BALL::TRRFile Class Reference
[Molecular
Dynamics Trajectory File Formats]
TRR Trajectory
file format. More...
#include <TRRFile.h>
Inheritance diagram for BALL::TRRFile:
[legend]
Classes |
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| class | TRRHeader |
| The header for each coordinate set
stored in the TRR file. More... |
|
Public Member Functions |
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Constructors and Destructor
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| TRRFile () | |
| Default constructor. |
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| TRRFile (const TRRFile &file) throw (Exception::FileNotFound) | |
| Copy constructor. |
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| TRRFile (const String &name, File::OpenMode open_mode=std::ios::in) | |
| Construct and open a
file. |
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| virtual | ~TRRFile () |
| Destructor. |
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Assignment
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| const TRRFile & | operator= (const TRRFile &file) |
| Assignment operator. |
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| virtual void | clear () |
| Clear method. |
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Predicates
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| bool | operator== (const TRRFile &file) const |
| Equality operator. |
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Public methods for file handling
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| virtual bool | init () |
| Initialize the file for
usage. |
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| virtual bool | writeNextHeader (const TRRHeader &header) |
| Writes the next header that shall
preceed the next data block. |
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| virtual bool | readNextHeader (TRRHeader &header) |
| Reads the next header preceding the
next data block. |
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| virtual bool | append (const SnapShot &snapshot) |
| Append a
SnapShot to an existing file. |
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| virtual bool | read (SnapShot &snapshot) |
| Read the next snapshot from the
file. |
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| virtual TRRFile & | operator>> (SnapShotManager &ssm) |
| Read the whole file into a SnapShotManager. |
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| virtual bool | flushToDisk (const std::vector< SnapShot > &buffer) throw (File::CannotWrite) |
| Write several SnapShots to disk.
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Accessors
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| bool | hasVelocities () const |
| void | setVelocityStorage (bool storage) |
| bool | hasForces () const |
| void | setForceStorage (bool storage) |
| Size | getPrecision () const |
| bool | setPrecision (const Size precision) |
| float | getTimestep () const |
| void | setTimestep (float timestep) |
| Vector3 | getBoundingBoxX () const |
| Vector3 | getBoundingBoxY () const |
| Vector3 | getBoundingBoxZ () const |
| void | setBoundingBox (const Vector3 &x, const Vector3 &y, const Vector3 &z) |
Protected Attributes |
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| TRRHeader | header_ |
| Size | precision_ |
| bool | has_velocities_ |
| bool | has_forces_ |
| Size | timestep_index_ |
| float | timestep_ |
| Vector3 | box1_ |
| Vector3 | box2_ |
| Vector3 | box3_ |
| BinaryFileAdaptor< Size > | adapt_size_ |
| BinaryFileAdaptor< char > | adapt_char_ |
| BinaryFileAdaptor< float > | adapt_float_ |
| BinaryFileAdaptor< double > | adapt_double_ |
Detailed Description
TRR Trajectory file format.This class enables BALL to read and write GROMACS TRR files. This format is portable.
- In a TRR file, each timestep is preceded by a header. The header is handled by the nested TRRHeader class.
Member Function Documentation
| virtual bool BALL::TRRFile::append | ( | const SnapShot & | snapshot | ) | [virtual] |
Append a SnapShot to an existing file.
- Parameters:
-
snapshot the SnapShot we want to store
- Returns:
- true, if writing was successful
Reimplemented from BALL::TrajectoryFile.
| virtual bool BALL::TRRFile::flushToDisk | ( | const std::vector< SnapShot > & | buffer | ) | throw (File::CannotWrite)
[virtual] |
Write several SnapShots to disk.
- Parameters:
-
buffer a vector of snapshots
- Returns:
- true, if flushing was successful, false ow.
Reimplemented from BALL::TrajectoryFile.
| virtual bool BALL::TRRFile::read | ( | SnapShot & | snapshot | ) | [virtual] |
Read the next snapshot from the file.
- Parameters:
-
snapshot a buffer for result delivery
- Returns:
- true, if a snapshot could be read, false otherwise.
Reimplemented from BALL::TrajectoryFile.
| virtual bool BALL::TRRFile::readNextHeader | ( | TRRHeader & | header | ) | [virtual] |
Reads the next header preceding the next data block.
- Parameters:
-
header a buffer for result delivery
- Returns:
- true, if a header could be read, false ow.
