NMRStarFile.h

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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: NMRStarFile.h,v 1.29 2005/12/23 17:01:44 amoll Exp $
//

#ifndef BALL_NMR_READ_STAR_H
#define BALL_NMR_READ_STAR_H

#ifndef BALL_FORMAT_LineBasedFile_H
# include<BALL/FORMAT/lineBasedFile.h>
#endif

#include <vector>

namespace BALL 
{

  struct BALL_EXPORT NMRAtomData
  {
    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;
  };

  struct BALL_EXPORT SampleCondition
  {
    SampleCondition() ;

    String  name;
    float   temperature;
    float   pH;
    float   pressure;
  };

  struct BALL_EXPORT ShiftReferenceElement
  {
    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;
  };

  struct BALL_EXPORT ShiftReferenceSet
  {
    ShiftReferenceSet() ;
    String name;
    std::vector<ShiftReferenceElement> elements;
  };

  struct BALL_EXPORT NMRAtomDataSet
  {
    NMRAtomDataSet() ;

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

  std::ostream& operator << (std::ostream& s, const NMRAtomData&            ad) ;
  std::ostream& operator << (std::ostream& s, const SampleCondition&        sc) ;
  std::ostream& operator << (std::ostream& s, const ShiftReferenceElement& sre) ;
  std::ostream& operator << (std::ostream& s, const ShiftReferenceSet&      sr) ;
  std::ostream& operator << (std::ostream& s, const NMRAtomDataSet&        set) ;
  

  class BALL_EXPORT NMRStarFile
    : public LineBasedFile
  {
    public:

      BALL_CREATE(NMRStarFile)

      

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

      NMRStarFile(const String& file_name)
        throw(Exception::FileNotFound, Exception::ParseError);

      const NMRStarFile& operator = (const NMRStarFile& f)  
        ;

      ~NMRStarFile()
        ;
        
      void clear() 
        ;




      Size getNumberOfAtoms() 
        const ;

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



      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_;

      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_;

      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_NMR_READ_STAR_H