votca::csg::BeadStructure Class Reference

Designed to determine if the structure beads passed in. More...

#include <beadstructure.h>

Inheritance diagram for votca::csg::BeadStructure:

Collaboration diagram for votca::csg::BeadStructure:

Classes
struct	BeadInfo
	Small structure to help store bead info relevant to the structure. More...

Public Member Functions
virtual	~BeadStructure ()=default
BeadStructure	getSubStructure (const std::vector< Index > &idx, const std::vector< tools::Edge > &edges) const
	Given indices and edges that exist are a subset of beadstructure, return the sub-beadstructure.
bool	isSingleStructure ()
	Determine if the bead structure consists of a single connected structure.
size_t	BeadCount () const noexcept
	returns the number of beads in the bead structure
template<class T >
void	AddBead (const T &bead)
	add a bead to the bead structure
virtual void	ConnectBeads (const Index &bead1_id, const Index &bead2_id)
	Create a connection between two beads in the structure.
std::vector< Index >	getNeighBeadIds (const Index &index)
	Return a vector of all the ids of the beads neighboring the index.
tools::Graph	getGraph ()
bool	isStructureEquivalent (BeadStructure &beadstructure)
	Compare the topology of two bead structures.
bool	BeadExist (Index bead_id) const
	Determine if a bead exists in the structure.
std::vector< Index >	getBeadIds () const
	Return the ids of the beads that are in the structure.

Protected Member Functions
virtual void	UpdateOnBeadAddition_ ()
void	InitializeGraph_ ()
void	CalculateStructure_ ()
tools::GraphNode	BeadInfoToGraphNode_ (const BeadInfo &)

Protected Attributes
bool	structureIdUpToDate = false
bool	graphUpToDate = false
bool	single_structureUpToDate_ = false
bool	single_structure_ = false
std::string	structure_id_ = ""
tools::Graph	graph_
std::set< tools::Edge >	connections_
std::unordered_map< Index, BeadInfo >	beads_
std::unordered_map< Index, tools::GraphNode >	graphnodes_

Detailed Description

Designed to determine if the structure beads passed in.

Essentially it will have the functionality to determine if the stored beads make up a single molecule. It can also break the stored beads up into molecules. It can compare two bead structures and determine if they are the same structure. The Ids of a bead will not determine if a structure is equivalent or not. Each bead must have a unique Id.

E.g. If a beadstructure is composed of the following:

BeadStructure 1 Name:"A" Id:1 -— Name:"B" Id:2

BeadStucture 2 Name:"A" Id:3 -— Name:"B" Id:4

Here BeadStructure 1 and 2 will compare equal

Definition at line 51 of file beadstructure.h.

Constructor & Destructor Documentation

~BeadStructure()

virtual votca::csg::BeadStructure::~BeadStructure ( )

virtualdefault

Member Function Documentation

AddBead()

template<class T >

void votca::csg::BeadStructure::AddBead

(

const T &

bead

)

add a bead to the bead structure

The same bead cannot be added twice.

Definition at line 159 of file beadstructure.h.

BeadCount()

size_t votca::csg::BeadStructure::BeadCount ( ) const

inlinenoexcept

returns the number of beads in the bead structure

Definition at line 87 of file beadstructure.h.

BeadExist()

bool votca::csg::BeadStructure::BeadExist ( Index  bead_id ) const

inline

Determine if a bead exists in the structure.

Definition at line 125 of file beadstructure.h.

BeadInfoToGraphNode_()

tools::GraphNode BeadStructure::BeadInfoToGraphNode_ ( const BeadInfo &  bead_info )

protected

Add graphnodes

Definition at line 63 of file beadstructure.cc.

CalculateStructure_()

void BeadStructure::CalculateStructure_ ( )

protected

Definition at line 54 of file beadstructure.cc.

ConnectBeads()

void BeadStructure::ConnectBeads ( const Index &  bead1_id, const Index &  bead2_id  )

virtual

Create a connection between two beads in the structure.

