read.trj {SOMMD} | R Documentation |
Read trj file
Description
Function to read a trajectory file
Usage
read.trj(trjfile, topfile)
Arguments
trjfile |
contains the name and the path to the reference file (pdb or gro files are accepted) |
topfile |
contains the name and the path to the trajectory file (xtc or dcd files are accepted) |
Value
Returns a list of class "trj" with the following components:
topfile |
the input topology file. |
topformat |
the format of the input topology. |
trjfile |
the input trajectory file. |
trjformat |
the format of the input trajectory. |
coord |
a three dimensional array containing atomic coordinates for all the frames. Dimensions are: Natoms:3:Nframes. |
top |
a data.frame containing topological informations with a row per atom and a column per record type (resno, resid, elety, eleno, chain). |
start |
a vector with the first frame of the simulation. When multiple simulations are concatenated with |
end |
a vector with the last frame of the simulation. When multiple simulations are concatenated with |
call |
the matched call. |
Author(s)
Alessandro Pandini
Examples
#Read trajectory
trj <- read.trj(trjfile = system.file("extdata", "HIF2a-MD.xtc", package = "SOMMD"),
topfile = system.file("extdata", "HIF2a.gro", package = "SOMMD"))