indigox Namespace Reference

Namespace for all graph related functionality. More...

Namespaces
	algorithm
	graph
	test
	utils

Classes
class	_ElectronGraph
class	_NTDecomp
class	_PermutableGraph
class	_TDecomp
class	Angle
class	Athenaeum
	Athenaeum class for fragment storage in CherryPicker algorithm. More...
class	Atom
class	AtomIterator
class	Bond
class	Dihedral
class	ElectronOpt
class	Element
	Read only class for storing elemental information. More...
struct	ElnVertProp
class	FFAngle
class	FFAtom
class	FFBond
class	FFDihedral
class	Forcefield
class	Fragment
	Fragment class for CherryPicker parameterisation algorithm. More...
class	Molecule
struct	NTDVertProp
class	ParamAngle
class	ParamAtom
class	ParamBond
class	ParamDihedral
class	ParamMolecule
class	PeriodicTable
	Singleton class for storing and access elemental information. More...
struct	PermVertProp
class	Residue
struct	TDVertProp

Typedefs
typedef utils::Graph< ElnVertProp >	_ElnGraph
typedef utils::Graph< NTDVertProp, utils::NoProperty, utils::DirectedGraph >	_NTDGraph
typedef utils::Graph< PermVertProp >	_PermGraph
typedef utils::Graph< TDVertProp, utils::NoProperty, utils::UndirectedGraph >	_TDGraph
using	AngleType = FFAngle::Type
using	AtomStereo = indigox::Atom::Stereo
	Type for the stereochemistry enum of an atom. More...
using	BondOrder = indigox::Bond::Order
	Type for the order of a bond. More...
using	BondStereo = indigox::Bond::Stereo
	Type for the stereochemistry enum of a bond. More...
using	BondType = FFBond::Type
using	DihedralType = FFDihedral::Type
typedef std::shared_ptr< _ElectronGraph >	ElectronGraph
typedef std::vector< PermVertex >	ElimOrder
typedef _ElnGraph::EdgeType	ElnEdge
typedef _ElnGraph::EdgeIter	ElnEdgeIter
typedef _ElnGraph::EdgeIterPair	ElnEdgeIterPair
typedef _ElnGraph::NbrsIterPair	ElnNbrsIterPair
typedef _ElnGraph::NbrsIter	ElnNeighboursIter
typedef _ElnGraph::VertType	ElnVertex
typedef _ElnGraph::VertIter	ElnVertexIter
typedef _ElnGraph::VertIterPair	ElnVertIterPair
using	FFFamily = Forcefield::Family
using	FFParam = std::initializer_list< double >
	type for collection of parameter inputs More...
typedef std::shared_ptr< _NTDecomp >	NTDecomp
typedef _NTDGraph::EdgeType	NTDEdge
typedef _NTDGraph::EdgeBool	NTDEdgeBool
typedef _NTDGraph::EdgeIter	NTDEdgeIter
typedef _NTDGraph::EdgeIterPair	NTDEdgeIterPair
typedef _NTDGraph::NbrsIterPair	NTDNbrsIterPair
typedef _NTDGraph::NbrsIter	NTDNeighboursIter
typedef _NTDGraph::PredIter	NTDPredecessorsIter
typedef _NTDGraph::PredIterPair	NTDPredIterPair
typedef _NTDGraph::VertBool	NTDVertBool
typedef _NTDGraph::VertType	NTDVertex
typedef _NTDGraph::VertIter	NTDVertexIter
typedef _NTDGraph::VertIterPair	NTDVertIterPair
typedef _NTDGraph::VertTypePair	NTDVertPair
typedef _PermGraph::EdgeIterPair	PermEdgeIterPair
typedef _PermGraph::NbrsIter	PermNbrsIter
typedef _PermGraph::NbrsIterPair	PermNbrsIterPair
typedef std::shared_ptr< _PermutableGraph >	PermutableGraph
typedef _PermGraph::VertType	PermVertex
typedef _PermGraph::VertIter	PermVertIter
typedef _PermGraph::VertIterPair	PermVertIterPair
using	ResidueType = Residue::Type
using	sAthenaeum = std::shared_ptr< Athenaeum >
using	sFragment = std::shared_ptr< Fragment >
using	State = uint32_t
typedef std::shared_ptr< _TDecomp >	TDecomp
typedef _TDGraph::EdgeType	TDEdge
typedef _TDGraph::EdgeBool	TDEdgeBool
typedef _TDGraph::EdgeIter	TDEdgeIter
typedef _TDGraph::EdgeIterPair	TDEdgeIterPair
typedef _TDGraph::NbrsIterPair	TDNbrsIterPair
typedef _TDGraph::NbrsIter	TDNeighboursIter
typedef _TDGraph::PredIter	TDPredecessorsIter
typedef _TDGraph::PredIterPair	TDPredIterPair
typedef _TDGraph::VertBool	TDVertBool
typedef _TDGraph::VertType	TDVertex
typedef _TDGraph::VertIter	TDVertexIter
typedef _TDGraph::VertIterPair	TDVertIterPair
typedef _TDGraph::VertTypePair	TDVertPair
using	wAthenaeum = std::weak_ptr< Athenaeum >
using	wFragment = std::weak_ptr< Fragment >

