BALL::Kekuliser Class Reference

#include <BALL/STRUCTURE/kekulizer.h>

Classes
struct	AtomInfo

Public Member Functions
	Kekuliser ()
virtual	~Kekuliser ()
bool	setup (Molecule &ac)
void	setAromaticRings (const std::vector< std::set< Atom * > > &rings)
void	setRings (const std::vector< std::set< Atom * > > &rings)
const std::vector< Bond * > &	getUnassignedBonds () const
void	clear ()
void	dump ()
void	setUseFormalCharges (bool state)
bool	useFormalCharges () const

Protected Member Functions
bool	fixAromaticRings_ ()
void	fixAromaticSystem_ (Position it)
virtual Size	getPenalty_ (Atom &atom, Index charge)
void	getMaximumValence_ ()
void	calculateAromaticSystems_ ()
void	collectSystems_ (Atom &atom)
void	collectAromaticAtoms_ ()
bool	hasAromaticBonds_ (Atom &atom)
void	applySolution_ (Position pos)
Position	calculateDistanceScores_ ()

Protected Attributes
bool	use_formal_charges_
std::vector< std::set< Atom * > >	aromatic_systems_
std::vector< std::set< Atom * > >	aromatic_rings_
std::vector< std::set< Atom * > >	rings_
std::vector< Bond * >	unassigned_bonds_
std::set< const Atom * >	aromatic_atoms_
std::set< const Atom * >	all_aromatic_atoms_
HashMap< Atom *, Index >	max_valence_
std::set< Atom * >	current_aromatic_system_
std::vector< AtomInfo >	atom_infos_
Molecule *	molecule_
Size	lowest_penalty_
Size	current_penalty_
std::vector< std::vector < AtomInfo > >	solutions_

Detailed Description

Class to transform bonds with type "aromatic" to conjugated single and double bonds.
Useage:

Kekulizer k;
k.setAromaticRings(...);
k.setRings(...);
k.setup(Molecule& m);
k.clear();

Definition at line 37 of file kekulizer.h.

Constructor & Destructor Documentation

BALL::Kekuliser::Kekuliser

(

)

virtual BALL::Kekuliser::~Kekuliser ( )

inlinevirtual

Definition at line 79 of file kekulizer.h.

Member Function Documentation

void BALL::Kekuliser::applySolution_ ( Position  pos )

protected

void BALL::Kekuliser::calculateAromaticSystems_ ( )

protected

Position BALL::Kekuliser::calculateDistanceScores_ ( )

protected

void BALL::Kekuliser::clear

(

)

void BALL::Kekuliser::collectAromaticAtoms_ ( )

protected

void BALL::Kekuliser::collectSystems_ ( Atom &  atom )

protected

void BALL::Kekuliser::dump

(

)

bool BALL::Kekuliser::fixAromaticRings_ ( )

protected

void BALL::Kekuliser::fixAromaticSystem_ ( Position  it )

protected

void BALL::Kekuliser::getMaximumValence_ ( )

protected

virtual Size BALL::Kekuliser::getPenalty_ ( Atom &  atom, Index  charge  )

protectedvirtual

const std::vector<Bond*>& BALL::Kekuliser::getUnassignedBonds ( ) const

inline

Definition at line 91 of file kekulizer.h.

bool BALL::Kekuliser::hasAromaticBonds_ ( Atom &  atom )

protected

void BALL::Kekuliser::setAromaticRings ( const std::vector< std::set< Atom * > > &  rings )

inline

Definition at line 85 of file kekulizer.h.

void BALL::Kekuliser::setRings ( const std::vector< std::set< Atom * > > &  rings )

inline

Definition at line 88 of file kekulizer.h.

bool BALL::Kekuliser::setup

(

Molecule &

ac

)

void BALL::Kekuliser::setUseFormalCharges ( bool  state )

inline

Definition at line 100 of file kekulizer.h.

bool BALL::Kekuliser::useFormalCharges ( ) const

inline

Definition at line 103 of file kekulizer.h.

Member Data Documentation

std::set<const Atom*> BALL::Kekuliser::all_aromatic_atoms_

protected

Definition at line 130 of file kekulizer.h.

std::set<const Atom*> BALL::Kekuliser::aromatic_atoms_

protected

Definition at line 129 of file kekulizer.h.

std::vector<std::set<Atom*> > BALL::Kekuliser::aromatic_rings_

protected

Definition at line 124 of file kekulizer.h.

std::vector<std::set<Atom*> > BALL::Kekuliser::aromatic_systems_

protected

Definition at line 123 of file kekulizer.h.

std::vector<AtomInfo> BALL::Kekuliser::atom_infos_

protected

Definition at line 136 of file kekulizer.h.

std::set<Atom*> BALL::Kekuliser::current_aromatic_system_

protected

Definition at line 133 of file kekulizer.h.

Size BALL::Kekuliser::current_penalty_

protected

Definition at line 139 of file kekulizer.h.

Size BALL::Kekuliser::lowest_penalty_

protected

Definition at line 138 of file kekulizer.h.

HashMap<Atom*, Index> BALL::Kekuliser::max_valence_

protected

Definition at line 131 of file kekulizer.h.

Molecule* BALL::Kekuliser::molecule_

protected

Definition at line 137 of file kekulizer.h.

std::vector<std::set<Atom*> > BALL::Kekuliser::rings_

protected

Definition at line 125 of file kekulizer.h.

std::vector<std::vector<AtomInfo> > BALL::Kekuliser::solutions_

protected

Definition at line 141 of file kekulizer.h.

std::vector<Bond*> BALL::Kekuliser::unassigned_bonds_

protected

Definition at line 126 of file kekulizer.h.

bool BALL::Kekuliser::use_formal_charges_

protected

Definition at line 121 of file kekulizer.h.