[R] Read trajectory file into R

[Prof Brian Ripley]

On Wed, 23 Jul 2003, Karim Elsawy wrote:

> 
> Prof Brian Ripley wrote:
> > 
> > On Wed, 23 Jul 2003, Karim Elsawy wrote:
> > 
> > > I wonder if there is a way to read a molecular dynamic trajectory file (
> > > binary file) produced by CHARMM into R. Something like that in matlab.
> > > Actually this will save tremendous effort in post processing.
> > 
> > If you know the file format, yes.  That's a main aim of connections and
> > function readBin().   Function read.S (in package foreign) is an example.
> > 
> > --
> > Brian D. Ripley,                  ripley at stats.ox.ac.uk
> > Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> > University of Oxford,             Tel:  +44 1865 272861 (self)
> > 1 South Parks Road,                     +44 1865 272866 (PA)
> > Oxford OX1 3TG, UK                Fax:  +44 1865 272595
> 
> 
> Thanks a lot for your help, actually I do not know the exact file format
> at the moment
> all what I know is :
> "The DCD files (the trajectory files) are single precision binary
> FORTRAN files, so are transportable
> between computer architectures. They are not, unfortunately,
> transportable between big-endian (most workstations) and little endian
> (Intel) architectures "
> 
> is this enough????

Possibly.  readBin can read those (at least on Unix-like OSes), and if you
can look at them some other way you can probably sort out the structure
of the values.

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595