BALL::AromaticityProcessor Class Reference

Processor method to detect aromaticity of AtomContainers. More...

#include <aromaticityProcessor.h>

Inheritance diagram for BALL::AromaticityProcessor:

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List of all members.

Classes
struct	Default
	Default values for options. More...
struct	Option
	Option names. More...
Public Member Functions
Constructors and Destructors
	AromaticityProcessor ()
	Default constructor.
	AromaticityProcessor (const AromaticityProcessor &aro)
	Copy constructor.
virtual	~AromaticityProcessor ()
	Destrcutor.
Assignment
AromaticityProcessor &	operator= (const AromaticityProcessor &aro)
	Assignment operator.
Accessors
void	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.
void	aromatizeSimple (vector< vector< Atom * > > &sssr)
	Method to set aromaticity with the use of simple rules.
Processor-related methods
Processor::Result	operator() (AtomContainer &ac)
	operator ()
virtual bool	start ()
	start method
Protected Member Functions
Predicates
bool	isValid_ (const AtomContainer &ac)
Public Attributes
Options	options
	options
void	setDefaultOptions ()
	reset the options to default values

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Detailed Description

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.

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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