#include <atom.h>

Collaboration diagram for votca::xtp::Atom:

[legend]

Classes
struct	data

Public Member Functions
	Atom (Index resnr, std::string md_atom_name, Index atom_id, Eigen::Vector3d pos, std::string element)
	Atom (Index atom_id, std::string element, Eigen::Vector3d pos)
	Atom (data &d)
Index	getId () const
const std::string &	getName () const
std::string	getElement () const
Index	getResnr () const
void	setResnr (Index resnr)
void	Translate (const Eigen::Vector3d &shift)
void	Rotate (const Eigen::Matrix3d &R, const Eigen::Vector3d &refPos)
const Eigen::Vector3d &	getPos () const
void	setPos (const Eigen::Vector3d &r)
bool	hasExternalBond () const
const Eigen::Vector3d &	getExternalBondDirection () const
Index	getExternalBondPartnerAtomId () const
void	setExternalBondDirection (const Eigen::Vector3d &dir, Index partner_atom_id)
Index	getExternalBondPartnerSegmentId () const
void	setExternalBondPartnerSegmentId (Index segment_id)
const Index *	getBondedPartnerIds () const
void	AddBondedPartner (Index partner_id)
std::string	identify () const
void	WriteData (data &d) const
void	ReadData (const data &d)

Static Public Member Functions
static std::string	GetElementFromString (const std::string &MDName)
static void	SetupCptTable (CptTable &table)

Static Public Attributes
static constexpr Index	kMaxBondedPartners = 4

Private Attributes
Index	id_ = -1
std::string	name_ = ""
std::string	element_ = ""
Index	resnr_ = -1
Eigen::Vector3d	pos_ = Eigen::Vector3d::Zero()
bool	has_external_bond_ = false
Eigen::Vector3d	external_bond_direction_ = Eigen::Vector3d::Zero()
Index	external_bond_partner_atom_id_ = -1
Index	external_bond_partner_segment_id_ = -1
Index	bonded_partner_ids_ [kMaxBondedPartners] = {-1, -1, -1, -1}

Friends
std::ostream &	operator<< (std::ostream &out, const Atom &atom)

Detailed Description

Definition at line 35 of file atom.h.

Constructor & Destructor Documentation

◆ Atom() [1/3]

votca::xtp::Atom::Atom	(	Index	resnr,
		std::string	md_atom_name,
		Index	atom_id,
		Eigen::Vector3d	pos,
		std::string	element )

Definition at line 30 of file atom.cc.

◆ Atom() [2/3]

votca::xtp::Atom::Atom	(	Index	atom_id,
		std::string	element,
		Eigen::Vector3d	pos )

Definition at line 68 of file atom.cc.

◆ Atom() [3/3]

votca::xtp::Atom::Atom ( data & d )

inline

Definition at line 66 of file atom.h.

Member Function Documentation

◆ AddBondedPartner()

void votca::xtp::Atom::AddBondedPartner ( Index partner_id )

inline

Definition at line 168 of file atom.h.

◆ getBondedPartnerIds()

const Index * votca::xtp::Atom::getBondedPartnerIds ( ) const

inline

Definition at line 167 of file atom.h.

◆ getElement()

std::string votca::xtp::Atom::getElement ( ) const

inline

Definition at line 72 of file atom.h.

◆ GetElementFromString()

std::string votca::xtp::Atom::GetElementFromString ( const std::string & MDName )

static

Definition at line 71 of file atom.cc.

◆ getExternalBondDirection()

const Eigen::Vector3d & votca::xtp::Atom::getExternalBondDirection ( ) const

inline

Definition at line 114 of file atom.h.

◆ getExternalBondPartnerAtomId()

Index votca::xtp::Atom::getExternalBondPartnerAtomId ( ) const

inline

Definition at line 117 of file atom.h.

◆ getExternalBondPartnerSegmentId()

Index votca::xtp::Atom::getExternalBondPartnerSegmentId ( ) const

inline

Definition at line 141 of file atom.h.

◆ getId()

Index votca::xtp::Atom::getId ( ) const

inline

Definition at line 70 of file atom.h.

◆ getName()

const std::string & votca::xtp::Atom::getName ( ) const

inline

Definition at line 71 of file atom.h.

◆ getPos()

const Eigen::Vector3d & votca::xtp::Atom::getPos ( ) const

inline

Definition at line 81 of file atom.h.

◆ getResnr()

Index votca::xtp::Atom::getResnr ( ) const

inline

Definition at line 74 of file atom.h.

◆ hasExternalBond()

bool votca::xtp::Atom::hasExternalBond ( ) const

inline

Definition at line 113 of file atom.h.

