| print.core {bio3d} | R Documentation |
Print method for core.find objects.
print.core(x, vol = NULL, ...)
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’. |
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 |
The produced plot.core function can be useful for deciding on the
core/non-core boundary.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
## 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)