dm {bio3d}R Documentation

Distance Matrix Analysis

Description

Construct a distance matrix for a given protein structure.

Usage

dm(pdb, selection = "calpha", verbose=TRUE)
dm.xyz(xyz, grpby = NULL, scut = NULL, mask.lower = TRUE)

Arguments

pdb a pdb structure object as returned by read.pdb or a numeric vector of ‘xyz’ coordinates.
selection a character string for selecting the pdb atoms to undergo comparison (see atom.select).
verbose logical, if TRUE possible warnings are printed.
xyz a numeric vector 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.

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.

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


##--- Distance Matrix Plot
pdb <- read.pdb( system.file("examples/d1bg2__.ent", package = "bio3d") )
k <- dm(pdb,selection="calpha")
filled.contour(k, nlevels = 4)

##--- DDM: Difference Distance Matrix
# Read aligned PDBs
aln <- read.fasta(system.file("examples/kif1a.fa",package="bio3d"))
pdb.path=paste(system.file(package="bio3d"),"/examples/",sep="")
m <- read.fasta.pdb(aln, pdb.path = pdb.path, pdbext = ".ent")

# Get distance matrix
a <- dm(m$xyz[2,])
b <- dm(m$xyz[3,])

# Calculate DDM
c <- a - b

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

plot(c, axis.tick.space=10,
     resnum.1=m$resno[1,],
     resnum.2=m$resno[2,],
     grid.col="gray",
     xlab="Residue No. (1i6i)", ylab="Residue No. (1i5s)")

## 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)

##--- Extract all-atom contacts
pdb <- read.pdb( system.file("examples/d1bg2__.ent", package = "bio3d") )
l <- dm(pdb,selection="all")
l[upper.tri(l)]=NA  # make top diagonal NA

# Find residues with contacting atoms (<=5 Angstrom)
inds.stru <- which(l<=5, arr.ind=TRUE)   

# Find non-consecutive residues (>5 residues sequence separation)
seq.sep  <- abs(as.numeric(pdb$atom[inds.stru[,1],"resno"]) -
               as.numeric(pdb$atom[inds.stru[,2],"resno"]))
inds.seq <- which(seq.sep>5) # seperated by > 5 residues

# All-atom contacts (indices)
inds <- inds.stru[inds.seq,]

# All-atom contacts (now in terms of residue numbers)
tmp <- unique( paste(pdb$atom[inds[,1],"resno"],
                     pdb$atom[inds[,2],"resno"], sep="#") )

contacts <- matrix(as.numeric(unlist(strsplit(tmp,split="#"))),
                   ncol=2, byrow=TRUE )

# Plot residue contacts
freq  <- table(contacts)
xaxis <-as.vector(bounds(as.numeric(names(freq)))[,c(1,2)])
x11()
plot(freq, typ="h", xlab="Residue Number",
     xaxt="n",ylab="Number of Contacts" )
axis(1,at=xaxis,labels=xaxis)
## End(Not run)

[Package bio3d version 1.0-5 Index]