BALL::RingAnalyser Class Reference

Methods for the analysis of the structure of ringsystems. More...

#include <BALL/STRUCTURE/ringAnalyser.h>

Inheritance diagram for BALL::RingAnalyser:

Classes
class	Ring

Public Types
enum	RingType {   NONE, TEMPLATE, FUSED, BRIDGED,   SPIRO, CORE }
Public Types inherited from BALL::UnaryFunctor< AtomContainer, Processor::Result >
typedef Processor::Result	result_type
typedef AtomContainer	argument_type
typedef AtomContainer &	argument_reference
typedef const AtomContainer &	const_argument_reference
typedef AtomContainer *	argument_pointer
typedef const AtomContainer *	const_argument_pointer

Public Member Functions
void	clear ()
bool	isInRing (const Atom *atom, std::vector< Atom * > const &ring) const
	helper-function; determines, whether an atom is part of a certain ring More...
bool	isInRingSystem (const Atom *atom, Index i) const
	helper-function; determines, whether an atom is part of a certain ring More...
void	sequenceRing (std::vector< Atom * > &ring)
Size	getNumberOfRingSystems ()
std::vector< Ring >	getRingSystem (Position i)
std::vector< Position >	getPeelingOrder (Position i)
Constructors and destructors.
	RingAnalyser ()
	Default-Constructor. More...
virtual	~RingAnalyser ()
	Destructor. More...
Processor-related methods
virtual bool	start ()
	Processor method which is called before the operator()-call. More...
virtual Processor::Result	operator() (AtomContainer &ac)
virtual bool	finish ()
	Processor method which is called after the operator()-call. More...
Public Member Functions inherited from BALL::UnaryProcessor< AtomContainer >
	UnaryProcessor ()
	UnaryProcessor (const UnaryProcessor &)
virtual	~UnaryProcessor ()

Protected Member Functions
void	clusterRings_ ()
	performs an agglomerative clustering of single rings to ringsystems More...
void	findSharedBonds_ ()
void	peelRings_ ()
	performs an analysis of the structure of a ringsystem More...
bool	isCentralRing_ (std::list< Position >::iterator ring, std::list< Position > &unassigned_rings)
bool	peelNextRing_ (std::list< Position > &unassigned_rings, bool peel_fused=false)
bool	assignRTD_ (std::list< Position > &trial_system)
	interface for a Ring Template Database (RTD), no functionality yet More...

Protected Attributes
std::vector< Ring >	rings_
	the smallest set of smallest rings of our molecule More...
std::vector< std::vector < Position > >	ring_systems_
	the ring systems, stored as indices into the smallest set of smallest rings More...
HashMap< Bond const *, std::deque< Position > >	rings_per_bond_
	the ring memberships per bond More...
std::vector< std::vector < Position > >	peeling_order_
	the order in which rings are peeled from their respective ring systems More...

Detailed Description

Methods for the analysis of the structure of ringsystems.

Definition at line 36 of file ringAnalyser.h.

Member Enumeration Documentation

enum BALL::RingAnalyser::RingType

Enumerator
NONE
TEMPLATE
FUSED
BRIDGED
SPIRO
CORE

Definition at line 41 of file ringAnalyser.h.

Constructor & Destructor Documentation

BALL::RingAnalyser::RingAnalyser

(

)

Default-Constructor.

virtual BALL::RingAnalyser::~RingAnalyser ( )

virtual

Destructor.

Member Function Documentation

bool BALL::RingAnalyser::assignRTD_ ( std::list< Position > &  trial_system )

protected

interface for a Ring Template Database (RTD), no functionality yet

Returns

always returns false by now

void BALL::RingAnalyser::clear

(

)

Clears the datastructures. NOTE: The options remain! Use setDefaultOptions() to clear the options.

void BALL::RingAnalyser::clusterRings_ ( )

protected

performs an agglomerative clustering of single rings to ringsystems

void BALL::RingAnalyser::findSharedBonds_ ( )

protected

Find the bonds shared between rings in the sssr Precondition: the rings must be sorted such that a_i, a_i+1 share a bond (and a_size-1, a_0)

virtual bool BALL::RingAnalyser::finish ( )

virtual

Processor method which is called after the operator()-call.

Reimplemented from BALL::UnaryProcessor< AtomContainer >.

Size BALL::RingAnalyser::getNumberOfRingSystems

(

)

Return the number of ring systems.

std::vector<Position> BALL::RingAnalyser::getPeelingOrder

(

Position

i

)

Returns the peeling order for the i-th ring system.

std::vector<Ring> BALL::RingAnalyser::getRingSystem

(

Position

i

)

Returns the i-th ring system.

bool BALL::RingAnalyser::isCentralRing_ ( std::list< Position >::iterator  ring, std::list< Position > &  unassigned_rings  )

protected

bool BALL::RingAnalyser::isInRing	(	const Atom *	atom,
		std::vector< Atom * > const &	ring
	)		const

helper-function; determines, whether an atom is part of a certain ring

Parameters

atom	the atom
ring	the ring

Returns

true, if the atom is part of the ring, otherwise returns false

bool BALL::RingAnalyser::isInRingSystem	(	const Atom *	atom,
		Index	i
	)		const

helper-function; determines, whether an atom is part of a certain ring

Parameters

atom	the atom
i	the index of the ring system to test

Returns

true, if the atom is part of the ring system, otherwise returns false

virtual Processor::Result BALL::RingAnalyser::operator() ( AtomContainer &  ac )

virtual

Operator () for the processor

Parameters

ac	the AtomContainer to which the processor is applied.

Reimplemented from BALL::UnaryProcessor< AtomContainer >.

bool BALL::RingAnalyser::peelNextRing_ ( std::list< Position > &  unassigned_rings, bool  peel_fused = false  )

protected

void BALL::RingAnalyser::peelRings_ ( )

protected

performs an analysis of the structure of a ringsystem

void BALL::RingAnalyser::sequenceRing

(

std::vector< Atom * > &

ring

)

Puts the Atoms in the input ring into the correct order

After calling this function, for i, i+1 it holds that atom i is bonded to atom i+1, and that the last is bonded to the first entry

Parameters

ring	the input ring to sequence

virtual bool BALL::RingAnalyser::start ( )

virtual

Processor method which is called before the operator()-call.

Reimplemented from BALL::UnaryProcessor< AtomContainer >.

Member Data Documentation

std::vector<std::vector<Position> > BALL::RingAnalyser::peeling_order_

protected

the order in which rings are peeled from their respective ring systems

Definition at line 192 of file ringAnalyser.h.

std::vector<std::vector<Position> > BALL::RingAnalyser::ring_systems_

protected

the ring systems, stored as indices into the smallest set of smallest rings

Definition at line 186 of file ringAnalyser.h.

std::vector<Ring> BALL::RingAnalyser::rings_

protected

the smallest set of smallest rings of our molecule

Definition at line 183 of file ringAnalyser.h.

HashMap<Bond const*, std::deque<Position> > BALL::RingAnalyser::rings_per_bond_

protected

the ring memberships per bond

Definition at line 189 of file ringAnalyser.h.