#include <BALL/STRUCTURE/sdGenerator.h>

Classes
class	AtomComparator

struct	Default
	Default values for options. More...

struct	Option
	Option names. More...

Public Types
enum	Property { FIRST_SDGENERATOR_PROPERTY = PDBAtom::NUMBER_OF_PROPERTIES+1, IN_RING, CORE_CHAIN, DEPOSITED, FXAS, EQAS, HEAD, EDGE, ASSEMBLED, ZIG, ZAG, INITIALIZED_HEAD_CFS, LAST_SDGENERATOR_PROPERTY }
	Properties, used to describe atoms and their status. More...

Public Member Functions
void	generateSD (System &molecule_sys)
	Generates a structure Diagram from the input System. More...

void	clear ()

Constructors and Destructors.
	SDGenerator (bool show_hydrogens=false)

virtual	~SDGenerator ()

Accessors
void	setDefaultOptions ()

Public Attributes
Public Attributes
Options	options
	options More...

Protected Member Functions
void	prepare_ ()
	Distinguishes between ring-atoms and core-chain-atoms, removes all H-Atoms from the System. More...

void	constructRingSystem_ (Position current_ring_system)
	Constructs a ringsystem, providing the atoms with relative 2D-coordinates, starting in the point of origin. More...

Angle	getCFS_ (Atom const *atom, bool hi)

Angle	computeCFS_ (Vector3 const &input)

void	setCFS_ (Atom *atom, Angle cfs, bool high)

void	pushCFS_ (Atom *atom)

Angle	getBackupCFS_ (Atom const *, bool hi)

void	computeCoreCFS_ (RingAnalyser::Ring &ring, bool clockwise)

Angle	computeAngularSeparation_ (Atom *seed)

Angle	computeAngularDemand_ (Atom *seed)

std::vector< Atom * >	sequenceSubstituents_ (Atom *seed)

void	computeShelleyPriorities_ ()

void	buildRegularPolygon_ (RingAnalyser::Ring &ring, Position first_anchor_index, bool clockwise)

void	buildOpenPolygon_ (RingAnalyser::Ring &ring, Position first_anchor_index, Position second_anchor_index)

void	attachCore_ (Position current_ring, std::vector< RingAnalyser::Ring > &current_system, float x_start)
	construct the core-ring as a regular polygon More...

void	attachTemplate_ (Position current_ring, std::vector< RingAnalyser::Ring > &current_system)
	attach a ring template to a (partially) constructed ringsystem (no functionality yet) More...

void	attachFused_ (Position current_ring, std::vector< RingAnalyser::Ring > &current_system)
	attach a fused ring to a (partially) constructed ringsystem More...

void	attachBridged_ (Position current_ring, std::vector< RingAnalyser::Ring > &current_system)
	attach a bridged ring to a (partially) constructed ringsystem More...

void	attachSpiro_ (Position current_ring, std::vector< RingAnalyser::Ring > &current_system)
	attach a spiro ring to a (partially) constructed ringsystem More...

void	computeAdjacencyMatrix_ (std::vector< Atom * > &chain, std::vector< bool > &result)
	Compute adjacency matrix of the given atoms. More...

void	treatChains_ ()
	cluster and arrange all chains in the system More...

void	smoothCFSAngle_ (Atom *seed)

void	placeSubstituent_ (Atom seed, Atom head, Atom *next)

void	depositPFU_ (Atom seed_atom, Atom next_neighbour)

void	checkOverlap_ (Atom *atom)

bool	ringIsClockwise_ (const RingAnalyser::Ring &ring, Index start_index=0) const

void	assembleSD_ ()

void	findFloydWarshallPath_ (std::vector< int > &path, std::vector< Index > &next, Size remaining_atoms, Position i, Position j, std::list< Index > &output)

Static Protected Member Functions
static bool	compareChains_ (const vector< Atom * > &x, const vector< Atom * > &y)
	Comparator for chains of atoms. More...

Protected Attributes
RingAnalyser	ring_analyser_
	The ring analyser containing all information about ring systems. More...

std::list< std::list< Atom * > >	chains_
	all chains More...

std::priority_queue< Atom , std::vector< Atom > , AtomComparator >	redraw_queue_
	our redraw queue More...

System *	system_
	the system we are working on More...

Detailed Description

Structure Diagram Generation.

This class provides methods for analysis of the input.

Definition at line 33 of file sdGenerator.h.

Member Enumeration Documentation

enum BALL::SDGenerator::Property

Properties, used to describe atoms and their status.

Enumerator
FIRST_SDGENERATOR_PROPERTY
IN_RING
CORE_CHAIN
DEPOSITED
FXAS
EQAS
HEAD
EDGE
ASSEMBLED
ZIG
ZAG
INITIALIZED_HEAD_CFS
LAST_SDGENERATOR_PROPERTY

Definition at line 40 of file sdGenerator.h.

