LOOS  v2.3.2
loos::AmberNetcdf Class Reference

Class for reading Amber Trajectories in NetCDF format. More...

#include <amber_netcdf.hpp>

Inheritance diagram for loos::AmberNetcdf:
Collaboration diagram for loos::AmberNetcdf:

Public Member Functions

 AmberNetcdf (const std::string &s, const uint na)
 
std::string description () const
 Return a string describing trajectory format.
 
uint natoms () const
 

of atoms per frame


 
uint nframes () const
 Number of frames in the trajectory.
 
float timestep () const
 Timestep per frame.
 
bool hasPeriodicBox () const
 
GCoord periodicBox () const
 Returns the periodic box for the current frame/trajectory.
 
std::vector< GCoordcoords ()
 Returns the current frames coordinates as a vector of GCoords. More...
 
- Public Member Functions inherited from loos::Trajectory
 Trajectory (const std::string &s)
 Automatically open the file named s.
 
 Trajectory (std::istream &fs)
 Open using the given stream...
 
bool rewind (void)
 Rewinds the readFrame() iterator.
 
void updateGroupCoords (AtomicGroup &g)
 Update the coordinates in an AtomicGroup with the current frame. More...
 
void seekNextFrame (void)
 
void seekFrame (const uint i)
 
bool readFrame (void)
 Reads the next frame in a trajectory, returning false if at the end.
 
bool readFrame (const int i)
 Reads a specific frame in a trajectory. More...
 

Static Public Member Functions

static pTraj create (const std::string &fname, const AtomicGroup &model)
 

Additional Inherited Members

- Protected Attributes inherited from loos::Trajectory
StreamWrapper ifs
 
bool cached_first
 
std::string _filename
 

Detailed Description

Class for reading Amber Trajectories in NetCDF format.

Definition at line 67 of file amber_netcdf.hpp.

Member Function Documentation

std::vector<GCoord> loos::AmberNetcdf::coords ( )
inlinevirtual

Returns the current frames coordinates as a vector of GCoords.

Some formats, notably DCDs, do not interleave their coordinates. This means that this could be a potentially expensive operation.

Implements loos::Trajectory.

Definition at line 111 of file amber_netcdf.hpp.

bool loos::AmberNetcdf::hasPeriodicBox ( ) const
inlinevirtual

Tests whether or not the given frame/trajectory has periodic boundary information. The presence of periodic box information does not necessarily indicate that said information has been read in yet. For example, the presence of crystal data is in the header so this can be detected before any frame is read, but the crystal data itself is only read when a frame is read in.

Implements loos::Trajectory.

Definition at line 108 of file amber_netcdf.hpp.


The documentation for this class was generated from the following files: