BALL::ChainBuilder Class Reference

This class provides methods for analysis of the chains in a molecule. More...

#include <BALL/STRUCTURE/chainBuilder.h>


Public Member Functions
	ChainBuilder ()
	Default-Constructor.
	~ChainBuilder ()
	Destructor.
vector< vector< Atom * > >	buildChains (System &molecule_sys)
	Determines the the main chain and side chains of a structure diagram.
Static Public Member Functions
static bool	compareChains (const vector< Atom * > &x, const vector< Atom * > &y)
	comparator for sorting the chains by their length
Private Member Functions
vector< vector< Size > >	calcAdjMatrix (vector< Atom * > &core_chain_atoms)
	creates a matrix, holding a "1" if two atoms a connected and "0" if they are not
void	visit_c_areas (Size &k, vector< vector< Size > > &adj_matrix, vector< int > &val, Size &nodes, Size &id, vector< Atom * > &core_chain_atoms, vector< Atom * > &chain_area)
	recursive visit-finction, used by findChainAreas()
void	findChainAreas (Size &nodes, vector< vector< Size > > &adj_matrix, vector< Atom * > &core_chain_atoms, vector< vector< Atom * > > &chain_areas)
	performs a depth-first-search for chain-areas in a molecule
void	findEdges (vector< Atom * > &chain_area)
	finds all edges in one chain area
void	visit_chains (Size &k, vector< vector< Size > > &adj_matrix, vector< int > &val, Size &id, vector< Atom * > &chain_area, Size &end, bool &breaker, Size &t, vector< Atom * > &prev_nodes)
	visit-function used by findPath()
vector< Atom * >	findPath (Atom &first_edge, Atom &second_edge, vector< Atom * > &chain_area, vector< vector< Size > > &adj_matrix)
	breadth-first-search, finding the shortest path between two edges of a chain-area
vector< vector< Atom * > >	findChains (vector< Atom * > &chain_area, vector< vector< Size > > &adj_matrix)
	finds all relevant chains in one chain-area
Size	getIndex (Atom &atom, vector< Atom > &container)
	helper-function to determine an Atom's index in a certain vector<Atom*>

Detailed Description

This class provides methods for analysis of the chains in a molecule.

Constructor & Destructor Documentation

BALL::ChainBuilder::ChainBuilder ( )

Default-Constructor.

BALL::ChainBuilder::~ChainBuilder ( )

Destructor.

Member Function Documentation

vector<vector<Atom*> > BALL::ChainBuilder::buildChains ( System & molecule_sys )

Determines the the main chain and side chains of a structure diagram.

Parameters:

molecule_sys

the input System

Returns:: the chains sorted by their length

vector<vector<Size> > BALL::ChainBuilder::calcAdjMatrix ( vector< Atom * > & core_chain_atoms ) [private]

creates a matrix, holding a "1" if two atoms a connected and "0" if they are not

Parameters:

core_chain_atoms

the core chain atoms of a molecule

Returns:: the adjacence-matrix representing the molecule-graph

static bool BALL::ChainBuilder::compareChains	(	const vector< Atom * > &	x,
		const vector< Atom * > &	y
	)			`[static]`

comparator for sorting the chains by their length

Parameters:

	x	chain
	y	chain

void BALL::ChainBuilder::findChainAreas	(	Size &	nodes,
		vector< vector< Size > > &	adj_matrix,
		vector< Atom * > &	core_chain_atoms,
		vector< vector< Atom * > > &	chain_areas
	)			`[private]`

performs a depth-first-search for chain-areas in a molecule

Parameters:

	nodes	number of nodes in the molecule-graph
	adj_matrix	adjacence-matrix representing the molecule-graph
	core_chain_atoms	the core chain atoms of the molecule
	chain_areas	the chain areas that are to be found

vector<vector<Atom*> > BALL::ChainBuilder::findChains	(	vector< Atom * > &	chain_area,
		vector< vector< Size > > &	adj_matrix
	)			`[private]`

finds all relevant chains in one chain-area

Parameters:

	chain_area	the chain area that is to be searched
	adj_matrix	adjacence-matrix representing the molecule-graph

Returns:: all relevant chains in chain_area

void BALL::ChainBuilder::findEdges ( vector< Atom * > & chain_area ) [private]

finds all edges in one chain area

Parameters:

chain_area

vector<Atom*> BALL::ChainBuilder::findPath	(	Atom *&	first_edge,
		Atom *&	second_edge,
		vector< Atom * > &	chain_area,
		vector< vector< Size > > &	adj_matrix
	)			`[private]`

breadth-first-search, finding the shortest path between two edges of a chain-area

Parameters:

	first_edge	the first of the two edges
	second_edge	the second of the two edges
	chain_area	the chain area that is to be searched
	adj_matrix	adjacence-matrix representing the molecule-graph

Returns:: the shortest path between first_edge and second_edge

Size BALL::ChainBuilder::getIndex	(	Atom *&	atom,
		vector< Atom * > &	container
	)			`[private]`

helper-function to determine an Atom's index in a certain vector<Atom*>

Parameters:

	atom	the Atom
	container	the vector<Atom*>

Returns:: the Atom's index

void BALL::ChainBuilder::visit_c_areas	(	Size &	k,
		vector< vector< Size > > &	adj_matrix,
		vector< int > &	val,
		Size &	nodes,
		Size &	id,
		vector< Atom * > &	core_chain_atoms,
		vector< Atom * > &	chain_area
	)			`[private]`

recursive visit-finction, used by findChainAreas()

Parameters:

	k	counter for the sequence-vector
	adj_matrix	adjacence-matrix representing the molecule-graph
	val	sequence, in which the atoms are visited
	nodes	number of nodes in the molecule-graph
	id	indicates, at which point in the sequence a certain atom has been visited
	core_chain_atoms	the core chain atoms of the molecule
	chain_area	the chain area that is to be filled with its atoms

void BALL::ChainBuilder::visit_chains	(	Size &	k,
		vector< vector< Size > > &	adj_matrix,
		vector< int > &	val,
		Size &	id,
		vector< Atom * > &	chain_area,
		Size &	end,
		bool &	breaker,
		Size &	t,
		vector< Atom * > &	prev_nodes
	)			`[private]`

visit-function used by findPath()

Parameters:

	k	counter for the sequence-vector
	adj_matrix	adjacence-matrix representing the molecule-graph
	val	sequence, in which the atoms are visited
	id	indicates, at which point in the sequence a certain atom has been visited
	chain_area	the chain area whos chains are to be found
	end	Index of the second edge - atom in the chain-area-vector
	breaker	flag, indicating, whether athe second edge has been reached
	t	starting point for the traceback
	prev_nodes	traceback-vector

BALL::ChainBuilder Class Reference

Public Member Functions

Static Public Member Functions

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation