BALL::DCDFile Class Reference
[Molecular
Dynamics Trajectory File Formats]
DCD Trajectory
file format. More...
#include <DCDFile.h>
Inheritance diagram for BALL::DCDFile:
[legend]
Public Member Functions |
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Constructors and Destructor
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| DCDFile () | |
| Default constructor. |
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| DCDFile (const DCDFile &file) throw (Exception::FileNotFound) | |
| Copy constructor. |
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| DCDFile (const String &name, File::OpenMode open_mode=std::ios::in) throw (Exception::FileNotFound) | |
| Detailed constructor. |
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| virtual | ~DCDFile () |
| Destructor. |
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Assignment
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| const DCDFile & | operator= (const DCDFile &file) |
| Assignment operator. |
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| virtual void | clear () |
| Clear method. |
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Predicates
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| bool | operator== (const DCDFile &file) const |
| Equality operator. |
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| bool | isSwappingBytes () const |
| bool | hasVelocities () const |
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Public methods for file handling
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| virtual bool | open (const String &name, File::OpenMode open_mode=std::ios::in) throw (Exception::FileNotFound) |
| open a DCDFile |
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| bool | init () |
| Initialize this instance, i.
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| virtual bool | readHeader () |
| Read the header of an existing file.
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| virtual bool | writeHeader () |
| Write a header Return true if the
header could be written successfully, false ow. |
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| virtual bool | seekAndWriteHeader () |
| 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 bool | flushToDisk (const std::vector< SnapShot > &buffer) throw (File::CannotWrite) |
| Write several SnapShots to disk.
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Accessors
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| void | enableVelocityStorage () |
| void | disableVelocityStorage () |
Protected Member Functions |
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| void | writeSize_ (const Size &data) |
| void | writeFloat_ (const 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) |
Protected Attributes |
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| Size | verbosity_ |
| bool | swap_bytes_ |
| 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_ |
| Position | current_snapshot_ |
| BinaryFileAdaptor< Size > | adapt_size_ |
| BinaryFileAdaptor< float > | adapt_float_ |
Detailed Description
DCD Trajectory file format.This class enables BALL to write DCD files that can be read by VMD. The format stems from the xplor package. This format is NOT portable.
- The header is described in the documentation for the nested DCDHeader class.
- Header of a DCD file: Got this description from http://www.arl.hpc.mil/PET/cta/ccm/software/fmd/Docs/html/fmd_ug.html. Quote: "The exact format of these files is quite ugly, as it reproduces the binary record format of unformatted FORTRAN files. Each such "record" begins with 4 bytes containing the integer value of the number of bytes in the following record. It ends with a record containing the same 4 bytes."
- The header consists of several blocks. Each block starts and ends with the number of bytes enclosed between those numbers, i. e. a block consisting of 8 bytes starts with the number 8 followed by 8 bytes of data and ends with the number 8.
- TODO: complete header description
Member Function Documentation
| virtual bool BALL::DCDFile::append | ( | const SnapShot & | snapshot | ) | [virtual] |
Append a SnapShot to an existing file.
Note that this method does not update the header.
- Parameters:
-
snapshot the snapshot we want to save
- Returns:
- true, if writing was successful
Reimplemented from BALL::TrajectoryFile.
| virtual bool BALL::DCDFile::flushToDisk | ( | const std::vector< SnapShot > & | buffer | ) | throw (File::CannotWrite)
[virtual] |
Write several SnapShots to disk.
- Parameters:
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buffer a vector of snapshots
- Returns:
- true, if flushing was successful, false ow.
Reimplemented from BALL::TrajectoryFile.
| bool BALL::DCDFile::init | ( | ) |
Initialize this instance, i.
e. read the header and update members
| virtual bool BALL::DCDFile::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 ow.
Reimplemented from BALL::TrajectoryFile.
| virtual bool BALL::DCDFile::readHeader | ( | ) | [virtual] |
Read the header of an existing file.
Return true if the header could be read successfully, false ow.
Reimplemented from BALL::TrajectoryFile.
