smilesParser.h

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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//

#ifndef BALL_STRUCTURE_SMILES_PARSER_H
#define BALL_STRUCTURE_SMILES_PARSER_H

#ifndef BALL_COMMON_H
# include <BALL/common.h>
#endif

#ifndef BALL_KERNEL_ATOM_H
# include <BALL/KERNEL/atom.h>
#endif

#ifndef BALL_KERNEL_BOND_H
# include <BALL/KERNEL/bond.h>
#endif

#ifndef BALL_KERNEL_SYSTEM_H
# include <BALL/KERNEL/system.h>
#endif

namespace BALL 
{

  class BALL_EXPORT SmilesParser
  {
    public:
    enum ZEIsomerType
    {
      NONE,
      Z,
      E
    };

    enum ChiralClass
    {
      NONCHIRAL,
      TH,
      AL,
      SP,
      TB,
      OH
    };

    enum
    {
      MAX_CONNECTIONS = 100
    };

    typedef std::pair<ChiralClass, Position> ChiralDef;

    class SPAtom;
    class BALL_EXPORT SPBond 
      : public Bond
    {
      public:
      virtual ~SPBond() ;

      SPBond(SPAtom* first, SPAtom* second, Index order = 1);

      ZEIsomerType getZEType() const;
      void setZEType(ZEIsomerType type);

      protected:
      ZEIsomerType  ze_type_;
    };
    
    class BALL_EXPORT SPAtom
      : public Atom
    {
      public:
        
      SPAtom(const String& symbol, bool in_brackets);
      virtual ~SPAtom() ;

      Size getDefaultValence() const;
      Size countRealValences() const;

      Size getIsotope() const { return isotope_; }
      void setIsotope(Size isotope) { isotope_ = isotope; };

      Index getFormalCharge() const { return formal_charge_; }
      void setFormalCharge(Index charge) { formal_charge_ = charge; }
      
      const ChiralDef& getChirality() const { return chirality_; }
      void setChirality(const ChiralDef& chirality) { chirality_ = chirality; }
      
      bool isAromatic() const { return is_aromatic_; }
      void setAromatic(bool is_aromatic) { is_aromatic_ = is_aromatic; };
      bool isInBrackets() const { return in_brackets_; }
      void setInBrackets(bool in_brackets) { in_brackets_ = in_brackets; };

      protected:
      Size        isotope_;
      Index       formal_charge_;
      ChiralDef   chirality_;
      bool        is_aromatic_;
      bool        in_brackets_;
    };
    
    typedef std::list<Position> ConnectionList;


    SmilesParser();
      
    SmilesParser(const SmilesParser& parser);

    virtual ~SmilesParser();
    
    void parse(const String& s)
      throw(Exception::ParseError);

    const System& getSystem() const;
    
    SPAtom* createAtom(const String& symbol, bool in_bracket = false);

    void createBonds(SPAtom* atom, const ConnectionList* list);   

    void createBond(SPAtom* left, SPAtom* right, Index order);

    void addMissingHydrogens();
    

    struct State
    {
      Size          char_count;
      SmilesParser* current_parser;
      const char*   buffer;
    };
    
    static State state;

    protected:
    System                system_;
    std::vector<SPAtom*>  connections_;
    std::vector<SPAtom*>  all_atoms_;
    static SmilesParser*  current_parser_;
  };
  
} // namespace BALL

#endif // BALL_STRUCTURE_SMILES_PARSER_H