File frames.hpp

This file contains a management class for framesets and specifies framesets for different trajectory types.

Author

Benjamin Lindner ben@benlabs.net

Version

See VERSION in CMakeLists.txt

Copyright

GNU General Public License

class Frames

#include <frames.hpp>

Management class for framesets.

Public Functions

inline Frames()

size_t size()

size_t add_frameset(const std::string filename, const std::string filetype, size_t first, size_t last, bool last_set, size_t stride, const std::string index_filename, bool index_default, size_t clones)

Frame load(size_t framenumber)

Private Functions

template<class Archive>
inline void serialize(Archive &ar, const unsigned int version)

Frameset &find_frameset(size_t framenumber)

void test_framenumber(size_t framenumber)

Private Members

std::vector<Frameset*> framesets

size_t number_of_frames

Friends

friend class boost::serialization::access

class Frameset

#include <frames.hpp>

Interface for framesets. Real framesets are based on a particular format.

Subclassed by CloneFrameset, FileFrameset

Public Functions

virtual void read_frame(size_t framenumber, Frame &cf) = 0

Public Members

size_t frame_number_offset

size_t number_of_frames

size_t number_of_atoms

Private Functions

template<class Archive>
inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class FileFrameset : public Frameset

#include <frames.hpp>

Derived frameset which implements file access functionality.

Subclassed by DCDFrameset, PDBFrameset, TRRFrameset, XTCFrameset

Public Functions

inline virtual ~FileFrameset()

void trim_index(size_t first, size_t last, bool last_set, size_t stride)

void load_index(std::string cache_filename)

void save_index(std::string cache_filename)

virtual void generate_index() = 0

Public Members

FramesetIndex frameset_index_

std::string filename

Private Functions

template<class Archive>
inline void serialize(Archive &ar, const unsigned int version)

Friends

friend class boost::serialization::access

class DCDHeader

#include <frames.hpp>

Type class representing the DCD file header structure.

Public Members

int32_t headsize

int32_t fingerprint

int32_t number_of_frames

int32_t dummy1

int32_t timesteps_between_frames

char buf1[24]

float size_of_timestep

int32_t flag_ext_block1

int32_t flag_ext_block2

class DCDFrameset : public FileFrameset

#include <frames.hpp>

Frameset class for the DCD trajectory file format.

Public Functions

inline DCDFrameset()

~DCDFrameset()

void init(std::string filename, size_t framenumber_offset)

inline DCDFrameset(std::string filename, size_t frame_number_offset)

virtual void read_frame(size_t framenumber, Frame &cf)

virtual void generate_index()

void close()

Private Functions

template<class Archive>
inline void serialize(Archive &ar, const unsigned int version)

bool detect(const std::string filename)

Private Members

std::streamoff init_byte_pos

unsigned long flag_ext_block1

unsigned long flag_ext_block2

std::streamoff block_size_byte

std::streamoff x_byte_offset

std::streamoff y_byte_offset

std::streamoff z_byte_offset

std::streamoff block1_byte_offset

std::streamoff block2_byte_offset

std::ifstream dcdfile

Friends

friend class boost::serialization::access

class PDBFrameset : public FileFrameset

#include <frames.hpp>

Frameset class for the PDB trajectory file format, based on VMD animate write.

Public Functions

inline PDBFrameset()

void init(std::string filename, size_t framenumber_offset)

inline PDBFrameset(std::string filename, size_t frame_number_offset)

virtual void read_frame(size_t framenumber, Frame &cf)

virtual void generate_index()

Private Functions

template<class Archive>
inline void serialize(Archive &ar, const unsigned int version)

bool detect(const std::string filename)

Private Members

std::vector<CartesianCoor3D> default_uc

Friends

friend class boost::serialization::access

class XTCFrameset : public FileFrameset

#include <frames.hpp>

Frameset class for the XTC trajectory file format.

Public Functions

inline XTCFrameset()

~XTCFrameset()

void init(std::string filename, size_t framenumber_offset)

inline XTCFrameset(std::string filename, size_t frame_number_offset)

virtual void read_frame(size_t framenumber, Frame &cf)

virtual void generate_index()

void close()

Private Functions

template<class Archive>
inline void serialize(Archive &ar, const unsigned int version)

bool detect(const std::string filename)

Private Members

XDRFILE *p_xdrfile

Friends

friend class boost::serialization::access

class TRRFrameset : public FileFrameset

#include <frames.hpp>

Frameset class for the TRR trajectory file format.

Public Functions

inline TRRFrameset()

~TRRFrameset()

void init(std::string filename, size_t framenumber_offset)

inline TRRFrameset(std::string filename, size_t frame_number_offset)

virtual void read_frame(size_t framenumber, Frame &cf)

virtual void generate_index()

void close()

Private Functions

template<class Archive>
inline void serialize(Archive &ar, const unsigned int version)

bool detect(const std::string filename)

Private Members

XDRFILE *p_xdrfile

Friends

friend class boost::serialization::access

class CloneFrameset : public Frameset

#include <frames.hpp>

Pseudo frameset which is a reference to another one and can be used to efficiently multiply coordinates.

Public Functions

inline CloneFrameset()

CloneFrameset(Frameset *original, size_t nof)

virtual void read_frame(size_t framenumber, Frame &cf)

Private Functions

template<class Archive>
inline void serialize(Archive &ar, const unsigned int version)

Private Members

Frameset *p_originalframeset

Friends

friend class boost::serialization::access