bio3d: filter.cmap – R documentation

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filter.cmap

Contact Map Consensus Filtering

Description

This function filters a tridimensional contact matrix (NxNxZ), where N is the residue number and Z is the simulation number) selecting only contacts present in at least P simulations.

Usage

filter.cmap(cm, cutoff.sims = NULL)

Arguments

`cm`	An array of dimensions NxNxZ or a list of NxN matrices containing binary contact values as obtained from `cmap`. Here, ‘N’ is the residue number and ‘Z’ the simulation number. The matrix elements should be 1 if two residues are in contact and 0 if they are not in contact.
`cutoff.sims`	A single element numeric vector corresponding to the minimum number of simulations a contact between two residues must be present. If not, it will be set to 0 in the output matrix.

Value

The output matrix is a nXn binary matrix (n = residue number). Elements equal to 1 correspond to residues in contact, elements equal to 0 to residues not in contact.

Examples

## Not run: 
   ## load example data
  pdbfile <- system.file("examples/hivp.pdb", package="bio3d")
  pdb <- read.pdb(pdbfile)

  trtfile <- system.file("examples/hivp.dcd", package="bio3d")
  trj <- read.dcd(trtfile, verbose=FALSE)

  ## split the trj example in two
  num.of.frames <- dim(trj)[1]
  trj1 <- trj[1:(num.of.frames/2),]
  trj2 <- trj[((num.of.frames/2)+1):num.of.frames,]

  ## Lets work with Calpha atoms only
  ca.inds <- atom.select(pdb, "calpha")
  #noh.inds <- atom.select(pdb, "noh")

  ## calculate single contact map matrices
  cms <- list()
  cms[[1]] <- cmap(trj1[,ca.inds$xyz], pcut=0.3, scut=0, dcut=7, mask.lower=FALSE)
  cms[[2]] <- cmap(trj1[,ca.inds$xyz], pcut=0.3, scut=0, dcut=7, mask.lower=FALSE)

  ## calculate average contact matrix
  cm.filter <- filter.cmap(cms, cutoff.sims=2)

  ## plot the result
  par(pty="s", mfcol=c(1,3))
  plot.cmap(cms[[1]])
  plot.cmap(cms[[2]])
  plot.cmap(cm.filter)

## End(Not run)

bio3d

Biological Structure Analysis

v2.4-2

GPL (>= 2)

Authors

Barry Grant [aut, cre], Xin-Qiu Yao [aut], Lars Skjaerven [aut], Julien Ide [aut]

Initial release