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