vl::RingExtractor Class Reference

The RingExtractor class traverses a molecule's graph and detects various types of cycles, mainly used for aromatic ring detection. More...

#include <RingExtractor.hpp>

Public Member Functions
	RingExtractor (Molecule *mol)
void	setMolecule (Molecule *mol)
Molecule *	molecule () const
void	run ()
void	bootstrap ()
void	depthFirstVisit (Atom *atom, std::vector< ref< Atom > > &current_path)
void	keepAromaticCycles ()
void	sortCycles ()
void	keepPlanarCycles (float epsilon)
void	removeDoubles ()
void	keepMinimalCycles ()

Protected Attributes
Molecule *	mMolecule

Detailed Description

The RingExtractor class traverses a molecule's graph and detects various types of cycles, mainly used for aromatic ring detection.

Definition at line 44 of file RingExtractor.hpp.

Constructor & Destructor Documentation

RingExtractor()

vl::RingExtractor::RingExtractor ( Molecule *  mol )

inline

Definition at line 47 of file RingExtractor.hpp.

Member Function Documentation

bootstrap()

void vl::RingExtractor::bootstrap ( )

inline

Definition at line 66 of file RingExtractor.hpp.

References vl::Molecule::atom(), vl::Molecule::atomCount(), vl::Molecule::computeAtomAdjacency(), depthFirstVisit(), molecule(), and vl::Atom::setVisited().

Referenced by run().

depthFirstVisit()

void vl::RingExtractor::depthFirstVisit ( Atom *  atom, std::vector< ref< Atom > > &  current_path  )

inline

Definition at line 78 of file RingExtractor.hpp.

References vl::Atom::adjacentAtoms(), vl::Molecule::cycles(), molecule(), vl::Atom::setVisited(), and vl::Atom::visited().

Referenced by bootstrap().

keepAromaticCycles()

void vl::RingExtractor::keepAromaticCycles ( )

inline

Definition at line 108 of file RingExtractor.hpp.

References vl::Molecule::bond(), vl::Bond::bondType(), vl::BT_Aromatic, vl::Molecule::cycle(), vl::Molecule::cycles(), and molecule().

Referenced by run().

keepMinimalCycles()

void vl::RingExtractor::keepMinimalCycles ( )

inline

Definition at line 206 of file RingExtractor.hpp.

References vl::Molecule::atoms(), vl::Molecule::cycles(), and molecule().

Referenced by run().

keepPlanarCycles()

void vl::RingExtractor::keepPlanarCycles ( float  epsilon )

inline

Definition at line 155 of file RingExtractor.hpp.

References vl::AABB::center(), vl::Atom::coordinates(), vl::cross(), vl::Molecule::cycle(), vl::Molecule::cycles(), vl::dot(), molecule(), vl::Vector3< T_Scalar >::normalize(), and vl::normalize().

molecule()

Molecule* vl::RingExtractor::molecule ( ) const

inline

Definition at line 51 of file RingExtractor.hpp.

References mMolecule.

Referenced by bootstrap(), depthFirstVisit(), keepAromaticCycles(), keepMinimalCycles(), keepPlanarCycles(), removeDoubles(), run(), and sortCycles().

removeDoubles()

void vl::RingExtractor::removeDoubles ( )

inline

Definition at line 194 of file RingExtractor.hpp.

References vl::Molecule::cycle(), vl::Molecule::cycles(), and molecule().

Referenced by run().

run()

void vl::RingExtractor::run ( )

inline

Definition at line 53 of file RingExtractor.hpp.

References bootstrap(), keepAromaticCycles(), keepMinimalCycles(), molecule(), removeDoubles(), and sortCycles().

setMolecule()

void vl::RingExtractor::setMolecule ( Molecule *  mol )

inline

Definition at line 49 of file RingExtractor.hpp.

References mMolecule.

sortCycles()

void vl::RingExtractor::sortCycles ( )

inline

Definition at line 133 of file RingExtractor.hpp.

References vl::Molecule::cycle(), vl::Molecule::cycles(), vl::Atom::isAtomAdjacent(), and molecule().

Referenced by run().

Member Data Documentation

mMolecule

Molecule* vl::RingExtractor::mMolecule

protected

Definition at line 245 of file RingExtractor.hpp.

Referenced by molecule(), and setMolecule().

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The documentation for this class was generated from the following file:

• C:/git/VL/src/vlMolecule/RingExtractor.hpp