. Install with pip install 'pydseams[solvis]'.

pydseams.solvis.to_solvis(frame, expand_box=True)

Wrap a Frame as a solvis.System.

Parameters:

• frame (Frame) – Configuration to view. Converted through to_ase().

• expand_box (bool, optional) – Passed to solvis.system.System. Default True.

Return type:

solvis.system.System

Raises:

ImportError – If solvis is not installed (pip install 'pydseams[solvis]').

Compiled module (pydseams.yoda)

yoda is mocked in the Sphinx build (autodoc_mock_imports), so automodule cannot list live signatures. The tables below are every public name registered in src/bindings.cpp: 111 names (98 functions, 13 types). Four functions are compile-gated and absent from builds that did not link the extra: readChemfiles (SEAMS_HAS_CHEMFILES), readCon (SEAMS_HAS_READCON), ira_match and sofi_point_group (SEAMS_HAS_IRA).

Application code uses Frame / read() / from_ase(). Call yoda directly for the raw engine.

I/O

name	role
readXYZ	Read atom coordinates from an XYZ file.
readLammpsTrjreduced	Read a LAMMPS trajectory frame, keeping only atoms of the given type.
readLammpsTrjO	Read a LAMMPS trajectory frame, keeping only oxygen atoms.
readLammpsTrj	Read a LAMMPS trajectory frame with all atom types.
readBonds	Read bond connectivity from a formatted bond file.
atomInSlice	Check whether a point (x, y, z) lies within a volume slice.
readChemfiles	Read any trajectory format supported by chemfiles (PDB, GRO, DCD, …). Linked when SEAMS_HAS_CHEMFILES.
readCon	Read a .con file (eOn saddle-point search trajectories). Linked when SEAMS_HAS_READCON.
writeDump	Write a LAMMPS dump file for the current point cloud.

Neighbours and hydrogen bonds

name	role
clearNeighbourList	Free memory for a neighbour list.
getNewNeighbourListByIndex	Build a neighbour list by index using a distance cutoff.
kNearestNeighbourList	Exact k-nearest bonded graph, union- or mutually-symmetrized.
shellSeparation	Certificate pair (max k-th distance, min (k+1)-th distance) for the exact reduction of the k-nearest graph to a cutoff graph.
halfNeighList	Build a half neighbour list (each pair stored once) for one atom type.
neighbourListByIndex	Convert an atom-ID neighbour list to an index-based neighbour list.
neighList	Build a full neighbour list for two atom types within a cutoff.
neighListO	Build a full neighbour list for a single atom type within a cutoff.
createBondsFromCages	Create bond connectivity from rings and cage information.
getHbondDistanceOH	Compute the O-H hydrogen bond distance between two atoms.
populateHbonds	Build the hydrogen-bond network from a trajectory and neighbour list.
populateHbondsWithInputClouds	Build hydrogen bonds from pre-loaded oxygen and hydrogen point clouds.
trimBonds	Remove duplicate bonds from a bond list.

Rings and cages

name	role
clearGraph	Free memory for a graph object.
countAllRingsFromIndex	Find all possible rings (including non-shortest-path) up to maxDepth.
ringNetwork	Find all primitive (shortest-path) rings up to maxDepth.
cageAffiliation	Order-free per-ring cage classification: (hc, ddc) flag vectors.
seededCageAffiliation	Seeded (hysteresis) per-atom cage flags: strict-graph seeds, permissive-graph completion.
RingUpdater	Exact incremental primitive rings for a neighbour list.
AffiliationUpdater	Exact incremental per-ring cage classification for one frame.
populateGraphFromIndices	Create a graph object from an index-based neighbour list.
populateGraphFromNListID	Create a graph object from an atom-ID neighbour list and point cloud.
removeNonSPrings	Remove non-shortest-path rings using the Franzblau criterion.
restoreEdgesFromIndices	Restore graph edges from an index-based neighbour list.

Ring classification

name	role
assignPolygonType	Assign atom types based on the ring size of n-membered rings.
assignPrismType	Assign atom types for atoms belonging to prism rings.
clearRingList	Free memory for a list of rings.
compareRings	Check whether two unordered rings contain the same elements.
commonElementsInThreeRings	Check whether three rings share at least one common element.
deformedPrismTypes	Get atom type values for deformed prisms.
discardExtraTetragonBlocks	Discard duplicate 4-membered ring pairs that are parallel in one dimension.
findPrisms	Identify which rings form prism blocks.
findsCommonElements	Return the common elements shared by two rings.
findTripletInRing	Search for a triplet of atoms within a ring.
getSingleRingSize	Extract rings of a specific size from a list of all rings.
hasCommonElements	Check whether two rings share any common elements.
basalPrismConditions	Test whether two rings satisfy strict basal prism conditions.
relaxedPrismConditions	Test whether two rings satisfy relaxed prism conditions (at least one bond).
getEdgeMoleculesInRings	Select edge molecules in rings that straddle the slice boundary.
printSliceGetEdgeMoleculesInRings	Select edge molecules in rings and write slice output files.

