R: Distance Matrix Analysis

dm {bio3d} | R Documentation

## Distance Matrix Analysis

### Description

Construct a distance matrix for a given protein structure.

### Usage

    dm(...)

    ## S3 method for class 'pdb'
    dm(pdb, inds = NULL, grp = TRUE, verbose=TRUE, ...)
    ## S3 method for class 'pdbs'
    dm(pdbs, ...)

    ## S3 method for class 'xyz'
    dm(xyz, grpby = NULL, scut = NULL, mask.lower = TRUE,
                      gc.first=FALSE, ncore=1, ...)

### Arguments

`pdb` | a `pdb` structure object as returned by `read.pdb` or a numeric vector of ‘xyz’ coordinates.
`inds` | atom and xyz coordinate indices obtained from `atom.select` that selects the elements of `pdb` upon which the calculation should be based.
`grp` | logical, if TRUE atomic distances will be grouped according to their residue membership. See ‘grpby’.
`verbose` | logical, if TRUE possible warnings are printed.
`pdbs` | a ‘pdbs’ object as returned by `read.fasta.pdb` or `pdbaln`.
`xyz` | a numeric vector or matrix of Cartesian coordinates.
`grpby` | a vector counting connective duplicated elements that indicate the elements of `xyz` that should be considered as a group (e.g. atoms from a particular residue).
`scut` | a cutoff neighbour value which has the effect of excluding atoms, or groups, that are sequentially within this value.
`mask.lower` | logical, if TRUE the lower matrix elements (i.e. those below the diagonal) are returned as NA.
`gc.first` | logical, if TRUE will call gc() first before calculation of distance matrix. This is to solve the memory overload problem when `ncore > 1` and `xyz` has many rows/columns, with a bit sacrifice on speed.
`ncore` | number of CPU cores used to do the calculation. `ncore>1` requires package ‘parallel’ installed.
`...` | arguments passed to and from functions.

### Details

Distance matrices, also called distance plots or distance maps, are an established means of describing and comparing protein conformations (e.g. Phillips, 1970; Holm, 1993).

A distance matrix is a 2D representation of 3D structure that is independent of the coordinate reference frame and, ignoring chirality, contains enough information to reconstruct the 3D Cartesian coordinates (e.g. Havel, 1983).

### Value

Returns a numeric matrix of class `"dmat"`, with all N by N distances, where N is the number of selected atoms. With multiple frames the output is provided in a three dimensional array.

### Note

The input `selection` can be any character string or pattern interpretable by the function `atom.select`. For example, shortcuts `"calpha"`, `"back"`, `"all"` and selection strings of the form `/segment/chain/residue number/residue name/element number/element name/`; see `atom.select` for details.

If a coordinate vector is provided as input (rather than a `pdb` object) the `selection` option is redundant and the input vector should be pruned instead to include only desired positions.

### Author(s)

Barry Grant

### References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

Phillips (1970) Biochem. Soc. Symp. 31, 11–28.

Holm (1993) J. Mol. Biol. 233, 123–138.

Havel (1983) Bull. Math. Biol. 45, 665–720.

### See Also

`plot.dmat`, `read.pdb`, `atom.select`

### Examples

    # PDB server connection required - testing excluded

    ##--- Distance Matrix Plot
    pdb <- read.pdb( "4q21" )
    k <- dm(pdb,inds="calpha")
    filled.contour(k, nlevels = 10)

    ## NOTE: FOLLOWING EXAMPLE NEEDS MUSCLE INSTALLED
    if(check.utility("muscle")) {

    ##--- DDM: Difference Distance Matrix
    # Downlaod and align two PDB files
    pdbs <- pdbaln( get.pdb( c( "4q21", "521p"), path = tempdir() ), outfile = tempfile() )

    # Get distance matrix
    a <- dm.xyz(pdbs$xyz[1,])
    b <- dm.xyz(pdbs$xyz[2,])

    # Calculate DDM
    c <- a - b

    # Plot DDM
    plot(c,key=FALSE, grid=FALSE)

    plot(c, axis.tick.space=10,
         resnum.1=pdbs$resno[1,],
         resnum.2=pdbs$resno[2,],
         grid.col="black",
         xlab="Residue No. (4q21)", ylab="Residue No. (521p)")
    }

    ## Not run:
    ##-- Residue-wise distance matrix based on the
    ##   minimal distance between all available atoms
    l <- dm.xyz(pdb$xyz, grpby=pdb$atom[,"resno"], scut=3)

    ## End(Not run)

[Package bio3d version 2.3-4 Index]