disables aromaticity prediction More...

#include <AP_disabled.hh>

Inheritance diagram for ggl::chem::AP_disabled:

Public Types
typedef AromaticityPerception::RingDescriptor	RingDescriptor
	ring describing class More...

typedef std::list< size_t >	RingList
	type of a list of node indices that form a ring More...

typedef std::set< size_t >	RingNodes
	type of a set of node indices that form a ring More...

typedef std::vector< std::pair < size_t, double > >	RingWeightVec
	Vector that holds ( index, weight ) pairs. More...

Public Member Functions
	AP_disabled ()

	AP_disabled (const AP_disabled &toCopy)

virtual AP_disabled *	clone () const

virtual void	correctAromaticity (Molecule &mol, const bool checkValence) throw (std::runtime_error)

virtual void	findAllRings (const Molecule &mol)

void	identifyAromaticEdges (const Molecule &mol)

virtual void	reportRing (const sgm::Graph_Interface &graph, const RingList &ringList)

virtual	~AP_disabled ()

Static Public Member Functions
static RingNodes	toRing (const Graph_Interface &graph, const RingList &ringList)

Protected Types
typedef AromaticityPerception::Edge	Edge
	defines an edge; NOTE: use as ordered pairs, i.e. first <= second More...

typedef AromaticityPerception::EdgeSet	EdgeSet
	defines an aromatic ring via the set of aromatic edges More...

Protected Member Functions
void	clearData ()

void	relabelMolecule (Molecule &mol, const bool checkValence) throw (std::runtime_error)

Static Protected Member Functions
static void	pruneFusedRings (std::vector< RingDescriptor * > &rings)

static void	pruneNonSingleDoubleBondRings (std::vector< RingDescriptor * > &rings, const Molecule &mol)

Protected Attributes
std::vector< RingDescriptor * >	allRings

EdgeSet	aromaticEdges
	the list of edges part of aromatic rings to be identified More...

Detailed Description

   Dummy aromaticity perception implementation that actually performs NO
   AROMATICITY PERCEPTION at all and thus disables aromaticity perception
   wherever used.

   The current aromaticity assignment is preserved.

Author: Martin Mann (c) 2014 http://www.bioinf.uni-freiburg.de/~mmann/

Definition at line 34 of file AP_disabled.hh.

Member Typedef Documentation

typedef AromaticityPerception::Edge ggl::chem::AP_disabled::Edge

protected

Definition at line 49 of file AP_disabled.hh.

typedef AromaticityPerception::EdgeSet ggl::chem::AP_disabled::EdgeSet

protected

Definition at line 51 of file AP_disabled.hh.

typedef AromaticityPerception::RingDescriptor ggl::chem::AP_disabled::RingDescriptor

Definition at line 40 of file AP_disabled.hh.

typedef std::list<size_t> sgm::RingReporter::RingList

inherited

Definition at line 27 of file RingReporter.hh.

typedef std::set<size_t> sgm::RingReporter::RingNodes

inherited

Definition at line 25 of file RingReporter.hh.

typedef std::vector< std::pair<size_t,double> > ggl::chem::AP_disabled::RingWeightVec

Definition at line 43 of file AP_disabled.hh.

Constructor & Destructor Documentation

ggl::chem::AP_disabled::AP_disabled ( )

inline

Construction

Parameters

model the aromaticity model to be used

Definition at line 67 of file AP_disabled.hh.

ggl::chem::AP_disabled::AP_disabled ( const AP_disabled & toCopy )

inline

Copy construction

Parameters

toCopy the object to make this a copy of

Definition at line 75 of file AP_disabled.hh.

virtual ggl::chem::AP_disabled::~AP_disabled ( )

inlinevirtual

destruction

Definition at line 82 of file AP_disabled.hh.

