SOMMD (version 0.1.2)

native.cont: Select native contact distances

Description

Function to select only distances between residues making contacts in reference file or a frame of the simulation

Usage

native.cont(
  struct = NULL,
  trj = NULL,
  trj.frame = 1,
  distance,
  mol.2 = FALSE,
  atoms = NULL
)

Value

A vector containing the index of a subset of selected distances

Arguments

struct

a struct object read with read.struct() to compute the native.cont

trj

a trj object to compute the native.cont

trj.frame

The frame of the trj on which the native.cont are computed

distance

the distance cut-off

mol.2

can be FALSE (default), use the whole distance matrix, or a vector containing the atomic number of the second molecule (and compute only intermolecular distances)

atoms

can be NULL (default), consider all the atoms present in coords, or a vector containing a set of atomic numbers to consider in the calculation (e.g. only CB). atoms can be obtained with the bio3d atom.select function

Author

Stefano Motta

Examples

# Read reference structure file with native conformation
struct <- read.struct(system.file("extdata", "HIF2a.gro", package = "SOMMD"))
#Select only Cbeta atoms to perform the analysis
sele_atoms <- which(struct$atom$elety=="CB")
#Choose only native contacts
sele_dists <- native.cont(struct=struct, distance=1.0, atoms=sele_atoms)