write.ncdf {bio3d}

Write AMBER Binary netCDF files

Description

Write coordinate data to a binary netCDF trajectory file.

Usage

write.ncdf(x, trjfile = "R.ncdf", cell = NULL)

Arguments

x

A numeric matrix of xyz coordinates with a frame/structure per row and a Cartesian coordinate per column.

trjfile

name of the output trajectory file.

cell

A numeric matrix of cell information with a frame/structure per row and a cell length or angle per column. If NULL cell will not be written.

Details

Writes an AMBER netCDF (Network Common Data Form) format trajectory file with the help of David W. Pierce's (UCSD) ncdf4 package available from CRAN.

Value

Called for its effect.

Note

See AMBER documentation for netCDF format description.

NetCDF binary trajectory files are supported by the AMBER modules sander, pmemd and ptraj. Compared to formatted trajectory files, the binary trajectory files are smaller, higher precision and significantly faster to read and write.

NetCDF provides for file portability across architectures, allows for backwards compatible extensibility of the format and enables the files to be self-describing. Support for this format is available in VMD.

Author(s)

Barry Grant

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696. https://www.unidata.ucar.edu/software/netcdf/ https://cirrus.ucsd.edu/~pierce/ncdf/ https://ambermd.org/FileFormats.php#netcdf

See Also

read.dcd, read.ncdf, read.pdb, write.pdb, atom.select

Examples

## Not run: 
##-- Read example trajectory file
trtfile <- system.file("examples/hivp.dcd", package="bio3d")
trj <- read.dcd(trtfile)

## Write to netCDF format
write.ncdf(trj, "newtrj.nc")

## Read trj
trj <- read.ncdf("newtrj.nc")

## End(Not run)