Constructor & Destructor Documentation

BALL::SDGenerator::SDGenerator ( bool show_hydrogens = false )

Default-Constructor

virtual BALL::SDGenerator::~SDGenerator ( )

virtual

Destructor

Member Function Documentation

void BALL::SDGenerator::assembleSD_ ( )

protected

Assemble the final structure diagram

void BALL::SDGenerator::attachBridged_	(	Position	current_ring,
		std::vector< RingAnalyser::Ring > &	current_system
	)

protected

attach a bridged ring to a (partially) constructed ringsystem

Parameters

current_ring	the index of the ring to attach
current_system	the index of the ring system

void BALL::SDGenerator::attachCore_	(	Position	current_ring,
		std::vector< RingAnalyser::Ring > &	current_system,
		float	x_start
	)

protected

construct the core-ring as a regular polygon

Parameters

current_ring	the index of the ring to attach
current_system	the ring system
x_start	the ring is created in (x_start, 0, 0)

void BALL::SDGenerator::attachFused_	(	Position	current_ring,
		std::vector< RingAnalyser::Ring > &	current_system
	)

protected

attach a fused ring to a (partially) constructed ringsystem

Parameters

current_ring	the index of the ring to attach
current_system	the index of the ring system

void BALL::SDGenerator::attachSpiro_	(	Position	current_ring,
		std::vector< RingAnalyser::Ring > &	current_system
	)

protected

attach a spiro ring to a (partially) constructed ringsystem

Parameters

current_ring	the index of the ring to attach
current_system	the index of the ring system

void BALL::SDGenerator::attachTemplate_	(	Position	current_ring,
		std::vector< RingAnalyser::Ring > &	current_system
	)

protected

attach a ring template to a (partially) constructed ringsystem (no functionality yet)

Parameters

current_ring	the index of the ring to attach
current_system	the ring system

void BALL::SDGenerator::buildOpenPolygon_	(	RingAnalyser::Ring &	ring,
		Position	first_anchor_index,
		Position	second_anchor_index
	)

protected

Build an open polygon for a ring with two fixed points.

void BALL::SDGenerator::buildRegularPolygon_	(	RingAnalyser::Ring &	ring,
		Position	first_anchor_index,
		bool	clockwise
	)

protected

Build a regular polygon for a ring with two fixed points.

void BALL::SDGenerator::checkOverlap_ ( Atom * atom )

protected

void BALL::SDGenerator::clear ( )

Clear all internal data structures.

static bool BALL::SDGenerator::compareChains_	(	const vector< Atom * > &	x,
		const vector< Atom * > &	y
	)

staticprotected

Comparator for chains of atoms.

void BALL::SDGenerator::computeAdjacencyMatrix_	(	std::vector< Atom * > &	chain,
		std::vector< bool > &	result
	)

protected

Compute adjacency matrix of the given atoms.

Angle BALL::SDGenerator::computeAngularDemand_ ( Atom * seed )

protected

Angle BALL::SDGenerator::computeAngularSeparation_ ( Atom * seed )

protected

Angle BALL::SDGenerator::computeCFS_ ( Vector3 const & input )

protected

void BALL::SDGenerator::computeCoreCFS_	(	RingAnalyser::Ring &	ring,
		bool	clockwise
	)

protected

void BALL::SDGenerator::computeShelleyPriorities_ ( )

protected

Compute the Shelley priority values for each atom

void BALL::SDGenerator::constructRingSystem_ ( Position current_ring_system )

protected

Constructs a ringsystem, providing the atoms with relative 2D-coordinates, starting in the point of origin.

Parameters

current_ring_system consecutive numbering of the molecule's ringsystems

void BALL::SDGenerator::depositPFU_	(	Atom *	seed_atom,
		Atom *	next_neighbour
	)

protected

void BALL::SDGenerator::findFloydWarshallPath_	(	std::vector< int > &	path,
		std::vector< Index > &	next,
		Size	remaining_atoms,
		Position	i,
		Position	j,
		std::list< Index > &	output
	)

protected

void BALL::SDGenerator::generateSD ( System & molecule_sys )

Generates a structure Diagram from the input System.

Parameters

molecule_sys

Angle BALL::SDGenerator::getBackupCFS_	(	Atom const *	,
		bool	hi
	)

protected

Angle BALL::SDGenerator::getCFS_	(	Atom const *	atom,
		bool	hi
	)

protected

void BALL::SDGenerator::placeSubstituent_	(	Atom *	seed,
		Atom *	head,
		Atom *	next
	)

protected

void BALL::SDGenerator::prepare_ ( )

protected

Distinguishes between ring-atoms and core-chain-atoms, removes all H-Atoms from the System.

Parameters

molecule_sys

void BALL::SDGenerator::pushCFS_ ( Atom * atom )

protected

bool BALL::SDGenerator::ringIsClockwise_	(	const RingAnalyser::Ring &	ring,
		Index	start_index = `0`
	)		const

protected

std::vector<Atom*> BALL::SDGenerator::sequenceSubstituents_ ( Atom * seed )

protected

void BALL::SDGenerator::setCFS_	(	Atom *	atom,
		Angle	cfs,
		bool	high
	)

protected

void BALL::SDGenerator::setDefaultOptions ( )

Resets the options to default values.

void BALL::SDGenerator::smoothCFSAngle_ ( Atom * seed )

protected

void BALL::SDGenerator::treatChains_ ( )

protected

cluster and arrange all chains in the system

Member Data Documentation

std::list<std::list<Atom*> > BALL::SDGenerator::chains_

protected

all chains

Definition at line 264 of file sdGenerator.h.

Options BALL::SDGenerator::options

options

Definition at line 101 of file sdGenerator.h.

std::priority_queue<Atom*, std::vector<Atom*>, AtomComparator> BALL::SDGenerator::redraw_queue_

protected

our redraw queue

Definition at line 267 of file sdGenerator.h.

RingAnalyser BALL::SDGenerator::ring_analyser_

protected

The ring analyser containing all information about ring systems.

Definition at line 261 of file sdGenerator.h.

System* BALL::SDGenerator::system_

protected

the system we are working on

Definition at line 270 of file sdGenerator.h.

Classes

Public Types

Public Member Functions

Public Attributes

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation