BALL::Kekuliser Class Reference
[Miscellaneous]

#include <BALL/STRUCTURE/kekulizer.h>

List of all members.

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

(

)

[inline, virtual]

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
	)			[protected, virtual]

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.