calc.distances {SOMMD} | R Documentation |
calc.distances
Description
Function to compute distances to be used to train the SOM
Usage
calc.distances(trj, mol.2 = FALSE, sele = FALSE, atoms = NULL, cap = NULL)
Arguments
trj |
contains the trajectory coordinates (array with three dimensions obtained by rioxdr) |
mol.2 |
contains the atom indexes of the second molecule in case only intermolecular distances should be computed |
sele |
contains the selection of distances coming from the native_contacts function |
atoms |
contains a list of atoms indexes on which the distances will be computed |
cap |
If a number is given, distances greater than this value are set at the cap value |
Value
A matrix containing the set of distances computed for all the frames.
Author(s)
Stefano Motta stefano.motta@unimib.it
Examples
# Read reference structure file with native conformation
struct <- read.struct(system.file("extdata", "HIF2a.gro", package = "SOMMD"))
# Read the trajectory
trj <- read.trj(trjfile = system.file("extdata", "HIF2a-MD.xtc", package = "SOMMD"),
topfile = system.file("extdata", "HIF2a.gro", package = "SOMMD"))
# Select only Cbeta atoms to perform the analysis
sele_atoms <- which(trj$top$elety=="CB")
# Choose only native contacts
sele_dists <- native.cont(struct=struct, distance=1.0, atoms=sele_atoms)
# Compute distances for SOM training.
DIST <- calc.distances(trj, mol.2=FALSE, sele=sele_dists, atoms=sele_atoms)
[Package SOMMD version 0.1.2 Index]