◆ identify()

std::string votca::xtp::Atom::identify ( ) const

inline

Definition at line 180 of file atom.h.

◆ ReadData()

void votca::xtp::Atom::ReadData ( const data & d )

Definition at line 143 of file atom.cc.

◆ Rotate()

void votca::xtp::Atom::Rotate	(	const Eigen::Matrix3d &	R,
		const Eigen::Vector3d &	refPos )

Definition at line 82 of file atom.cc.

◆ setExternalBondDirection()

void votca::xtp::Atom::setExternalBondDirection	(	const Eigen::Vector3d &	dir,
		Index	partner_atom_id )

inline

Definition at line 120 of file atom.h.

◆ setExternalBondPartnerSegmentId()

void votca::xtp::Atom::setExternalBondPartnerSegmentId ( Index segment_id )

inline

Definition at line 144 of file atom.h.

◆ setPos()

void votca::xtp::Atom::setPos ( const Eigen::Vector3d & r )

inline

Definition at line 82 of file atom.h.

◆ setResnr()

void votca::xtp::Atom::setResnr ( Index resnr )

inline

Definition at line 76 of file atom.h.

◆ SetupCptTable()

void votca::xtp::Atom::SetupCptTable ( CptTable & table )

static

Definition at line 88 of file atom.cc.

◆ Translate()

void votca::xtp::Atom::Translate ( const Eigen::Vector3d & shift )

inline

Definition at line 77 of file atom.h.

◆ WriteData()

void votca::xtp::Atom::WriteData ( data & d ) const

Definition at line 125 of file atom.cc.

◆ operator<<

std::ostream & operator<<	(	std::ostream &	out,
		const Atom &	atom )

friend

Definition at line 182 of file atom.h.

Member Data Documentation

◆ bonded_partner_ids_

Index votca::xtp::Atom::bonded_partner_ids_[kMaxBondedPartners] = {-1, -1, -1, -1}

private

Definition at line 207 of file atom.h.

◆ element_

std::string votca::xtp::Atom::element_ = ""

private

Definition at line 200 of file atom.h.

◆ external_bond_direction_

Eigen::Vector3d votca::xtp::Atom::external_bond_direction_ = Eigen::Vector3d::Zero()

private

Definition at line 204 of file atom.h.

◆ external_bond_partner_atom_id_

Index votca::xtp::Atom::external_bond_partner_atom_id_ = -1

private

Definition at line 205 of file atom.h.

◆ external_bond_partner_segment_id_

Index votca::xtp::Atom::external_bond_partner_segment_id_ = -1

private

Definition at line 206 of file atom.h.

◆ has_external_bond_

bool votca::xtp::Atom::has_external_bond_ = false

private

Definition at line 203 of file atom.h.

◆ id_

Index votca::xtp::Atom::id_ = -1

private

Definition at line 197 of file atom.h.

◆ kMaxBondedPartners

Index votca::xtp::Atom::kMaxBondedPartners = 4

staticconstexpr

Definition at line 44 of file atom.h.

◆ name_

std::string votca::xtp::Atom::name_ = ""

private

Definition at line 198 of file atom.h.

◆ pos_

Eigen::Vector3d votca::xtp::Atom::pos_ = Eigen::Vector3d::Zero()

private

Definition at line 202 of file atom.h.

◆ resnr_

Index votca::xtp::Atom::resnr_ = -1

private

Definition at line 201 of file atom.h.

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

xtp/include/votca/xtp/atom.h
xtp/src/libxtp/atom.cc

Classes

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ Atom() [1/3]

◆ Atom() [2/3]

◆ Atom() [3/3]

Member Function Documentation

◆ AddBondedPartner()

◆ getBondedPartnerIds()

◆ getElement()

◆ GetElementFromString()

◆ getExternalBondDirection()

◆ getExternalBondPartnerAtomId()

◆ getExternalBondPartnerSegmentId()

◆ getId()

◆ getName()

◆ getPos()

◆ getResnr()

◆ hasExternalBond()

◆ identify()

◆ ReadData()

◆ Rotate()

◆ setExternalBondDirection()

◆ setExternalBondPartnerSegmentId()

◆ setPos()

◆ setResnr()

◆ SetupCptTable()

◆ Translate()

◆ WriteData()

Friends And Related Symbol Documentation

◆ operator<<

Member Data Documentation

◆ bonded_partner_ids_

◆ element_

◆ external_bond_direction_

◆ external_bond_partner_atom_id_

◆ external_bond_partner_segment_id_

◆ has_external_bond_

◆ id_

◆ kMaxBondedPartners

◆ name_

◆ pos_

◆ resnr_