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>

List of all members.

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

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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.

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Constructor & Destructor Documentation

vl::RingExtractor::RingExtractor

(

Molecule *

mol )

[inline]

Definition at line 47 of file RingExtractor.hpp.

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Member Function Documentation

void vl::RingExtractor::setMolecule

(

Molecule *

mol )

[inline]

Definition at line 49 of file RingExtractor.hpp.

References mMolecule.

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().

void vl::RingExtractor::run

(

)

[inline]

Definition at line 53 of file RingExtractor.hpp.

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

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().

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().

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().

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().

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().

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().

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().

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Member Data Documentation

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:

• /home/master/UCL/VisualizationLibrary/src/vlMolecule/RingExtractor.hpp