, including all inherited members.
| adapt_float_ (defined in DCDFile) | DCDFile | [protected] |
| adapt_size_ (defined in DCDFile) | DCDFile | [protected] |
| append(const SnapShot &snapshot) | DCDFile | [virtual] |
| charmm_extra_block_A_ (defined in DCDFile) | DCDFile | [protected] |
| charmm_extra_block_B_ (defined in DCDFile) | DCDFile | [protected] |
| clear() | DCDFile | [virtual] |
| close() | File | |
| copy(String source_name, String destination_name, Size buffer_size=4096) | File | [static] |
| copyTo(const String &destination_name, Size buffer_size=4096) | File | |
| CORD_ (defined in DCDFile) | DCDFile | [protected] |
| createTemporaryFilename(String &temporary) | File | [static] |
| current_snapshot_ (defined in DCDFile) | DCDFile | [protected] |
| DCDFile() | DCDFile | |
| DCDFile(const DCDFile &file) | DCDFile | |
| DCDFile(const String &name, File::OpenMode open_mode=std::ios::in) | DCDFile | |
| disableTransformation(Transformation transformation) (defined in File) | File | [static] |
| disableVelocityStorage() (defined in DCDFile) | DCDFile | |
| enableTransformation(Transformation transformation) (defined in File) | File | [static] |
| enableVelocityStorage() (defined in DCDFile) | DCDFile | |
| File() | File | |
| File(const String &name, OpenMode open_mode=std::ios::in) | File | |
| File(const File &file) | File | |
| flushToDisk(const std::vector< SnapShot > &buffer) | DCDFile | [virtual] |
| getFileStream() | File | |
| getName() const | File | |
| getNumberOfAtoms() const | TrajectoryFile | |
| getNumberOfSnapShots() const | TrajectoryFile | |
| getOpenMode() const | File | |
| getOriginalName() const (defined in File) | File | |
| getSize() | File | |
| getSize(String name) | File | [static] |
| getTransformationManager() | File | |
| getTransformationManager() const | File | |
| getType(String name, bool trace_link) | File | [static] |
| getType(bool trace_link) const | File | |
| has_velocities_ (defined in DCDFile) | DCDFile | [protected] |
| hasVelocities() const (defined in DCDFile) | DCDFile | |
| init() | DCDFile | |
| is_open_ (defined in File) | File | [protected] |
| is_temporary_ (defined in File) | File | [protected] |
| isAccessible(String name) | File | [static] |
| isAccessible() const | File | |
| isCanonized() const | File | |
| isClosed() const | File | |
| isExecutable(String name) | File | [static] |
| isExecutable() const | File | |
| isOpen() const | File | |
| isReadable(String name) | File | [static] |
| isReadable() const | File | |
| isSwappingBytes() const (defined in DCDFile) | DCDFile | |
| isTransformationEnabled(Transformation transformation) (defined in File) | File | [static] |
| isValid() const | File | |
| isWritable(String name) | File | [static] |
| isWritable() const | File | |
| MODE_APP | File | [static] |
| MODE_ATE | File | [static] |
| MODE_BINARY | File | [static] |
| MODE_IN | File | [static] |
| MODE_OUT | File | [static] |
| MODE_TRUNC | File | [static] |
| move(const String &source_name, const String &destination_name) | File | [static] |
| moveTo(const String &destination_name) | File | |
| name_ (defined in File) | File | [protected] |
| number_of_atoms_ (defined in TrajectoryFile) | TrajectoryFile | [protected] |
| number_of_comments_ (defined in DCDFile) | DCDFile | [protected] |
| number_of_snapshots_ (defined in TrajectoryFile) | TrajectoryFile | [protected] |
| open(const String &name, File::OpenMode open_mode=std::ios::in) | DCDFile | [virtual] |
| open_mode_ (defined in File) | File | [protected] |
