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AromaticityProcessor Class Reference

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

#include <aromaticityProcessor.h>

Inheritance diagram for AromaticityProcessor:

UnaryProcessor< AtomContainer > UnaryFunctor< AtomContainer, Processor::Result > List of all members.

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 ()

Protected Member Functions

Predicates
bool isValid_ (const AtomContainer &ac)

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.

Member Function Documentation

void 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 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