Classes
struct	LocalKey
struct	FrameFingerprint
struct	KeyLibrary
	A dictionary from local keys to labels: the keys of reference structures (a polymorph library), so any molecule whose rooted neighbourhood matches a reference gets that reference's name. More...
struct	LibraryMatch

Typedefs
using	Rows = std::vector<std::vector<int>>
	Neighbour rows by index, each row leading with the atom itself, as nneigh::neighbourListByIndex returns them.

Functions
std::vector< int >	hopNeighbourhood (const Rows &rows, int atom, int hops)
	Atoms within hops bonds of atom, the atom itself first, then in breadth-first order.
std::uint64_t	wlHash (const std::vector< std::vector< int > > &adjacency, int root, int rounds, const std::vector< int > &colours={})
	Weisfeiler-Lehman refinement hash of a graph given by local adjacency lists; root (or -1) starts in its own colour; colours (empty or one integer per vertex, such as the atom type) seeds the initial colours.
LocalKey	localKey (const Rows &rows, int atom, int hops, const std::vector< int > &colours={})
	Key of the rooted neighbourhood of atom.
FrameFingerprint	fingerprint (const Rows &rows, int hops=2, int maxRingSize=7, const std::vector< int > &colours={})
	Keys of every atom, their histogram, the ring census up to maxRingSize, and the frame key.
FrameFingerprint	incrementalFingerprint (const FrameFingerprint &prev, const Rows &rows, const std::vector< int > &dirtyAtoms, int hops, int maxRingSize=7, const std::vector< int > &colours={})
	Recompute local keys only for the hop-ball of dirtyAtoms and keep the rest of prev.
std::string	hex (std::uint64_t value)
	Hex string of a 64-bit hash.
void	addToLibrary (KeyLibrary &lib, const FrameFingerprint &fp, const std::string &label)
	Add every distinct key of fp under label; a key already present under other labels carries all of them, sorted and joined by '\|'.
std::string	writeLibrary (const KeyLibrary &lib)
	Text form: a header line # method M hops H colours C (C is 0 or 1; a header without it means uncoloured), then key label lines.
KeyLibrary	readLibrary (const std::string &text)
LibraryMatch	matchLibrary (const FrameFingerprint &fp, const KeyLibrary &lib)
	Look every atom key of fp up in lib.
LibraryMatch	matchLibraries (const Rows &rows, const std::vector< KeyLibrary > &libs, int maxRingSize=7, const std::vector< int > &colours={})
	Match against libraries at several depths: an atom takes the label of the deepest library that holds its key, and a molecule whose wide neighbourhood is disturbed (a defect two bonds away, a jittered dense polymorph) still gets named by its inner shells.

Typedef Documentation

◆ Rows

using topo::Rows = std::vector<std::vector<int>>

Neighbour rows by index, each row leading with the atom itself, as nneigh::neighbourListByIndex returns them.

Definition at line 38 of file topo_fingerprint.hpp.

Function Documentation

◆ addToLibrary()

void topo::addToLibrary	(	KeyLibrary &	lib,
		const FrameFingerprint &	fp,
		const std::string &	label )

Add every distinct key of fp under label; a key already present under other labels carries all of them, sorted and joined by '|'.

◆ fingerprint()

FrameFingerprint topo::fingerprint	(	const Rows &	rows,
		int	hops = 2,
		int	maxRingSize = 7,
		const std::vector< int > &	colours = {} )

Keys of every atom, their histogram, the ring census up to maxRingSize, and the frame key.

colours as in localKey.

◆ hex()

std::string topo::hex ( std::uint64_t value )

Hex string of a 64-bit hash.

◆ hopNeighbourhood()

std::vector< int > topo::hopNeighbourhood	(	const Rows &	rows,
		int	atom,
		int	hops )

Atoms within hops bonds of atom, the atom itself first, then in breadth-first order.

◆ incrementalFingerprint()

FrameFingerprint topo::incrementalFingerprint	(	const FrameFingerprint &	prev,
		const Rows &	rows,
		const std::vector< int > &	dirtyAtoms,
		int	hops,
		int	maxRingSize = 7,
		const std::vector< int > &	colours = {} )

Recompute local keys only for the hop-ball of dirtyAtoms and keep the rest of prev.

The ring census is taken on rows. A size or hop mismatch falls back to a full fingerprint.

◆ localKey()

LocalKey topo::localKey	(	const Rows &	rows,
		int	atom,
		int	hops,
		const std::vector< int > &	colours = {} )

Key of the rooted neighbourhood of atom.

colours is empty or one class per row (atom type, species); coloured vertices never match vertices of another colour.

◆ matchLibraries()

LibraryMatch topo::matchLibraries	(	const Rows &	rows,
		const std::vector< KeyLibrary > &	libs,
		int	maxRingSize = 7,
		const std::vector< int > &	colours = {} )

Match against libraries at several depths: an atom takes the label of the deepest library that holds its key, and a molecule whose wide neighbourhood is disturbed (a defect two bonds away, a jittered dense polymorph) still gets named by its inner shells.

depth records the hops that named each atom. Every library must share the method of this build and the colouring (colours empty or one per row); throws std::invalid_argument otherwise, or when two libraries share a depth.

◆ matchLibrary()

LibraryMatch topo::matchLibrary	(	const FrameFingerprint &	fp,
		const KeyLibrary &	lib )

Look every atom key of fp up in lib.

Throws std::invalid_argument when the methods, hop counts or colourings differ.

◆ readLibrary()

KeyLibrary topo::readLibrary ( const std::string & text )

◆ wlHash()

std::uint64_t topo::wlHash	(	const std::vector< std::vector< int > > &	adjacency,
		int	root,
		int	rounds,
		const std::vector< int > &	colours = {} )

Weisfeiler-Lehman refinement hash of a graph given by local adjacency lists; root (or -1) starts in its own colour; colours (empty or one integer per vertex, such as the atom type) seeds the initial colours.

rounds refinements.

◆ writeLibrary()

std::string topo::writeLibrary ( const KeyLibrary & lib )

Text form: a header line # method M hops H colours C (C is 0 or 1; a header without it means uncoloured), then key label lines.

Classes

Typedefs

Functions