DCDFile.h

Go to the documentation of this file.

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

#ifndef BALL_FORMAT_DCDFILE_H
#define BALL_FORMAT_DCDFILE_H

#ifndef BALL_FORMAT_TRAJECTORYFILE_H
# include <BALL/FORMAT/trajectoryFile.h>
#endif

#ifndef BALL_SYSTEM_BINARYFILEADAPTOR_H
# include <BALL/SYSTEM/binaryFileAdaptor.h>
#endif

namespace BALL
{
  class BALL_EXPORT DCDFile
    : public TrajectoryFile
  {
    public:


    DCDFile();

    DCDFile(const String& name, File::OpenMode open_mode = std::ios::in);

    virtual ~DCDFile();



    virtual void clear();



    bool operator == (const DCDFile& file) const;

    bool isSwappingBytes() const;

    bool hasVelocities() const;



    virtual bool open(const String& name, File::OpenMode open_mode = std::ios::in);

    bool init();

    virtual bool readHeader();

    virtual bool writeHeader();

    virtual bool seekAndWriteHeader();

    // ?????:
    // should append() also write the header? what is more intuitive?
    virtual bool append(const SnapShot& snapshot);

    virtual bool read(SnapShot& snapshot);

    virtual bool flushToDisk(const std::vector<SnapShot>& buffer);



    void enableVelocityStorage();

    void disableVelocityStorage();


    private:
      const DCDFile& operator = (const DCDFile& file);

    protected:

    //_ 
    void writeSize_(const Size& data)
       { *this << BinaryFileAdaptor<Size>(data);}

    //_ 
    void writeFloat_(const float& data)
       { *this << BinaryFileAdaptor<float>(data);}

    //_
    void writeVector_(const vector<Vector3>& v);
    
    //_
    float readFloat_(); 

    //_
    Size readSize_();

    //_
    bool readSize_(Size expected_size, const String& what);

    //_
    bool readVector_(vector<Vector3>& v);

    //_
    Size verbosity_;

    // a flag indicating that we have to swap bytes when reading data
    bool swap_bytes_;

    // a floag indicating that this DCD file contains atom velocities
    bool has_velocities_;

    //_
    bool charmm_extra_block_A_;

    //_
    bool charmm_extra_block_B_;

    //_
    String CORD_;

    //_
    Size step_number_of_starting_time_;

    //_
    Size steps_between_saves_;

    //_
    double time_step_length_;

    //_
    Size number_of_comments_;

    /*_ We had a problem with read(Snapshot), as it
        still returned true at the end of file. No idea
        why the stream was still good! To fix this,
        I added this member to count the current read snapshot.
    */
    Position current_snapshot_;

    BinaryFileAdaptor<Size>  adapt_size_;
    BinaryFileAdaptor<float> adapt_float_;
  };
} // namespace BALL

#endif // BALL_FORMAT_DCDFILE_H