dm. bio3d 2.3-0

Usage

dm(...)
"dm"(pdb, inds = NULL, grp = TRUE, verbose=TRUE, ...)
"dm"(pdbs, ...)
"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.

Description

Construct a distance matrix for a given protein structure.

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.

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.

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.

Examples


# PDB server connection required - testing excluded

##--- Distance Matrix Plot
pdb <- read.pdb( "4q21" )

  Note: Accessing on-line PDB file

k <- dm(pdb,inds="calpha")
filled.contour(k, nlevels = 10)

## NOTE: FOLLOWING EXAMPLE NEEDS MUSCLE INSTALLED

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

Warning message:
/tmp/RtmpTDihxb/4q21.pdb  exists. Skipping download

Reading PDB files:
/tmp/RtmpTDihxb/4q21.pdb
/tmp/RtmpTDihxb/521p.pdb
..

Extracting sequences

pdb/seq: 1   name: /tmp/RtmpTDihxb/4q21.pdb 
pdb/seq: 2   name: /tmp/RtmpTDihxb/521p.pdb 


# 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)")




##-- Residue-wise distance matrix based on the
##   minimal distance between all available atoms
l <- dm.xyz(pdb$xyz, grpby=pdb$atom[,"resno"], scut=3)

Author

Barry Grant

Distance Matrix Analysis