| OpenMode typedef | File | |
| operator!=(const File &file) const | File | |
| operator=(const DCDFile &file) | DCDFile | |
| TrajectoryFile::operator=(const TrajectoryFile &file) | TrajectoryFile | |
| File::operator=(const File &file) | File | |
| operator==(const DCDFile &file) const | DCDFile | |
| TrajectoryFile::operator==(const TrajectoryFile &file) const | TrajectoryFile | |
| File::operator==(const File &file) const | File | |
| original_name_ (defined in File) | File | [protected] |
| read(SnapShot &snapshot) | DCDFile | [virtual] |
| readFloat_() (defined in DCDFile) | DCDFile | [protected] |
| readHeader() | DCDFile | [virtual] |
| readSize_() (defined in DCDFile) | DCDFile | [protected] |
| readSize_(Size expected_size, const String &what) (defined in DCDFile) | DCDFile | [protected] |
| readVector_(vector< Vector3 > &v) (defined in DCDFile) | DCDFile | [protected] |
| registerTransformation(const String &pattern, const String &exec) (defined in File) | File | [static] |
| remove(String name) | File | [static] |
| remove() | File | |
| rename(String old_path, String new_path) | File | [static] |
| renameTo(const String &new_path) | File | |
| reopen() | File | |
| reopen(File::OpenMode open_mode) | File | |
| seekAndWriteHeader() (defined in DCDFile) | DCDFile | [virtual] |
| setName(const String &name) | File | |
| step_number_of_starting_time_ (defined in DCDFile) | DCDFile | [protected] |
| steps_between_saves_ (defined in DCDFile) | DCDFile | [protected] |
| swap_bytes_ (defined in DCDFile) | DCDFile | [protected] |
| time_step_length_ (defined in DCDFile) | DCDFile | [protected] |
| TrajectoryFile() | TrajectoryFile | |
| TrajectoryFile(const TrajectoryFile &file) | TrajectoryFile | |
| TrajectoryFile(const String &filename, File::OpenMode open_mode=std::ios::in) | TrajectoryFile | |
| Transformation enum name | File | |
| TRANSFORMATION__EXEC enum value (defined in File) | File | |
| TRANSFORMATION__FILTER enum value (defined in File) | File | |
| TRANSFORMATION__URL enum value (defined in File) | File | |
| TRANSFORMATION_EXEC_PREFIX | File | [static] |
| TRANSFORMATION_FILE_PREFIX | File | [static] |
| TRANSFORMATION_FTP_PREFIX | File | [static] |
| TRANSFORMATION_HTTP_PREFIX | File | [static] |
| transformation_manager_ (defined in File) | File | [protected, static] |
| transformation_methods_ (defined in File) | File | [protected, static] |
| truncate(String path, Size size=0) | File | [static] |
| truncate(Size size=0) | File | |
| Type enum name | File | |
| TYPE__BLOCK_SPECIAL_FILE enum value (defined in File) | File | |
| TYPE__CHAR_SPECIAL_FILE enum value (defined in File) | File | |
| TYPE__DIRECTORY enum value (defined in File) | File | |
| TYPE__FIFO_SPECIAL_FILE enum value (defined in File) | File | |
| TYPE__REGULAR_FILE enum value (defined in File) | File | |
| TYPE__SOCKET enum value (defined in File) | File | |
| TYPE__SYMBOLIC_LINK enum value (defined in File) | File | |
| TYPE__UNKNOWN enum value (defined in File) | File | |
| unregisterTransformation(const String &pattern) (defined in File) | File | [static] |
| verbosity_ (defined in DCDFile) | DCDFile | [protected] |
| writeFloat_(const float &data) (defined in DCDFile) | DCDFile | [protected] |
| writeHeader() | DCDFile | [virtual] |
| writeSize_(const Size &data) (defined in DCDFile) | DCDFile | [protected] |
| writeVector_(const vector< Vector3 > &v) (defined in DCDFile) | DCDFile | [protected] |
| ~DCDFile() | DCDFile | [virtual] |
| ~File() | File | [virtual] |
| ~TrajectoryFile() | TrajectoryFile | [virtual] |