votca::csg::CGMoleculeDef Class Reference

definition of a coarse grained molecule More...

#include <cgmoleculedef.h>

Collaboration diagram for votca::csg::CGMoleculeDef:

Classes
struct	beaddef_t

Public Member Functions
	CGMoleculeDef ()=default
	~CGMoleculeDef ()
Molecule *	CreateMolecule (Topology &top)
Map	CreateMap (const Molecule &in, Molecule &out)
void	Load (std::string filename)
const std::string &	getName ()
const std::string &	getIdent ()

Private Member Functions
void	ParseTopology (tools::Property &options)
void	ParseBeads (tools::Property &options)
void	ParseBonded (tools::Property &options)
void	ParseMapping (tools::Property &options)
beaddef_t *	getBeadByName (const std::string &name)
tools::Property *	getMapByName (const std::string &name)

Private Attributes
tools::Property	options_
std::string	name_
std::string	ident_
std::vector< beaddef_t * >	beads_
std::map< std::string, beaddef_t * >	beads_by_name_
std::map< std::string, tools::Property * >	maps_
std::vector< tools::Property * >	bonded_

Detailed Description

definition of a coarse grained molecule

This class is to define a coarse grained molecule, which includes the topology, mapping, ...

Todo:

clean up this class, do the bonded interactions right!!!!

check for consistency of xml file, seperate xml parser and class!!

Definition at line 49 of file cgmoleculedef.h.

Constructor & Destructor Documentation

CGMoleculeDef()

votca::csg::CGMoleculeDef::CGMoleculeDef ( )

default

~CGMoleculeDef()

votca::csg::CGMoleculeDef::~CGMoleculeDef

(

)

Definition at line 51 of file cgmoleculedef.cc.

Member Function Documentation

CreateMap()

Map votca::csg::CGMoleculeDef::CreateMap	(	const Molecule &	in,
		Molecule &	out
	)

TODO: change this to factory, do not hardcode!!

Definition at line 202 of file cgmoleculedef.cc.

CreateMolecule()

Molecule * votca::csg::CGMoleculeDef::CreateMolecule

(

Topology &

top

)

Definition at line 118 of file cgmoleculedef.cc.

getBeadByName()

CGMoleculeDef::beaddef_t * votca::csg::CGMoleculeDef::getBeadByName ( const std::string &  name )

private

Definition at line 242 of file cgmoleculedef.cc.

getIdent()

const std::string & votca::csg::CGMoleculeDef::getIdent ( )

inline

Definition at line 60 of file cgmoleculedef.h.

getMapByName()

tools::Property * votca::csg::CGMoleculeDef::getMapByName ( const std::string &  name )

private

Definition at line 251 of file cgmoleculedef.cc.

getName()

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

inline

Definition at line 59 of file cgmoleculedef.h.

Load()

void votca::csg::CGMoleculeDef::Load

(

std::string

filename

)

Definition at line 58 of file cgmoleculedef.cc.

ParseBeads()

void votca::csg::CGMoleculeDef::ParseBeads ( tools::Property &  options )

private

Definition at line 75 of file cgmoleculedef.cc.

ParseBonded()

void votca::csg::CGMoleculeDef::ParseBonded ( tools::Property &  options )

private

Definition at line 108 of file cgmoleculedef.cc.

ParseMapping()

void votca::csg::CGMoleculeDef::ParseMapping ( tools::Property &  options )

private

Definition at line 112 of file cgmoleculedef.cc.

ParseTopology()

void votca::csg::CGMoleculeDef::ParseTopology ( tools::Property &  options )

private

Definition at line 68 of file cgmoleculedef.cc.

Member Data Documentation

beads_

std::vector<beaddef_t *> votca::csg::CGMoleculeDef::beads_

private

Definition at line 80 of file cgmoleculedef.h.

beads_by_name_

std::map<std::string, beaddef_t *> votca::csg::CGMoleculeDef::beads_by_name_

private

Definition at line 81 of file cgmoleculedef.h.

bonded_

std::vector<tools::Property *> votca::csg::CGMoleculeDef::bonded_

private

Definition at line 86 of file cgmoleculedef.h.

ident_

std::string votca::csg::CGMoleculeDef::ident_

private

Definition at line 77 of file cgmoleculedef.h.

maps_

std::map<std::string, tools::Property *> votca::csg::CGMoleculeDef::maps_

private

Definition at line 84 of file cgmoleculedef.h.

name_

std::string votca::csg::CGMoleculeDef::name_

private

Definition at line 75 of file cgmoleculedef.h.

options_

tools::Property votca::csg::CGMoleculeDef::options_

private

Definition at line 63 of file cgmoleculedef.h.

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

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