#include <BALL/STRUCTURE/kekulizer.h>
Class to transform bonds with type "aromatic" to conjugated single and double bonds.
Useage:
BALL_EXTERN_VARIABLE const double k
Definition at line 37 of file kekulizer.h.
◆ Kekuliser()
BALL::Kekuliser::Kekuliser |
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◆ ~Kekuliser()
virtual BALL::Kekuliser::~Kekuliser |
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inlinevirtual |
◆ applySolution_()
void BALL::Kekuliser::applySolution_ |
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Position |
pos | ) |
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protected |
◆ calculateAromaticSystems_()
void BALL::Kekuliser::calculateAromaticSystems_ |
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protected |
◆ calculateDistanceScores_()
Position BALL::Kekuliser::calculateDistanceScores_ |
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◆ clear()
void BALL::Kekuliser::clear |
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◆ collectAromaticAtoms_()
void BALL::Kekuliser::collectAromaticAtoms_ |
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protected |
◆ collectSystems_()
void BALL::Kekuliser::collectSystems_ |
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Atom & |
atom | ) |
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protected |
◆ dump()
void BALL::Kekuliser::dump |
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◆ fixAromaticRings_()
bool BALL::Kekuliser::fixAromaticRings_ |
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◆ fixAromaticSystem_()
void BALL::Kekuliser::fixAromaticSystem_ |
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Position |
it | ) |
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protected |
◆ getMaximumValence_()
void BALL::Kekuliser::getMaximumValence_ |
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protected |
◆ getPenalty_()
virtual Size BALL::Kekuliser::getPenalty_ |
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Atom & |
atom, |
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Index |
charge |
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protectedvirtual |
◆ getUnassignedBonds()
const std::vector< Bond * > & BALL::Kekuliser::getUnassignedBonds |
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const |
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inline |
◆ hasAromaticBonds_()
bool BALL::Kekuliser::hasAromaticBonds_ |
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Atom & |
atom | ) |
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protected |
◆ setAromaticRings()
void BALL::Kekuliser::setAromaticRings |
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const std::vector< std::set< Atom * > > & |
rings | ) |
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inline |
◆ setRings()
void BALL::Kekuliser::setRings |
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const std::vector< std::set< Atom * > > & |
rings | ) |
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inline |
◆ setup()
◆ setUseFormalCharges()
void BALL::Kekuliser::setUseFormalCharges |
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bool |
state | ) |
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inline |
◆ useFormalCharges()
bool BALL::Kekuliser::useFormalCharges |
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const |
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inline |
◆ all_aromatic_atoms_
std::set<const Atom*> BALL::Kekuliser::all_aromatic_atoms_ |
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protected |
◆ aromatic_atoms_
std::set<const Atom*> BALL::Kekuliser::aromatic_atoms_ |
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protected |
◆ aromatic_rings_
std::vector<std::set<Atom*> > BALL::Kekuliser::aromatic_rings_ |
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protected |
◆ aromatic_systems_
std::vector<std::set<Atom*> > BALL::Kekuliser::aromatic_systems_ |
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protected |
◆ atom_infos_
std::vector<AtomInfo> BALL::Kekuliser::atom_infos_ |
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◆ current_aromatic_system_
std::set<Atom*> BALL::Kekuliser::current_aromatic_system_ |
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◆ current_penalty_
Size BALL::Kekuliser::current_penalty_ |
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protected |
◆ lowest_penalty_
Size BALL::Kekuliser::lowest_penalty_ |
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protected |
◆ max_valence_
◆ molecule_
◆ rings_
std::vector<std::set<Atom*> > BALL::Kekuliser::rings_ |
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protected |
◆ solutions_
std::vector<std::vector<AtomInfo> > BALL::Kekuliser::solutions_ |
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protected |
◆ unassigned_bonds_
std::vector<Bond*> BALL::Kekuliser::unassigned_bonds_ |
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◆ use_formal_charges_
bool BALL::Kekuliser::use_formal_charges_ |
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protected |