Bond Class Reference

#include <indigox/classes/bond.hpp>

Classes
struct	Impl

Public Types
using	BondAtoms = std::array< Atom, 2 >
	Container for storing Atom references assigned to an Bond. More...
enum	Order
	Enum for the different possible bond orders. More...
enum	Stereo
	Enum for the different possible bond stereochemistry states. More...

Public Member Functions
	Bond ()=default
	Bond (const Bond &)=default
	Bond (Bond &&)=default
	~ Bond ()=default
const BondAtoms &	GetAtoms () const
	Get the atoms of the bond. More...
int64_t	GetID () const
int64_t	GetIndex () const
	Get the index from the molecule. More...
const Molecule &	GetMolecule () const
	Molecule this bond is associated with. More...
Order	GetOrder () const
	Get the bond order of the bond. More...
Stereo	GetStereochemistry () const
	Get the stereochemistry of the bond. More...
int64_t	GetTag () const
	Tag of the bond. More...
const FFBond &	GetType () const
	Get the type of the bond. More...
bool	HasType () const
bool	IsAmideBond () const
bool	IsCarbonylBond () const
constexpr int64_t	NumAtoms () const
	Number of atoms this bond is between. More...
	operator bool () const
bool	operator!= (const Bond &bnd) const
bool	operator< (const Bond &bnd) const
bool	operator<= (const Bond &bnd) const
Bond &	operator= (const Bond &)=default
Bond &	operator= (Bond &&)=default
bool	operator== (const Bond &bnd) const
bool	operator> (const Bond &bnd) const
bool	operator>= (const Bond &bnd) const
void	SetOrder (Order order)
	Set the bond order. More...
void	SetStereochemistry (Stereo stereo)
	Set the stereochemistry of the bond. More...
void	SetTag (int64_t tag)
	Set the tag of this bond. More...
void	SetType (const FFBond &type)
	Set the type of the bond. More...

Friends
class	cereal::access
	Friendship allows serialisation. More...
class	indigox::Molecule
	Friendship allows IXMolecule to create new bonds. More...
std::ostream &	operator<< (std::ostream &os, const Bond &bnd)

Member Typedef Documentation

BondAtoms

using BondAtoms = std::array<Atom, 2>

Container for storing Atom references assigned to an Bond.

Member Enumeration Documentation

Order

enum Order

strong

Enum for the different possible bond orders.

Enumerator
UNDEFINED	No defined bond order.
SINGLE	Bond order of 1.
DOUBLE	Bond order of 2.
TRIPLE	Bond order of 3.
QUADRUPLE	Bond order of 4.
AROMATIC	Aromatic bond.
ONEANDAHALF	Non-aromatic bond order of 1.5.
TWOANDAHALF	Bond order of 2.5.

Stereo

enum Stereo

strong

Enum for the different possible bond stereochemistry states.

Enumerator
UNDEFINED	No defined stereochemistry.
NONE	Defined as no stereochemistry.
E	E isomer.
Z	Z isomer.

Constructor & Destructor Documentation

Bond() [1/3]

Bond ( )

default

Bond() [2/3]

Bond ( const Bond &  )

default

Bond() [3/3]

Bond ( Bond &&  )

default

~ Bond()

~ Bond ( )

default

Member Function Documentation

GetAtoms()

const BondAtoms& GetAtoms

(

)

const

Get the atoms of the bond.

Returns

pair of the atoms of the bond.

GetID()

int64_t GetID

(

)

const

GetIndex()

int64_t GetIndex

(

)

const

Get the index from the molecule.

Calculates the index of the bond in the container of bonds of the molecule it is a part of. If the molecule is dead, the index returned is the tag of the bond.

Returns

the index of the bond.

GetMolecule()

const Molecule& GetMolecule

(

)

const

Molecule this bond is associated with.

The returned shared_ptr is empty if the bond is not assigned to a valid molecule.

Returns

the molecule associated with this bond.

GetOrder()

Order GetOrder

(

)

const

Get the bond order of the bond.

Returns

the bond order.

Todo:

Obtain order based on molecule data.

GetStereochemistry()

Stereo GetStereochemistry

(

)

const

Get the stereochemistry of the bond.

Returns

the stereochemistry of the bond.

Todo:

Obtain stereochemistry based on molecule data.

GetTag()

int64_t GetTag

(

)

const

Tag of the bond.

This value may be modified without warning. Use with caution. For a constant identifier to the bond, use IXBond::GetUniqeID().

Returns

the tag assigned to the bond.

GetType()

const FFBond& GetType

(

)

const

Get the type of the bond.

Returns

the type of the bond.

HasType()

bool HasType

(

)

const

IsAmideBond()

bool IsAmideBond

(

)

const

IsCarbonylBond()

bool IsCarbonylBond

(

)

const

NumAtoms()

constexpr int64_t NumAtoms ( ) const

inline

Number of atoms this bond is between.

Returns

2.

operator bool()

operator bool ( ) const

inline

operator!=()

bool operator!= ( const Bond &  bnd ) const

inline

operator<()

bool operator<

(

const Bond &

bnd

)

const

operator<=()

bool operator<= ( const Bond &  bnd ) const

inline

operator=() [1/2]

Bond& operator= ( Bond &&  )

default

operator=() [2/2]

Bond& operator= ( const Bond &  )

default

operator==()

bool operator==

(

const Bond &

bnd

)

const

operator>()

bool operator>

(

const Bond &

bnd

)

const

operator>=()

bool operator>= ( const Bond &  bnd ) const

inline

SetOrder()

void SetOrder

(

Order

order

)

Set the bond order.

Parameters

order

the bond order to set.

SetStereochemistry()

void SetStereochemistry

(

Stereo

stereo

)

Set the stereochemistry of the bond.

Parameters

stereo

the stereochemistry to set.

SetTag()

void SetTag

(

int64_t

tag

)

Set the tag of this bond.

The tag of a bond should not be considered stable. Use with caution.

Parameters

tag	the tag to set.

SetType()

void SetType

(

const FFBond &

type

)

Set the type of the bond.

Parameters

type	the type of bond to set.

Friends And Related Function Documentation

cereal::access

friend class cereal::access

friend

Friendship allows serialisation.

indigox::Molecule

friend class indigox::Molecule

friend

Friendship allows IXMolecule to create new bonds.

operator<<

std::ostream& operator<< ( std::ostream &  os, const Bond &  bnd  )

friend

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The documentation for this class was generated from the following file:

• include/indigox/classes/bond.hpp