print.core {bio3d}R Documentation

Printing Core Positions and Returning Indices

Description

Print method for core.find objects.

Usage

print.core(x, vol = NULL, ...)

Arguments

x a list object obtained with the function core.find.
vol the maximal cumulative volume value at which core positions are detailed.
... additional arguments to ‘print’.

Value

Returns a three component list of indices:

atom atom indices of core positions
xyz xyz indices of core positions
resno residue numbers of core positions

Note

The produced plot.core function can be useful for deciding on the core/non-core boundary.

Author(s)

Barry Grant

References

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

See Also

core.find, plot.core

Examples


## Not run: 
##-- Read kinesin alignment and structures
aln <- read.fasta(system.file("examples/kinesin_xray.fa",package="bio3d"))
pdb.path = system.file("examples/",package="bio3d")
pdbs <- read.fasta.pdb(aln, pdb.path = pdb.path, pdbext = ".ent")

## Find core
core <- core.find(pdbs,
                  #write.pdbs = TRUE,
                  verbose=TRUE)
## End(Not run)

##-- OR read previously saved kinesin data
data(kinesin)
attach(kinesin)

col=rep("black", length(core$volume))
col[core$volume<2]="pink"; col[core$volume<1]="red"
plot(core, col=col)

inds.1 <- print(core, vol=1)
inds.0.5 <- print(core, vol=0.5)


[Package bio3d version 1.0-5 Index]