Topology writers

name	role
polygonRingAnalysis	Classify rings in a quasi-2D monolayer and write output.
bulkPolygonRingAnalysis	Classify rings in a bulk system and write output.
prismAnalysis	Prism identification on rings up to maxDepth; writes output.
rmAxialTranslations	Remove axial translations from an ice nanotube for visualization.

Topological unit matching

name	role
atomsFromCages	Get atom indices belonging to cages in a given cluster.
averageRMSDatom	Average the per-atom RMSD over the number of shared cages.
buildRefDDC	Build a reference double-diamond cage from a template XYZ file.
buildRefHC	Build a reference hexagonal cage from a template XYZ file.
clusterCages	Cluster cages using Stillinger’s algorithm and write XYZ output.
shapeMatchDDC	Shape-match a target double-diamond cage against a reference.
shapeMatchHC	Shape-match a target hexagonal cage against a reference.
topoBulkCriteria	Find HCs and DDCs in a bulk system using topological criteria.
topoUnitMatchingBulk	Run full topological unit matching for bulk water.
updateRMSDatom	Update per-atom RMSD from a cage shape-matching result.

Selection

name	role
getPointCloudOneAtomType	Extract a point cloud containing only atoms of a given type.
atomsInSingleSlice	Mark atoms inside a rectangular volume slice.
moleculesInSingleSlice	Mark whole molecules as in-slice if any atom is inside the region.
setAtomsWithSameMolID	Set the inSlice flag for all atoms sharing a given molecule ID.

CHILL / CHILL+

name	role
BondClassifier	Bond-classification rule set (staggered / eclipsed windows).
chillRule	The CHILL water rule set.
chillPlusRule	The CHILL+ water rule set.
bondClassifier	Look up a registered bond-classification rule set by name.
registerBondClassifier	Register (or replace) a named bond-classification rule set.
bondClassifierNames	Names of every registered bond-classification rule set.
classifyBonds	Compute and classify bond correlations under an arbitrary rule set.
getCorrelPlus	Compute CHILL+ bond-order correlations and classify bond types.
getIceTypePlusNoPrint	Classify each atom’s ice type using CHILL+. Does not write a file.
getIceTypePlus	Classify each atom’s ice type using CHILL+ and write to file.
getCorrel	Compute CHILL bond-order correlations and classify bond types.
getIceTypeNoPrint	Classify each atom’s ice type using CHILL. Does not write a file.
getIceType	Classify each atom’s ice type using CHILL and write to file.
getq6	Compute the q6 bond order parameter for all atoms.
reclassifyWater	Reclassify water molecules using averaged q6 and q3 parameters.
printIceType	Print the ice type classification for the current frame.

Descriptors

name	role
steinhardtQl	Local and neighbour-averaged Steinhardt parameters of degree orderL.
steinhardtQlVoronoi	Voronoi facet-area weighted Steinhardt parameters.
classifyTemplates	IRA/Horn overlay onto FCC, HCP, BCC, and SC neighbour shells.
soapSpectrum	SOAP power spectrum of one particle.
soapSpectrumAll	SOAP power spectrum of every particle.
voronoiFeature	Per-atom [q4, q6, q8] from the Voronoi-weighted Steinhardt path.
voronoiFeatures	[q4, q6, q8] for every particle from one Voronoi pass per order.
voronoiFacetWeights	Voronoi facet neighbours and area weights for every particle.
LinearClassifier	Linear classifier used by Frame.fit_classifier.
ira_available	True when this build linked libira (IRA/SOFI).
ira_match	IRA overlay of two n x 3 point sets. Linked when SEAMS_HAS_IRA.
sofi_point_group	SOFI point group of an n x 3 cloud. Linked when SEAMS_HAS_IRA.
lookupTableQ4Vec	Lookup table for Q4 (m=0 to m=8).
lookupTableQ4	Lookup table for Q4 at a single m (m=0 to m=8).
lookupTableQ8Vec	Lookup table for Q8 (m=0 to m=16).
lookupTableQ8	Lookup table for Q8 at a single m (m=0 to m=16).

Clustering and RDF

name	role
clusterAnalysis	Cluster ice-like particles and return the largest ice cluster.
recenterClusterCloud	Recenter a cluster point cloud for visualization.
rdf2Danalysis_AA	2D radial distribution function for identical atom types.

Types

name	role
PointCloudDouble	Collection of points for a single frame, with box dimensions.
PointDouble	Per-particle data: coordinates, type, molecule ID, ice classification.
SteinhardtQl	Per-particle Steinhardt ql and neighbour-averaged qlBar.
AtomStateType	Per-atom ice phase classification from CHILL / CHILL+ / q6.
BondType	Bond classification: staggered, eclipsed, or out_of_range.
Result	Bond correlation result: classifier (bond type) and c_value.
CrystalKind	Crystal template kind: other, sc, fcc, hcp, bcc.
TemplateHit	IRA/Horn overlay hit: kind, rmsd, name.
VoronoiWeights	Facet-sharing neighbours and facet-area weights of one particle.