read.ncdf. bio3d 2.3-0

Usage

read.ncdf(trjfile, headonly = FALSE, verbose = TRUE, time = FALSE, first = NULL, last = NULL, stride = 1, cell = FALSE, at.sel = NULL)

Arguments

trjfile: name of trajectory file to read. A vector if treat a batch of files
headonly: logical, if TRUE only trajectory header information is returned. If FALSE only trajectory coordinate data is returned.
verbose: logical, if TRUE print details of the reading process.
time: logical, if TRUE the first and last have the time unit ps; Otherwise the unit is the frame number.
first: starting time or frame number to read; If NULL, start from the begining of the file(s).
last: read data until last time or frame number; If NULL or equal to -1, read until the end of the file(s).
stride: take at every stride frame(s)
cell: logical, if TRUE and headonly is FALSE return cell information only. Otherwise, return header or coordinates.
at.sel: an object of class ‘select’ indicating a subset of atomic coordinates to be read.

Description

Read coordinate data from a binary netCDF trajectory file.

Details

Reads a AMBER netCDF format trajectory file with the help of David W. Pierce's (UCSD) ncdf4 package available from CRAN.

Value

A list of trajectory header data, a numeric matrix of xyz coordinates with a frame/structure per row and a Cartesian coordinate per column, or a numeric matrix of cell information with a frame/structure per row and lengths and angles per column. If time=TRUE, row names of returned coordinates or cell are set to be the physical time of corresponding frames.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696. http://www.unidata.ucar.edu/software/netcdf/ http://cirrus.ucsd.edu/~pierce/ncdf/ http://ambermd.org/formats.html#netcdf

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.

If you experience problems reading your trajectory file with read.ncdf() consider first reading your file into VMD and from there exporting a new DCD trajectory file with the 'save coordinates' option. This new file should be easily read with read.dcd().

Examples

##-- Read example trajectory file
trtfile <- system.file("examples/hivp.dcd", package="bio3d")
trj <- read.dcd(trtfile)

 NATOM = 198 
 NFRAME= 117 
 ISTART= 0 
 last  = 117 
 nstep = 117 
 nfile = 117 
 NSAVE = 1 
 NDEGF = 0 
 version 24 
Reading (x100)
  |======================================================================| 100%


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

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

[1] "Reading file newtrj.nc"
[1] "Produced by program: bio3d"
[1] "File conventions AMBER version 1.0"
[1] "Frames: 117"
[1] "Atoms: 198"

Author

Barry Grant

Read AMBER Binary netCDF files