#include <indigox/classes/atom.hpp>

Classes
struct	Impl

Public Types
using	AtomAngles = std::vector< Angle >
	Container for storing IXAngle references. More...

using	AtomBonds = std::vector< Bond >
	Container for storing Bond references. More...

using	AtomDihedrals = std::vector< Dihedral >
	Container for storing IXDihedral references. More...

enum	Stereo
	Enum for the different types of atom stereochemistry. More...

Public Member Functions
	Atom ()=default

	Atom (const Atom &)=default

	Atom (Atom &&)=default

	~ Atom ()=default

int32_t	AddImplicitHydrogen ()
	Add an implicit hydrogen. More...

const AtomAngles &	GetAngles () const

const AtomBonds &	GetBonds () const

int32_t	GetChargeGroupID () const

const AtomDihedrals &	GetDihedrals () const

const Element &	GetElement () const
	Element of the atom. More...

int32_t	GetFormalCharge () const
	Formal charge on the atom. More...

int64_t	GetID () const

int32_t	GetImplicitCount () const
	Get number of implicit hydrogens. More...

int64_t	GetIndex () const
	Get the index from the molecule. More...

const Molecule &	GetMolecule () const
	Molecule this atom is associated with. More...

const std::string &	GetName () const
	Atom name. More...

double	GetPartialCharge () const
	Partial atomic charge on the atom. More...

const Eigen::Vector3d &	GetPosition () const
	Vector of the atom's position. More...

int32_t	GetResidueID ()

std::string	GetResidueName ()

Stereo	GetStereochemistry () const
	Get the stereochemistry of the atom. More...

int64_t	GetTag () const
	Tag of the atom. More...

const FFAtom &	GetType () const
	Get the FF type of the atom. More...

double	GetX () const
	Atom x position. More...

double	GetY () const
	Atom y position. More...

double	GetZ () const
	Atom z position. More...

bool	HasType () const

int64_t	NumAngles () const
	Number of valid angles this atom is a part of. More...

int64_t	NumBonds () const
	Number of valid bonds this atom is part of. More...

int64_t	NumDihedrals () const
	Number of valid dihedrals this atom is a part of. More...

int32_t	NumHeavyAtomBonds () const

int32_t	NumHydrogenBonds () const

	operator bool () const

bool	operator!= (const Atom &atm) const

bool	operator< (const Atom &atm) const

bool	operator<= (const Atom &atm) const

Atom &	operator= (const Atom &)=default

Atom &	operator= (Atom &&)=default

bool	operator== (const Atom &atm) const

bool	operator> (const Atom &atm) const

bool	operator>= (const Atom &atm) const

int32_t	RemoveImplicitHydrogen ()
	Remove an implicit hydrogen. More...

void	SetChargeGroupID (int32_t id)

void	SetElement (const Element &e)
	Set the element of this atom. More...

void	SetElement (std::string e)
	Set the element of this atom. More...

void	SetElement (int32_t e)
	Set the element of this atom. More...

void	SetFormalCharge (int32_t q)
	Set the formal charge of this atom. More...

void	SetImplicitCount (int32_t h)
	Set the number of implicit hydrogens. More...

void	SetName (std::string n)
	Set the atom name. More...

void	SetPartialCharge (double q)
	Set the partial charge of this atom. More...

void	SetPosition (double x, double y, double z)
	Set the x, y and z positions. More...

void	SetStereochemistry (Stereo s)
	Set the stereochemistry of an atomic center. More...

void	SetTag (int32_t i)
	Set the tag of this atom. More...

void	SetType (const FFAtom &type)
	Set the FF type of the atom. More...

Friends
class	cereal::access
	Friendship allows IXAtom to be serialised. More...

class	indigox::Molecule
	Friendship allows IXMolecule to create new atoms. More...

std::ostream &	operator<< (std::ostream &os, const Atom &atm)

Member Typedef Documentation

◆ AtomAngles

using AtomAngles = std::vector<Angle>

Container for storing IXAngle references.

◆ AtomBonds

using AtomBonds = std::vector<Bond>

Container for storing Bond references.

◆ AtomDihedrals

using AtomDihedrals = std::vector<Dihedral>

Container for storing IXDihedral references.

Member Enumeration Documentation

◆ Stereo

enum Stereo

strong

Enum for the different types of atom stereochemistry.

