BALL::Kekuliser Class Reference
[Miscellaneous]

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

#include <kekulizer.h>


Public Member Functions
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();