peptides.h

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

#ifndef BALL_STRUCTURE_PEPTIDES_H
#define BALL_STRUCTURE_PEPTIDES_H

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

#ifndef BALL_KERNEL_PROTEIN_H
# include <BALL/KERNEL/protein.h>
#endif

#ifndef BALL_DATATYPE_OPTIONS_H
# include <BALL/DATATYPE/options.h>
#endif

#ifndef BALL_CONCEPT_EMBEDDABLE_H
# include <BALL/CONCEPT/embeddable.h>
#endif

namespace BALL 
{

  namespace Peptides
  {

    typedef std::list<String> ThreeLetterAASequence;

    typedef String OneLetterAASequence;


    BALL_EXPORT char OneLetterCode(const String& aa);

    BALL_EXPORT String ThreeLetterCode(char aa);

    BALL_EXPORT bool IsOneLetterCode(char aa);
    
    BALL_EXPORT bool IsThreeLetterCode(const String& aa);

    BALL_EXPORT OneLetterAASequence ThreeLetterToOneLetter(const ThreeLetterAASequence& sequence);
  
    BALL_EXPORT ThreeLetterAASequence OneLetterToThreeLetter(const OneLetterAASequence& sequence);

    BALL_EXPORT OneLetterAASequence GetSequence(const Protein& protein);  
    
    BALL_EXPORT OneLetterAASequence GetSequence(const Chain& chain);

    BALL_EXPORT OneLetterAASequence GetSequence(ResidueConstIterator it);
   
//

    class BALL_EXPORT NameConverter
      : public Embeddable
    {
      public:
        BALL_EMBEDDABLE(NameConverter, Embeddable)

        
        
        static const String VALUE_NA;
      
        struct BALL_EXPORT Option
        { 
          static const char* INIFile; 
          
          static const char* PSEUDO_ATOMS_INIFile;  

        };

        struct BALL_EXPORT Default
        {
          static const String INIFile;
          static const String PSEUDO_ATOMS_INIFile;
        };
    
        NameConverter();
      
        virtual ~NameConverter() {}
    
        void setDefaultOptions();

        bool supportsNamingScheme(const String& scheme_name) const;

        bool supportsPseudoAtomNamingScheme(const String& scheme_name) const;
  
        String convertName(const String& amino_acid, const String& old_atom_name,
                           const String& old_naming_scheme, const String& new_naming_scheme) const;
          
        bool matches(const String& amino_acid, const String& old_atom_name,
                     const String& old_naming_scheme, const String& new_atom_name,
                     const String& new_naming_scheme) const;

        std::vector<String> resolvePseudoAtoms(const String& amino_acid, const String& atom_name, 
                                               const String& old_naming_scheme, const String& new_naming_scheme) const;

        Options options;

      protected:  
        
        void readConversionTable_()
          throw (Exception::FileNotFound());
      
        void readPseudoAtomsConversionTable_()
          throw (Exception::FileNotFound());

        std::vector<String>                 conventions_;
        std::vector< std::vector <String> > conversion_table_;  
        
        std::vector<String>                 pseudo_conventions_;
        std::vector< std::vector <std::vector <String> > > pseudo_conversion_table_;

        //TODO: unse a StringHashMap of amino acid names to simplify the access
    };

  }  // namespace Peptides

} // namespace BALL

#endif // BALL_STRUCTURE_PEPTIDES_H_