BALL::AromaticityProcessor Class Reference

This processor provides methods for detection and assignment of aromaticity. More...

#include <BALL/QSAR/aromaticityProcessor.h>

Inheritance diagram for BALL::AromaticityProcessor:

Classes
struct	Default
	Default values for options. More...
struct	Option
	Option names. More...

Public Member Functions
Constructors and Destructors
	AromaticityProcessor ()
	AromaticityProcessor (const AromaticityProcessor &aro)
virtual	~AromaticityProcessor ()
Assignment
AromaticityProcessor &	operator= (const AromaticityProcessor &aro)
Accessors
void	aromatize (const vector< vector< Atom * > > &sssr, AtomContainer &ac)
void	aromatizeSimple (vector< vector< Atom * > > &sssr)
Processor-related methods
Processor::Result	operator() (AtomContainer &ac)
virtual bool	start ()
Public Member Functions inherited from BALL::UnaryProcessor< AtomContainer >
	UnaryProcessor ()
	UnaryProcessor (const UnaryProcessor &)
virtual	~UnaryProcessor ()
virtual bool	finish ()

Protected Member Functions
Predicates
bool	isValid_ (const AtomContainer &ac)

Private Member Functions
bool	simpleCanBeAromatic_ (const HashSet< Atom * > &ring)
bool	simpleCanBeAromaticWeaker_ (const HashSet< Atom * > &ring)
void	extendAromaticSystem_ (vector< HashSet< Atom * > > &sssr, HashSet< Atom * > ring)
bool	hasConjugatedDoubleBonds_ (HashSet< Atom * > ring)
Size	countPiElectrons_ (HashSet< Atom * > &ring)

Private Attributes
bool	overwrite_bond_orders_

Public Attributes
Options	options
	options More...
void	setDefaultOptions ()

Additional Inherited Members
Public Types inherited from BALL::UnaryFunctor< AtomContainer, Processor::Result >
typedef Processor::Result	result_type
typedef AtomContainer	argument_type
typedef AtomContainer &	argument_reference
typedef const AtomContainer &	const_argument_reference
typedef AtomContainer *	argument_pointer
typedef const AtomContainer *	const_argument_pointer

Detailed Description

This processor provides methods for detection and assignment of aromaticity.

Aromaticity Processor

Processor method to detect aromaticity of AtomContainers. If it is called as a processor with the operator (), the RingPerceptionProcessor is called before, to calculate a ring set. It can be called explicitely with aromatize with a ringset as parameter.

Definition at line 28 of file aromaticityProcessor.h.

Constructor & Destructor Documentation

BALL::AromaticityProcessor::AromaticityProcessor

(

)

Default constructor

BALL::AromaticityProcessor::AromaticityProcessor

(

const AromaticityProcessor &

aro

)

Copy constructor

virtual BALL::AromaticityProcessor::~AromaticityProcessor ( )

virtual

Destrcutor

Member Function Documentation

void BALL::AromaticityProcessor::aromatize	(	const vector< vector< Atom * > > &	sssr,
		AtomContainer &	ac
	)

Calculated the aromaticity of the molcule and sets the properties "IsAromatic" for aromatic atoms, and Bond::ORDER__AROMATIC for bonds which are aromatic.

Parameters

SSSR	ring set as vector<vector<Atom*> >, (vector of rings in vector<Atom*>) after the processing this variable holds all aromatic systems, which are not necessarily single rings!

void BALL::AromaticityProcessor::aromatizeSimple

(

vector< vector< Atom * > > &

sssr

)

Method to set aromaticity with the use of simple rules. Each ring from the given SSSR set (which needs just to be a set of rings) is examined for itself. (needed for the implementation of the MMFF94 force field which does not agree with the advanced araomtaticity definition of the default method.).

It does not set any aromaticity flags, neither at the atoms nor bonds to bond order aromatic! sssr is the set to be examined, only aromatic rings will stay

Size BALL::AromaticityProcessor::countPiElectrons_ ( HashSet< Atom * > &  ring )

private

void BALL::AromaticityProcessor::extendAromaticSystem_ ( vector< HashSet< Atom * > > &  sssr, HashSet< Atom * >  ring  )

private

bool BALL::AromaticityProcessor::hasConjugatedDoubleBonds_ ( HashSet< Atom * >  ring )

private

bool BALL::AromaticityProcessor::isValid_ ( const AtomContainer &  ac )

protected

Processor::Result BALL::AromaticityProcessor::operator() ( AtomContainer &  )

virtual

operator ()

Reimplemented from BALL::UnaryProcessor< AtomContainer >.

AromaticityProcessor& BALL::AromaticityProcessor::operator=

(

const AromaticityProcessor &

aro

)

Assignment operator

void BALL::AromaticityProcessor::setDefaultOptions

(

)

reset the options to default values

bool BALL::AromaticityProcessor::simpleCanBeAromatic_ ( const HashSet< Atom * > &  ring )

private

bool BALL::AromaticityProcessor::simpleCanBeAromaticWeaker_ ( const HashSet< Atom * > &  ring )

private

virtual bool BALL::AromaticityProcessor::start ( )

virtual

start method

Reimplemented from BALL::UnaryProcessor< AtomContainer >.

Member Data Documentation

Options BALL::AromaticityProcessor::options

options

Definition at line 83 of file aromaticityProcessor.h.

bool BALL::AromaticityProcessor::overwrite_bond_orders_

private

Should we set the bond orders to aromatic or merely store the information as a property of the bond? This value depends on the value of the option OVERWRITE_BOND_ORDERS

Definition at line 166 of file aromaticityProcessor.h.