A bead cannot be connected to itself. It also may not be connected to a bead that has not yet been added to the structure.

Reimplemented in votca::csg::BeadMotif.

Definition at line 115 of file beadstructure.cc.

getBeadIds()

std::vector< Index > BeadStructure::getBeadIds

(

)

const

Return the ids of the beads that are in the structure.

Returns

vector of the ids

Do not use graph_.getVertices() because this would require that the graph is updated

Definition at line 187 of file beadstructure.cc.

getGraph()

tools::Graph BeadStructure::getGraph

(

)

Definition at line 134 of file beadstructure.cc.

getNeighBeadIds()

std::vector< Index > BeadStructure::getNeighBeadIds

(

const Index &

index

)

Return a vector of all the ids of the beads neighboring the index.

Definition at line 179 of file beadstructure.cc.

getSubStructure()

BeadStructure BeadStructure::getSubStructure	(	const std::vector< Index > &	idx,
		const std::vector< tools::Edge > &	edges
	)		const

Given indices and edges that exist are a subset of beadstructure, return the sub-beadstructure.

If the edges and and indices passed in do not exist within the current BeadStructure a runtime exception is thrown, as the the sub structure is not actually a sub structure of the current BeadStructure.

Parameters

idx	Indices of the substructure, must exist within the current BeadStructure
edges	Edges of the substructure, must exist within the current BeadStructure

Returns

BeadStructure which is a substructure of BeadStructure

Definition at line 83 of file beadstructure.cc.

InitializeGraph_()

void BeadStructure::InitializeGraph_ ( )

protected

Definition at line 38 of file beadstructure.cc.

isSingleStructure()

bool BeadStructure::isSingleStructure

(

)

Determine if the bead structure consists of a single connected structure.

This function will determine if all beads in the structure are connected somehow to everyother bead. The connection does not have to be direct

Returns

- returns a boolean true if it is a single Structure

Definition at line 139 of file beadstructure.cc.

isStructureEquivalent()

bool BeadStructure::isStructureEquivalent

(

BeadStructure &

beadstructure

)

Compare the topology of two bead structures.

This function looks at how the beads are arranged within the bead structure and determines if the topology is the same.

Parameters

[in]

beadstructure

- beadstructure to compare with

Returns

- if the same returns true else false

Definition at line 169 of file beadstructure.cc.

UpdateOnBeadAddition_()

virtual void votca::csg::BeadStructure::UpdateOnBeadAddition_ ( )

inlineprotectedvirtual

If extra initialization is needed by a child class when a bead is added this method can be overridden.

Reimplemented in votca::csg::BeadMotif.

Definition at line 142 of file beadstructure.h.

Member Data Documentation

beads_

std::unordered_map<Index, BeadInfo> votca::csg::BeadStructure::beads_

protected

Definition at line 154 of file beadstructure.h.

connections_

std::set<tools::Edge> votca::csg::BeadStructure::connections_

protected

Definition at line 153 of file beadstructure.h.

graph_

tools::Graph votca::csg::BeadStructure::graph_

protected

Definition at line 152 of file beadstructure.h.

graphnodes_

std::unordered_map<Index, tools::GraphNode> votca::csg::BeadStructure::graphnodes_

protected

Definition at line 155 of file beadstructure.h.

graphUpToDate

bool votca::csg::BeadStructure::graphUpToDate = false

protected

Definition at line 148 of file beadstructure.h.

single_structure_

bool votca::csg::BeadStructure::single_structure_ = false

protected

Definition at line 150 of file beadstructure.h.

single_structureUpToDate_

bool votca::csg::BeadStructure::single_structureUpToDate_ = false

protected

Definition at line 149 of file beadstructure.h.

structure_id_

std::string votca::csg::BeadStructure::structure_id_ = ""

protected

Definition at line 151 of file beadstructure.h.

structureIdUpToDate

bool votca::csg::BeadStructure::structureIdUpToDate = false

protected

Definition at line 147 of file beadstructure.h.

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

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