Fragment class for CherryPicker parameterisation algorithm. More...

#include <indigox/classes/athenaeum.hpp>

Public Types
using	AngType = stdx::triple< AtmType >

using	AtmType = graph::MGVertex

using	BndType = std::pair< AtmType, AtmType >

using	DhdType = stdx::quad< AtmType >

enum	OverlapType
	Type of overlapping vertex. More...

using	OverlapVertex = std::pair< OverlapType, graph::CMGVertex >
	Type used to match an overlap vertex to its type of overlap. More...

using	Vert = graph::MGVertex

Public Member Functions
	Fragment (const graph::MolecularGraph &G, std::vector< graph::MGVertex > &frag, std::vector< graph::MGVertex > &overlap)
	Normal constructor. More...

	Fragment (const Molecule &mol, std::vector< Atom > &frag, std::vector< Atom > &overlap)

const std::vector< AngType > &	GetAngles () const

const std::vector< AtmType > &	GetAtoms () const

const std::vector< BndType > &	GetBonds () const

const std::vector< DhdType > &	GetDihedrals () const

const std::vector< graph::CMGVertex > &	GetFragment () const

const graph::CondensedMolecularGraph &	GetGraph () const

const std::vector< OverlapVertex > &	GetOverlap () const

const boost::dynamic_bitset &	GetSupersets () const

bool	IsFragmentVertex (const graph::CMGVertex &v) const

bool	IsOverlapVertex (const graph::CMGVertex &v) const

size_t	Size () const

Friends
class	Athenaeum

class	cereal::access

Detailed Description

Fragment class for CherryPicker parameterisation algorithm.

Member Typedef Documentation

◆ AngType

using AngType = stdx::triple<AtmType>

◆ AtmType

using AtmType = graph::MGVertex

◆ BndType

using BndType = std::pair<AtmType, AtmType>

◆ DhdType

using DhdType = stdx::quad<AtmType>

◆ OverlapVertex

using OverlapVertex = std::pair<OverlapType, graph::CMGVertex>

Type used to match an overlap vertex to its type of overlap.

◆ Vert

using Vert = graph::MGVertex

Member Enumeration Documentation

◆ OverlapType

enum OverlapType

strong

Type of overlapping vertex.

Each vertex of an overlap is given a type. This is to enable more detailed isomorphism matching methods to be used when matching.

Enumerator
GenericOverlap

Constructor & Destructor Documentation

◆ Fragment() [1/2]

Fragment	(	const graph::MolecularGraph &	G,
		std::vector< graph::MGVertex > &	frag,
		std::vector< graph::MGVertex > &	overlap
	)

Normal constructor.

Constructs a fragment of the given graph from the combined fragment and overlap vertices.

Parameters

G	the graph to generate fragment from.
frag	the vertices of G that are part of the fragment.
overlap	the vertices of G that are part of the overlap region.

◆ Fragment() [2/2]

Fragment	(	const Molecule &	mol,
		std::vector< Atom > &	frag,
		std::vector< Atom > &	overlap
	)

Member Function Documentation

◆ GetAngles()

const std::vector<AngType>& GetAngles ( ) const

◆ GetAtoms()

const std::vector<AtmType>& GetAtoms ( ) const

◆ GetBonds()

const std::vector<BndType>& GetBonds ( ) const

◆ GetDihedrals()

const std::vector<DhdType>& GetDihedrals ( ) const

◆ GetFragment()

const std::vector<graph::CMGVertex>& GetFragment ( ) const

◆ GetGraph()

const graph::CondensedMolecularGraph& GetGraph ( ) const

◆ GetOverlap()

const std::vector<OverlapVertex>& GetOverlap ( ) const

◆ GetSupersets()

const boost::dynamic_bitset& GetSupersets ( ) const

◆ IsFragmentVertex()

bool IsFragmentVertex ( const graph::CMGVertex & v ) const

◆ IsOverlapVertex()

bool IsOverlapVertex ( const graph::CMGVertex & v ) const

◆ Size()

size_t Size ( ) const

Friends And Related Function Documentation

◆ Athenaeum

friend class Athenaeum

friend

◆ cereal::access

friend class cereal::access