votca::csg::BaseBead Class Reference

information about a base bead More...

#include <basebead.h>

Inheritance diagram for votca::csg::BaseBead:

Collaboration diagram for votca::csg::BaseBead:

Public Member Functions
virtual	~BaseBead ()=default
Index	getId () const noexcept
	Gets the id of the bead.
void	setId (const Index &id) noexcept
	Sets the id of the bead.
std::string	getName () const
	Gets the name of the bead.
void	setName (std::string name)
	Sets the name of the bead.
void	setMoleculeId (const Index &molecule_id) noexcept
	assign the bead to a molecule with the provided id
Index	getMoleculeId () const noexcept
	Get the id of the molecule the bead is a part of, if the molecule id has not been set return topology_constants::unassigned_molecule_id.
virtual const std::string	getType () const noexcept
virtual void	setType (const std::string &type) noexcept
std::string	getElement () const noexcept
	Returns the element type of the bead.
virtual const double &	getMass () const noexcept
virtual void	setMass (const double &m) noexcept
virtual void	setPos (const Eigen::Vector3d &bead_position)
virtual const Eigen::Vector3d &	getPos () const
virtual Eigen::Vector3d &	Pos ()
virtual const Eigen::Vector3d &	Pos () const
bool	HasPos () const noexcept
void	HasPos (const bool &true_or_false) noexcept

Protected Member Functions
	BaseBead ()=default

Protected Attributes
std::string	type_ = tools::topology_constants::unassigned_bead_type
Index	id_ = tools::topology_constants::unassigned_residue_id
Index	molecule_id_ = tools::topology_constants::unassigned_molecule_id
std::string	element_symbol_ = tools::topology_constants::unassigned_element
TOOLS::Name	name_
double	mass_ = 0.0
Eigen::Vector3d	bead_position_
bool	bead_position_set_ = false

Detailed Description

information about a base bead

The Base Bead class describes the core functionality of an atom or a coarse grained bead. It stores information like the id, the name, the mass, the charge and the residue it belongs to and the position

Definition at line 44 of file basebead.h.

Constructor & Destructor Documentation

~BaseBead()

virtual votca::csg::BaseBead::~BaseBead ( )

virtualdefault

destructor

BaseBead()

votca::csg::BaseBead::BaseBead ( )

protecteddefault

Member Function Documentation

getElement()

std::string votca::csg::BaseBead::getElement ( ) const

inlinenoexcept

Returns the element type of the bead.

Returns

either the element symbol i.e. "Si" for silcon or unassigned if it has not been specified.

Definition at line 98 of file basebead.h.

getId()

Index votca::csg::BaseBead::getId ( ) const

inlinenoexcept

Gets the id of the bead.

Definition at line 52 of file basebead.h.

getMass()

virtual const double & votca::csg::BaseBead::getMass ( ) const

inlinevirtualnoexcept

get the mass of the base bead

Returns

- base bead mass

Definition at line 104 of file basebead.h.

getMoleculeId()

Index votca::csg::BaseBead::getMoleculeId ( ) const

inlinenoexcept

Get the id of the molecule the bead is a part of, if the molecule id has not been set return topology_constants::unassigned_molecule_id.

Returns

Definition at line 78 of file basebead.h.

getName()

std::string votca::csg::BaseBead::getName ( ) const

inline

Gets the name of the bead.

Definition at line 58 of file basebead.h.

getPos()

const Eigen::Vector3d & votca::csg::BaseBead::getPos ( ) const

inlinevirtual

get the position of the base bead

Returns

base bead position

Definition at line 166 of file basebead.h.

getType()

virtual const std::string votca::csg::BaseBead::getType ( ) const

inlinevirtualnoexcept

get the bead type

Returns

const string

Definition at line 84 of file basebead.h.

HasPos() [1/2]

bool votca::csg::BaseBead::HasPos ( ) const

inlinenoexcept

does this configuration store positions?

Definition at line 139 of file basebead.h.

HasPos() [2/2]

void votca::csg::BaseBead::HasPos ( const bool & true_or_false )

inlinenoexcept

set has position to true

Definition at line 142 of file basebead.h.

Pos() [1/2]

virtual Eigen::Vector3d & votca::csg::BaseBead::Pos ( )

inlinevirtual

direct access (read/write) to the position of the base bead

Returns

reference to position

Definition at line 128 of file basebead.h.

Pos() [2/2]

virtual const Eigen::Vector3d & votca::csg::BaseBead::Pos ( ) const

inlinevirtual

Definition at line 133 of file basebead.h.

setId()

void votca::csg::BaseBead::setId ( const Index & id )

inlinenoexcept

Sets the id of the bead.

Definition at line 55 of file basebead.h.

setMass()

virtual void votca::csg::BaseBead::setMass ( const double & m )

inlinevirtualnoexcept

set the mass of the base bead

Parameters

m	- base bead mass

Definition at line 110 of file basebead.h.

setMoleculeId()

void votca::csg::BaseBead::setMoleculeId ( const Index & molecule_id )

inlinenoexcept

assign the bead to a molecule with the provided id

Parameters

molecule_id

Definition at line 68 of file basebead.h.

setName()

void votca::csg::BaseBead::setName ( std::string name )

inline

Sets the name of the bead.

Definition at line 61 of file basebead.h.

setPos()

void votca::csg::BaseBead::setPos ( const Eigen::Vector3d & bead_position )

inlinevirtual

set the position of the base bead

Parameters

bead_position

- base bead position

Definition at line 161 of file basebead.h.

setType()

virtual void votca::csg::BaseBead::setType ( const std::string & type )

inlinevirtualnoexcept

set the bead type

Parameters

type	bead type object

Definition at line 90 of file basebead.h.

Member Data Documentation

bead_position_

Eigen::Vector3d votca::csg::BaseBead::bead_position_

protected

Definition at line 156 of file basebead.h.

bead_position_set_

bool votca::csg::BaseBead::bead_position_set_ = false

protected

Definition at line 158 of file basebead.h.

element_symbol_

std::string votca::csg::BaseBead::element_symbol_ = tools::topology_constants::unassigned_element

protected

Definition at line 152 of file basebead.h.

id_

Index votca::csg::BaseBead::id_ = tools::topology_constants::unassigned_residue_id

protected

Definition at line 150 of file basebead.h.

mass_

double votca::csg::BaseBead::mass_ = 0.0

protected

Definition at line 155 of file basebead.h.

molecule_id_

Index votca::csg::BaseBead::molecule_id_ = tools::topology_constants::unassigned_molecule_id

protected

Definition at line 151 of file basebead.h.

name_

TOOLS::Name votca::csg::BaseBead::name_

protected

Definition at line 153 of file basebead.h.

type_

std::string votca::csg::BaseBead::type_ = tools::topology_constants::unassigned_bead_type

protected

Definition at line 149 of file basebead.h.

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

• csg/include/votca/csg/basebead.h