Enumerator
UNDEFINED	No defined stereochemistry.
ACHIRAL	Defined as no stereochemistry.
R	Has R stereochemistry.
S	Has S stereochemistry.

Constructor & Destructor Documentation

◆ Atom() [1/3]

Atom ( )

default

◆ Atom() [2/3]

Atom ( const Atom & )

default

◆ Atom() [3/3]

Atom ( Atom && )

default

◆ ~ Atom()

~ Atom ( )

default

Member Function Documentation

◆ AddImplicitHydrogen()

int32_t AddImplicitHydrogen ( )

Add an implicit hydrogen.

Returns: the new number of implicit hydrogens in the atom.

◆ GetAngles()

const AtomAngles& GetAngles ( ) const

◆ GetBonds()

const AtomBonds& GetBonds ( ) const

◆ GetChargeGroupID()

int32_t GetChargeGroupID ( ) const

◆ GetDihedrals()

const AtomDihedrals& GetDihedrals ( ) const

◆ GetElement()

const Element& GetElement ( ) const

Element of the atom.

Returns: the element of this atom.

◆ GetFormalCharge()

int32_t GetFormalCharge ( ) const

Formal charge on the atom.

Returns: the formal charge on the atom.

◆ GetID()

int64_t GetID ( ) const

◆ GetImplicitCount()

int32_t GetImplicitCount ( ) const

Get number of implicit hydrogens.

Returns: the number of implicit hydrogens in the atom.

◆ GetIndex()

int64_t GetIndex ( ) const

Get the index from the molecule.

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

Returns: the index of the atom.

◆ GetMolecule()

const Molecule& GetMolecule ( ) const

Molecule this atom is associated with.

The returned shared_ptr is empty of the atom is not assigned to a valid molecule.

Returns: the molecule associated with this atom.

◆ GetName()

const std::string& GetName ( ) const

Atom name.

Returns: name of the atom.

◆ GetPartialCharge()

double GetPartialCharge ( ) const

Partial atomic charge on the atom.

Returns: the partial atomic charge.

◆ GetPosition()

const Eigen::Vector3d& GetPosition ( ) const

Vector of the atom's position.

Returns: the atoms position.

◆ GetResidueID()

int32_t GetResidueID ( )

◆ GetResidueName()

std::string GetResidueName ( )

◆ GetStereochemistry()

Stereo GetStereochemistry ( ) const

Get the stereochemistry of the atom.

Returns: the stereochemistry of the atom.

◆ GetTag()

int64_t GetTag ( ) const

Tag of the atom.

This value may be modified without warning. Use with caution. For a constant identifier to the atom, use IXAtom::GetUniqueID.

Returns: the tag assigned to the atom.

◆ GetType()

const FFAtom& GetType ( ) const

Get the FF type of the atom.

Returns: the force field type of the atom.

◆ GetX()

double GetX ( ) const

Atom x position.

Returns: the x coordinate of this atom.

◆ GetY()

double GetY ( ) const

Atom y position.

Returns: the y coordinate of this atom.

◆ GetZ()

double GetZ ( ) const

Atom z position.

Returns: the z coordinate of this atom.

◆ HasType()

bool HasType ( ) const

◆ NumAngles()

int64_t NumAngles ( ) const

Number of valid angles this atom is a part of.

Returns: the number of valid assigned angles.

◆ NumBonds()

int64_t NumBonds ( ) const

Number of valid bonds this atom is part of.

Returns: the number of valid assigned bonds.

◆ NumDihedrals()

int64_t NumDihedrals ( ) const

Number of valid dihedrals this atom is a part of.

Returns: the number of valid assigned dihedrals.

◆ NumHeavyAtomBonds()

int32_t NumHeavyAtomBonds ( ) const

◆ NumHydrogenBonds()

int32_t NumHydrogenBonds ( ) const

◆ operator bool()

operator bool ( ) const

inline

◆ operator!=()

bool operator!= ( const Atom & atm ) const

inline

◆ operator<()

bool operator< ( const Atom & atm ) const

◆ operator<=()

bool operator<= ( const Atom & atm ) const

inline

◆ operator=() [1/2]

Atom& operator= ( const Atom & )

default

◆ operator=() [2/2]

Atom& operator= ( Atom && )

default

◆ operator==()

bool operator== ( const Atom & atm ) const

◆ operator>()

bool operator> ( const Atom & atm ) const

◆ operator>=()

bool operator>= ( const Atom & atm ) const

inline

◆ RemoveImplicitHydrogen()

int32_t RemoveImplicitHydrogen ( )

Remove an implicit hydrogen.

