NMRStarFile.h.REMOTE.23414.h

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

#ifndef BALL_FORMAT_NMRSTARFILE_H
#define BALL_FORMAT_NMRSTARFILE_H

#ifndef BALL_FORMAT_CIFFILE_H
# include<BALL/FORMAT/CIFFile.h>
#endif

#ifndef BALL_COMMON_LIMITS_H
# include<BALL/COMMON/limits.h>
#endif

#include <vector>

namespace BALL 
{
  
  class BALL_EXPORT NMRStarFile
    : public CIFFile
  {
    public:
      BALL_CREATE(NMRStarFile)

      static const float FLOAT_VALUE_NA;
      static const Position POSITION_VALUE_NA;

    
      class BALL_EXPORT NMRAtomData
      {
        public:
          NMRAtomData();

          Position  atom_ID;
          Position  residue_seq_code;
          String    residue_label;
          String    atom_name;
          char      atom_type;
          float     shift_value;
          float     error_value;
          Position  ambiguity_code;

          std::ostream& operator >> (std::ostream& s) throw();
      };

      class BALL_EXPORT SampleCondition
      {
        public:
          SampleCondition();
  
          String  name;
          float   temperature;
          float   pH;
          float   pressure;
  
          std::ostream& operator >> (std::ostream& s) throw();
      };

      class BALL_EXPORT ShiftReferenceElement
      {
        public:
          ShiftReferenceElement();

          String    mol_common_name;
          char      atom_type;
          Position  isotope_number;
          String    atom_group;
          String    shift_units;
          float     shift_value;
          char      reference_method;
          char      reference_type;
          float     indirect_shift_ratio;

          std::ostream& operator >> (std::ostream& s) throw();
      };

      class BALL_EXPORT ShiftReferenceSet
      {
        public: 
          ShiftReferenceSet();
        
          String name;
          std::vector<ShiftReferenceElement> elements;

          std::ostream& operator >> (std::ostream& s);
      };
      
      class BALL_EXPORT NMRAtomDataSet
      {
        public:
          NMRAtomDataSet();

          String                    name;
          std::vector<NMRAtomData>  atom_data;
          SampleCondition           condition;
          ShiftReferenceSet         reference;

          std::ostream& operator >> (std::ostream& s);
      };

      class BALL_EXPORT EntryInformation
      {
        public:
          EntryInformation();
          ~EntryInformation();
          std::ostream& operator >> (std::ostream& s);

          String entry_type;
          String BMRB_accession_code;
          String NMR_STAR_version;
          String experimental_method;
      };
  


      NMRStarFile();
      
      NMRStarFile(const NMRStarFile& f)
        throw(Exception::FileNotFound);

      NMRStarFile(const String& file_name, File::OpenMode open_mode = std::ios::in)
        throw(Exception::FileNotFound);

      ~NMRStarFile();

      const NMRStarFile& operator = (const NMRStarFile& f);
      
      bool read()
        throw(Exception::ParseError);

      void clear();




      Size getNumberOfAtoms()  // TODO!!!  
        const ;

      const std::vector<NMRAtomDataSet>& getData()
        const ;

      const EntryInformation& getEntryInformation() const {return entry_information_;};

    //  SaveFrame& getSaveframe(String category, Position db_pos = 0);
    //  const SaveFrame& getSaveframe(String category, Position db_pos = 0) const;

  //    const CIFFile::Item* hasColumn(const SaveFrame* sf, String name);
  // TODO ;; bool hasColumn(const SaveFrame* sf, String name);



      bool operator == (const NMRStarFile& f)  ;

      bool operator != (const NMRStarFile& f)  ;



      enum ReferenceMethod
      {
        INTERNAL_REFERENCE,
        EXTERNAL_REFERENCE,
        UNKNOWN_REFERENCE,
        UNSET_REFERENCE
      };

      enum ReferenceType
      {
        DIRECT_TYPE,
        INDIRECT_TYPE,
        UNKNOWN_TYPE,
        UNSET_TYPE
      };


    private:

      /*_ @name NMR-Star specific Help-Methods
       */
      //_@{

      //    NMRAtomData processShiftLine_()
      //      throw(Exception::ParseError);

      void readEntryInformation_()
        throw(Exception::ParseError, Exception::InvalidFormat);

      void readMolSystem_()
        ;

      void readSampleConditions_()
        ;

      void readShiftReferences_()
        ;

      void readShifts_()
        throw (Exception::ParseError);

      static void initializeReferenceOptions_()
        ;

      //_@}
      /*_ @name NMR-Star specific attributes
      */
      //_@{

      Size number_of_shifts_;
 
      //
      EntryInformation entry_information_;

      std::vector<NMRAtomDataSet> atom_data_sets_;

      std::vector<SampleCondition> sample_conditions_;

      std::vector<ShiftReferenceSet> shift_references_;

      String system_name_;

      static std::vector<String> reference_options_;
  
      // a dummy saveframe
      SaveFrame dummy_saveframe_; // TODO : add to clear... Constructor..

      enum ShiftReferenceTypes_
      {
        MOL_COMMON_NAME,
        ATOM_TYPE,
        ISOTOPE_NUMBER,
        ATOM_GROUP,
        SHIFT_UNITS,
        SHIFT_VALUE,
        REFERENCE_METHOD,
        REFERENCE_TYPE,
        INDIRECT_SHIFT_RATIO
      };

      //_@}
  };

} // Namespace BALL

#endif // BALL_FORMAT_NMRSTARFILE_H

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