votca::csg::Molecule Class Reference

information about molecules More...

#include <molecule.h>

Collaboration diagram for votca::csg::Molecule:

Public Member Functions
Index	getId () const
	get the molecule ID
const std::string &	getName () const
	get the name of the molecule
void	setName (const std::string &name)
	set the name of the molecule
void	AddBead (Bead *bead, const std::string &name)
	Add a bead to the molecule.
Bead *	getBead (Index bead)
	get the id of a bead in the molecule
const Bead *	getBead (Index bead) const
Index	getBeadId (Index bead) const
Index	getBeadIdByName (const std::string &name) const
Index	BeadCount () const
	get the number of beads in the molecule
const std::vector< Bead * > &	Beads () const
std::vector< Bead * > &	Beads ()
Index	getBeadByName (const std::string &name) const
	find a bead by it's name
std::string	getBeadName (const Index bead)
const std::string &	getBeadName (const Index bead) const
void	AddInteraction (Interaction *ic)
	Add an interaction to the molecule.
std::vector< Interaction * >	Interactions ()
const std::vector< Interaction * > &	Interactions () const

Private Member Functions
	Molecule (Index id, std::string name)
	constructor

Private Attributes
std::map< std::string, Index >	beadmap_
std::vector< Interaction * >	interactions_
Index	id_
std::string	name_
std::vector< Bead * >	beads_
std::vector< std::string >	bead_names_

Friends
class	Topology

Detailed Description

information about molecules

The Molecule class stores which beads belong to a molecule. The organization of beads into molecules is needed for the CG mapping.

Todo

sort atoms in molecule

Definition at line 45 of file molecule.h.

Constructor & Destructor Documentation

Molecule()

votca::csg::Molecule::Molecule ( Index id, std::string name )

inlineprivate

constructor

Definition at line 99 of file molecule.h.

Member Function Documentation

AddBead()

void votca::csg::Molecule::AddBead	(	Bead *	bead,
		const std::string &	name )

Add a bead to the molecule.

Definition at line 29 of file molecule.cc.

AddInteraction()

void votca::csg::Molecule::AddInteraction ( Interaction * ic )

inline

Add an interaction to the molecule.

Definition at line 77 of file molecule.h.

BeadCount()

Index votca::csg::Molecule::BeadCount ( ) const

inline

get the number of beads in the molecule

Definition at line 65 of file molecule.h.

Beads() [1/2]

std::vector< Bead * > & votca::csg::Molecule::Beads ( )

inline

Definition at line 68 of file molecule.h.

Beads() [2/2]

const std::vector< Bead * > & votca::csg::Molecule::Beads ( ) const

inline

Definition at line 67 of file molecule.h.

getBead() [1/2]

Bead * votca::csg::Molecule::getBead ( Index bead )

inline

get the id of a bead in the molecule

Definition at line 59 of file molecule.h.

getBead() [2/2]

const Bead * votca::csg::Molecule::getBead ( Index bead ) const

inline

Definition at line 60 of file molecule.h.

getBeadByName()

Index votca::csg::Molecule::getBeadByName

(

const std::string &

name

)

const

find a bead by it's name

Definition at line 37 of file molecule.cc.

getBeadId()

Index votca::csg::Molecule::getBeadId ( Index bead ) const

inline

Definition at line 61 of file molecule.h.

getBeadIdByName()

Index votca::csg::Molecule::getBeadIdByName ( const std::string & name ) const

inline

Definition at line 104 of file molecule.h.

getBeadName() [1/2]

std::string votca::csg::Molecule::getBeadName ( const Index bead )

inline

Definition at line 71 of file molecule.h.

getBeadName() [2/2]

const std::string & votca::csg::Molecule::getBeadName ( const Index bead ) const

inline

Definition at line 72 of file molecule.h.

getId()

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

inline

get the molecule ID

Definition at line 48 of file molecule.h.

getName()

const std::string & votca::csg::Molecule::getName ( ) const

inline

get the name of the molecule

Definition at line 51 of file molecule.h.

Interactions() [1/2]

std::vector< Interaction * > votca::csg::Molecule::Interactions ( )

inline

Definition at line 79 of file molecule.h.

Interactions() [2/2]

const std::vector< Interaction * > & votca::csg::Molecule::Interactions ( ) const

inline

Definition at line 80 of file molecule.h.

setName()

void votca::csg::Molecule::setName ( const std::string & name )

inline

set the name of the molecule

Definition at line 54 of file molecule.h.

Friends And Related Symbol Documentation

Topology

friend class Topology

friend

Definition at line 101 of file molecule.h.

Member Data Documentation

bead_names_

std::vector<std::string> votca::csg::Molecule::bead_names_

private

Definition at line 96 of file molecule.h.

beadmap_

std::map<std::string, Index> votca::csg::Molecule::beadmap_

private

Definition at line 86 of file molecule.h.

beads_

std::vector<Bead *> votca::csg::Molecule::beads_

private

Definition at line 95 of file molecule.h.

id_

Index votca::csg::Molecule::id_

private

Definition at line 90 of file molecule.h.

interactions_

std::vector<Interaction *> votca::csg::Molecule::interactions_

private

Definition at line 87 of file molecule.h.

name_

std::string votca::csg::Molecule::name_

private

Definition at line 93 of file molecule.h.

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

• csg/include/votca/csg/molecule.h
• csg/src/libcsg/molecule.cc