If GetImplicitCount() == 0, no hydrogen is removed.

Returns: the new number of implicit hydrogens in the atom.

◆ SetChargeGroupID()

void SetChargeGroupID ( int32_t id )

◆ SetElement() [1/3]

void SetElement ( const Element & e )

Set the element of this atom.

Parameters

e	the element to set to.

◆ SetElement() [2/3]

void SetElement ( std::string e )

Set the element of this atom.

Parameters

e	the name or atomic symbol of the element to set.

◆ SetElement() [3/3]

void SetElement ( int32_t e )

Set the element of this atom.

Parameters

e	the atomic number of the element to set.

◆ SetFormalCharge()

void SetFormalCharge ( int32_t q )

Set the formal charge of this atom.

Parameters

q	the formal charge value to set.

◆ SetImplicitCount()

void SetImplicitCount ( int32_t h )

Set the number of implicit hydrogens.

Parameters

h	the number of implicit hydrogens to set.

◆ SetName()

void SetName ( std::string n )

Set the atom name.

Parameters

n	name to set.

◆ SetPartialCharge()

void SetPartialCharge ( double q )

Set the partial charge of this atom.

Parameters

q	the partial charge value to set.

◆ SetPosition()

void SetPosition	(	double	x,
		double	y,
		double	z
	)

Set the x, y and z positions.

Parameters

x,y,z position to set.

◆ SetStereochemistry()

void SetStereochemistry ( Stereo s )

Set the stereochemistry of an atomic center.

Parameters

s	the stereochemistry to set.

◆ SetTag()

void SetTag ( int32_t i )

Set the tag of this atom.

The tag of an atom should not be considered stable. Use with caution.

Parameters

i	the tag to set.

◆ SetType()

void SetType ( const FFAtom & type )

Set the FF type of the atom.

Parameters

type	the type to set.

Friends And Related Function Documentation

◆ cereal::access

friend class cereal::access

friend

Friendship allows IXAtom to be serialised.

◆ indigox::Molecule

friend class indigox::Molecule

friend

Friendship allows IXMolecule to create new atoms.

◆ operator<<

std::ostream& operator<<	(	std::ostream &	os,
		const Atom &	atm
	)

friend

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

include/indigox/classes/atom.hpp

Classes

Public Types

Public Member Functions

Friends

Member Typedef Documentation

◆ AtomAngles

◆ AtomBonds

◆ AtomDihedrals

Member Enumeration Documentation

◆ Stereo

Constructor & Destructor Documentation

◆ Atom() [1/3]

◆ Atom() [2/3]

◆ Atom() [3/3]

◆ ~ Atom()

Member Function Documentation

◆ AddImplicitHydrogen()

◆ GetAngles()

◆ GetBonds()

◆ GetChargeGroupID()

◆ GetDihedrals()

◆ GetElement()

◆ GetFormalCharge()

◆ GetID()

◆ GetImplicitCount()

◆ GetIndex()

◆ GetMolecule()

◆ GetName()

◆ GetPartialCharge()

◆ GetPosition()

◆ GetResidueID()

◆ GetResidueName()

◆ GetStereochemistry()

◆ GetTag()

◆ GetType()

◆ GetX()

◆ GetY()

◆ GetZ()

◆ HasType()

◆ NumAngles()

◆ NumBonds()

◆ NumDihedrals()

◆ NumHeavyAtomBonds()

◆ NumHydrogenBonds()

◆ operator bool()

◆ operator!=()

◆ operator<()

◆ operator<=()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ operator>()

◆ operator>=()

◆ RemoveImplicitHydrogen()

◆ SetChargeGroupID()

◆ SetElement() [1/3]

◆ SetElement() [2/3]

◆ SetElement() [3/3]

◆ SetFormalCharge()

◆ SetImplicitCount()

◆ SetName()

◆ SetPartialCharge()

◆ SetPosition()

◆ SetStereochemistry()

◆ SetTag()

◆ SetType()

Friends And Related Function Documentation

◆ cereal::access

◆ indigox::Molecule

◆ operator<<