Enumerations
enum	CalculatedData : uint8_t
enum	IteratorType

Functions
template<class Iter >
double	CalculateMean (Iter begin, Iter end)
	Calculate the mean of a range of numbers. More...
template<class RandomIter >
double	CalculateMedian (RandomIter begin, RandomIter end)
	Calculate the median of a range of numbers. More...
template<class Iter >
double	CalculateStandardDeviation (Iter begin, Iter end)
template<typename InputIter , typename T >
size_t	Combinations (InputIter first, InputIter last, size_t r, std::vector< std::vector< T >> &out)
Forcefield	GenerateGROMOS54A7 ()
const PeriodicTable &	GetPeriodicTable ()
Athenaeum	LoadAthenaeum (std::string path)
Molecule	LoadMolecule (std::string path)
std::ostream &	operator<< (std::ostream &os, const Dihedral &dhd)
std::ostream &	operator<< (std::ostream &, const Element &)
std::ostream &	operator<< (std::ostream &os, const PeriodicTable &pt)
	Print a PeriodicTable to an output stream. More...
std::ostream &	operator<< (std::ostream &os, BondType type)
std::ostream &	operator<< (std::ostream &os, AngleType type)
std::ostream &	operator<< (std::ostream &os, DihedralType type)
void	SaveAthenaeum (const Athenaeum &ath, std::string path)
void	SaveMolecule (const Molecule &mol, std::string path)

Detailed Description

Namespace for all graph related functionality.

utils namespace for useful utility functions

Typedef Documentation

_ElnGraph

typedef utils::Graph<ElnVertProp> _ElnGraph

_NTDGraph

typedef utils::Graph<NTDVertProp, utils::NoProperty, utils::DirectedGraph> _NTDGraph

_PermGraph

typedef utils::Graph<PermVertProp> _PermGraph

_TDGraph

typedef utils::Graph<TDVertProp, utils::NoProperty, utils::UndirectedGraph> _TDGraph

AngleType

using AngleType = FFAngle::Type

AtomStereo

using AtomStereo = indigox::Atom::Stereo

Type for the stereochemistry enum of an atom.

BondOrder

using BondOrder = indigox::Bond::Order

Type for the order of a bond.

BondStereo

using BondStereo = indigox::Bond::Stereo

Type for the stereochemistry enum of a bond.

