native.cont: Select native contact distances

In SOMMD: Self Organising Maps for the Analysis of Molecular Dynamics Data

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
)

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

Value

A vector containing the index of a subset of selected distances

Author(s)

Stefano Motta [e-mail]

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)

SOMMD documentation built on Oct. 2, 2024, 5:07 p.m.