|Create a DCD file and write out the header. More...|
|Write out a model to the DCD file. More...|
DCDFile provides methods for creating DCD files.
DCD is a file format for storing simulation trajectories. It is supported by many programs, such as CHARMM, NAMD, and X-PLOR. Note, however, that different programs produce subtly different versions of the format. This class generates the CHARMM version. Also note that there is no standard byte ordering (big-endian or little-endian) for this format. This class always generates files with little-endian ordering.
Create a DCD file and write out the header.
|file||(file) A file to write to|
|topology||(Topology) The Topology defining the molecular system being written|
|dt||(time) The time step used in the trajectory|
|firstStep||(int=0) The index of the first step in the trajectory|
|interval||(int=1) The frequency (measured in time steps) at which states are written to the trajectory|
References DCDFile._file, DCDFile._firstStep, DCDFile._interval, DCDFile._modelCount, and DCDFile._topology.
Write out a model to the DCD file.
|positions||(list) The list of atomic positions to write|
|unitCellDimensions||(Vec3=None) The dimensions of the crystallographic unit cell. If None, the dimensions specified in the Topology will be used. Regardless of the value specified, no dimensions will be written if the Topology does not represent a periodic system.|
References DCDFile._file, DCDFile._firstStep, DCDFile._interval, and DCDFile._modelCount.