BondType

using BondType = FFBond::Type

DihedralType

using DihedralType = FFDihedral::Type

ElectronGraph

typedef std::shared_ptr<_ElectronGraph> ElectronGraph

ElimOrder

typedef std::vector<PermVertex> ElimOrder

ElnEdge

typedef _ElnGraph::EdgeType ElnEdge

ElnEdgeIter

typedef _ElnGraph::EdgeIter ElnEdgeIter

ElnEdgeIterPair

typedef _ElnGraph::EdgeIterPair ElnEdgeIterPair

ElnNbrsIterPair

typedef _ElnGraph::NbrsIterPair ElnNbrsIterPair

ElnNeighboursIter

typedef _ElnGraph::NbrsIter ElnNeighboursIter

ElnVertex

typedef _ElnGraph::VertType ElnVertex

ElnVertexIter

typedef _ElnGraph::VertIter ElnVertexIter

ElnVertIterPair

typedef _ElnGraph::VertIterPair ElnVertIterPair

FFFamily

using FFFamily = Forcefield::Family

FFParam

using FFParam = std::initializer_list<double>

type for collection of parameter inputs

NTDecomp

typedef std::shared_ptr<_NTDecomp> NTDecomp

NTDEdge

typedef _NTDGraph::EdgeType NTDEdge

NTDEdgeBool

typedef _NTDGraph::EdgeBool NTDEdgeBool

NTDEdgeIter

typedef _NTDGraph::EdgeIter NTDEdgeIter

NTDEdgeIterPair

typedef _NTDGraph::EdgeIterPair NTDEdgeIterPair

NTDNbrsIterPair

typedef _NTDGraph::NbrsIterPair NTDNbrsIterPair

NTDNeighboursIter

typedef _NTDGraph::NbrsIter NTDNeighboursIter

NTDPredecessorsIter

typedef _NTDGraph::PredIter NTDPredecessorsIter

NTDPredIterPair

typedef _NTDGraph::PredIterPair NTDPredIterPair

NTDVertBool

typedef _NTDGraph::VertBool NTDVertBool

NTDVertex

typedef _NTDGraph::VertType NTDVertex

NTDVertexIter

typedef _NTDGraph::VertIter NTDVertexIter

NTDVertIterPair

typedef _NTDGraph::VertIterPair NTDVertIterPair

NTDVertPair

typedef _NTDGraph::VertTypePair NTDVertPair

PermEdgeIterPair

typedef _PermGraph::EdgeIterPair PermEdgeIterPair

PermNbrsIter

typedef _PermGraph::NbrsIter PermNbrsIter

PermNbrsIterPair

typedef _PermGraph::NbrsIterPair PermNbrsIterPair

PermutableGraph

typedef std::shared_ptr<_PermutableGraph> PermutableGraph

PermVertex

typedef _PermGraph::VertType PermVertex

PermVertIter

typedef _PermGraph::VertIter PermVertIter

PermVertIterPair

typedef _PermGraph::VertIterPair PermVertIterPair

ResidueType

using ResidueType = Residue::Type

sAthenaeum

using sAthenaeum = std::shared_ptr<Athenaeum>

sFragment

using sFragment = std::shared_ptr<Fragment>

State

using State = uint32_t

TDecomp

typedef std::shared_ptr<_TDecomp> TDecomp

TDEdge

typedef _TDGraph::EdgeType TDEdge

TDEdgeBool

typedef _TDGraph::EdgeBool TDEdgeBool

TDEdgeIter

typedef _TDGraph::EdgeIter TDEdgeIter

TDEdgeIterPair

typedef _TDGraph::EdgeIterPair TDEdgeIterPair

TDNbrsIterPair

typedef _TDGraph::NbrsIterPair TDNbrsIterPair

TDNeighboursIter

typedef _TDGraph::NbrsIter TDNeighboursIter

TDPredecessorsIter

typedef _TDGraph::PredIter TDPredecessorsIter

TDPredIterPair

typedef _TDGraph::PredIterPair TDPredIterPair

TDVertBool

typedef _TDGraph::VertBool TDVertBool

TDVertex

typedef _TDGraph::VertType TDVertex

TDVertexIter

typedef _TDGraph::VertIter TDVertexIter

TDVertIterPair

typedef _TDGraph::VertIterPair TDVertIterPair

TDVertPair

typedef _TDGraph::VertTypePair TDVertPair

wAthenaeum

using wAthenaeum = std::weak_ptr<Athenaeum>

wFragment

using wFragment = std::weak_ptr<Fragment>

Enumeration Type Documentation

CalculatedData

enum CalculatedData : uint8_t

strong

Enumerator
Formula
AnglePerception
DihedralPerception
ResiduePerception
ChargeGroupDetermination
CondensedGraph
Number

IteratorType

enum IteratorType

Enumerator
ATOM_NEIGHBOUR
BOND_ATOM
MOLECULE_ATOM
ATOM_BOND
MOLECULE_BOND
UNDEFINED

Function Documentation

CalculateMean()

double indigox::CalculateMean	(	Iter	begin,
		Iter	end
	)

Calculate the mean of a range of numbers.

Template Parameters

Iter	type of the iterator defining the range.

Parameters

begin,end

iterators defining the range.

Returns

the mean of the range.

Referenced by CalculateStandardDeviation().

CalculateMedian()

double indigox::CalculateMedian	(	RandomIter	begin,
		RandomIter	end
	)

Calculate the median of a range of numbers.

If the range has an odd length, the median is the middle item in the sorted range. If it has an even length, the median is the mean of the two central items. If the range is empty, the median is undefined.

Template Parameters

RandomIter

random access itertor defining the range.

Parameters

begin,end

iterators defining the range.

Returns

the median of the range.

Exceptions

std::runtime_error

if the range is empty.

CalculateStandardDeviation()

double indigox::CalculateStandardDeviation	(	Iter	begin,
		Iter	end
	)

Combinations()

size_t indigox::Combinations	(	InputIter	first,
		InputIter	last,
		size_t	r,
		std::vector< std::vector< T >> &	out
	)

GenerateGROMOS54A7()

Forcefield indigox::GenerateGROMOS54A7

(

)

54A7 version

GetPeriodicTable()

const PeriodicTable& indigox::GetPeriodicTable

(

)

LoadAthenaeum()

Athenaeum indigox::LoadAthenaeum

(

std::string

path

)

LoadMolecule()

Molecule indigox::LoadMolecule

(

std::string

path

)

operator<<() [1/6]

std::ostream& indigox::operator<<	(	std::ostream &	os,
		const Dihedral &	dhd
	)

operator<<() [2/6]

std::ostream& indigox::operator<<	(	std::ostream &	,
		const Element &
	)

operator<<() [3/6]

std::ostream& indigox::operator<<	(	std::ostream &	os,
		const PeriodicTable &	pt
	)

Print a PeriodicTable to an output stream.

Prints number of elements in the PeriodicTable.

Parameters

os	output stream to print to.
pt	PeriodicTable to print.

Returns

the output stream.

operator<<() [4/6]

std::ostream& indigox::operator<<	(	std::ostream &	os,
		BondType	type
	)

operator<<() [5/6]

std::ostream& indigox::operator<<	(	std::ostream &	os,
		AngleType	type
	)

operator<<() [6/6]

std::ostream& indigox::operator<<	(	std::ostream &	os,
		DihedralType	type
	)

SaveAthenaeum()

void indigox::SaveAthenaeum	(	const Athenaeum &	ath,
		std::string	path
	)

SaveMolecule()

void indigox::SaveMolecule	(	const Molecule &	mol,
		std::string	path
	)