aromaticityProcessor.h

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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
//
 
#ifndef BALL_QSAR_AROMATICITYPROCESSOR_H
#define BALL_QSAR_AROMATICITYPROCESSOR_H
 
#ifndef BALL_KERNEL_ATOMCONTAINER_H
# include <BALL/KERNEL/atomContainer.h>
#endif
 
#ifndef BALL_DATATYPE_OPTIONS_H
  #include <BALL/DATATYPE/options.h>
#endif
 
namespace BALL
{
  class BALL_EXPORT AromaticityProcessor
    : public UnaryProcessor<AtomContainer>
  {
    public:


    struct BALL_EXPORT Option
    { 
      static const char* OVERWRITE_BOND_ORDERS; 
    };

    struct BALL_EXPORT Default
    {
      static const bool OVERWRITE_BOND_ORDERS;
    };


  
    BALL_CREATE(AromaticityProcessor)
 
    //@{    
    AromaticityProcessor();
  
    AromaticityProcessor(const AromaticityProcessor& aro);

    virtual ~AromaticityProcessor();



    AromaticityProcessor& operator = (const AromaticityProcessor& aro);


    Options options;

    void setDefaultOptions();


    void aromatize(const vector<vector<Atom*> >& sssr, AtomContainer& ac);

    void aromatizeSimple(vector<vector<Atom*> >& sssr);
    

    
    Processor::Result operator () (AtomContainer& ac);
    
    virtual bool start();
 
 
    protected:

    bool isValid_(const AtomContainer& ac);
 
 
    private:
 
    /*_ simple criterion if a ring can be aromatic
    */
    bool simpleCanBeAromatic_(const HashSet<Atom*>& ring);
 
    /*_ simple criterion if a ring can be aromatic, with weaker condition
        double bonds not need to be alternating inside the ring
    */
    bool simpleCanBeAromaticWeaker_(const HashSet<Atom*>& ring);
 
    /*_ Tries to extend an aromatic system. Main method that tries to extend 
        the aromaticity to intersecting rings.
        @param SSSR ring set as vector<HashSet<Atom*> >, (vector of rings in HashSet<Atom*>)
        @param ring as HashSet<Atom*>, the ring to extended
    */    
    void extendAromaticSystem_(vector<HashSet<Atom*> >& sssr, HashSet<Atom*> ring);
      
    /*_ Predicate that return true if the ring has conjugated double bonds. The criterion 
        is very weak, beacuse the predicate only considers carbon atoms, no hetero atoms
        are counted.
        @param ring as HashSet<Atom*>, to be tested
    */
    bool hasConjugatedDoubleBonds_(HashSet<Atom*> ring);
      
    /*_ This mthod return the number of pi electrons in the ring (aromatic system)
        @param ring as HashSet<Atom*>, from which the number of pi electrons to count
    */
    Size countPiElectrons_(HashSet<Atom*>& ring);

    bool overwrite_bond_orders_;
  };
} // namespace BALL
 
#endif // BALL_QSAR_AROMATICITYPROCESSOR_H