Member Function Documentation

void ggl::chem::AromaticityPerception::clearData ( )

protectedinherited

Resets internal temporary data structures.

virtual AP_disabled* ggl::chem::AP_disabled::clone ( ) const

inlinevirtual

Creates a heap copy of this instance that has to be deleted by the calling methods later on.

Returns: a new instance that is a copy of this object

Implements ggl::chem::AromaticityPerception.

Definition at line 161 of file AP_disabled.hh.

virtual void ggl::chem::AP_disabled::correctAromaticity	(	Molecule &	mol,
		const bool	checkValence
	)		throw (std::runtime_error)

inlinevirtual

Does nothing and thus fully disables aromaticity perception

Parameters

mol	the molecule to correct (not changed)
checkValence	whether or not the valence of nodes and bonds should be checked. (ignored)

Exceptions

std::runtime_error (never thrown)

Reimplemented from ggl::chem::AromaticityPerception.

Definition at line 149 of file AP_disabled.hh.

virtual void ggl::chem::AP_disabled::findAllRings ( const Molecule & mol )

inlinevirtual

Does nothing here...

Parameters

mol	the molecule to check for rings

Implements ggl::chem::AromaticityPerception.

Definition at line 93 of file AP_disabled.hh.

void ggl::chem::AP_disabled::identifyAromaticEdges ( const Molecule & mol )

inlinevirtual

Push all currently aromatic edges to the aromaticEdges container.

Parameters

mol	the molecule to check for aromatic rings

Implements ggl::chem::AromaticityPerception.

Definition at line 105 of file AP_disabled.hh.

static void ggl::chem::AromaticityPerception::pruneFusedRings ( std::vector< RingDescriptor * > & rings )

staticprotectedinherited

Performs a pruning of rings (within the "allRings" container) that are fused versions of smaller rings sharing only one bond.

Parameters

rings the rings to be pruned

static void ggl::chem::AromaticityPerception::pruneNonSingleDoubleBondRings	(	std::vector< RingDescriptor * > &	rings,
		const Molecule &	mol
	)

staticprotectedinherited

Performs a pruning of rings (within the "allRings" container) that are not composed of single and double bonds only.

Parameters

rings	the rings to be pruned
mol	the molecule to relabel

void ggl::chem::AromaticityPerception::relabelMolecule	(	Molecule &	mol,
		const bool	checkValence
	)		throw (std::runtime_error)

protectedinherited

Relabels the given molecule according to the aromatic rings defined by the aromaticEdges container. All other nodes and edges are set non-aromatic.

Parameters

mol	the molecule to relabel (done inplace)
checkValence	whether or not the valence of nodes and bonds should be checked. In error case a std::runtime_error is thrown.

Exceptions

std::runtime_error if a canonical relabeling is not possible or the valence checks fail

virtual void ggl::chem::AromaticityPerception::reportRing	(	const sgm::Graph_Interface &	graph,
		const RingList &	ringList
	)

virtualinherited

Is called to report a ring identified by a RingPerception instance.

Here it is used to store each ring within the allRings container.

Parameters

graph	the graph that contains the ring
ringList	the ring to report

Implements sgm::RingReporter.

static RingNodes sgm::RingReporter::toRing	(	const Graph_Interface &	graph,
		const RingList &	ringList
	)

staticinherited

Utility class that converts a RingList, i.e. a list of nodes when traversing a ring within a graph, into the set of nodes that form the ring.

Parameters

graph	the graph that contains the ring
ringList	the ring list to convert

Returns: the list of nodes traversing the ring

Field Documentation

std::vector< RingDescriptor* > ggl::chem::AromaticityPerception::allRings

protectedinherited

container that will hold all rings of the current molecule -> this list is later pruned to the rings of interest

Definition at line 76 of file AromaticityPerception.hh.

EdgeSet ggl::chem::AromaticityPerception::aromaticEdges

protectedinherited

Definition at line 72 of file AromaticityPerception.hh.

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

src/ggl/chem/AP_disabled.hh

Public Types

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Field Documentation