bio3d (version 2.2-4)

print.core: Printing Core Positions and Returning Indices

Description

Print method for core.find objects.

Usage

"print"(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

References

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

See Also

core.find, plot.core

Examples

## Not run: 
# ##-- Generate a small kinesin alignment and read corresponding structures
# pdbfiles <- get.pdb(c("1bg2","2ncd","1i6i","1i5s"), URLonly=TRUE)
# pdbs <- pdbaln(pdbfiles)
# 
# ##-- Find 'core' positions
# core <- core.find(pdbs)
# plot(core)
# 
# ##-- Fit on these relatively invarient subset of positions 
# core.inds <- print(core, vol=0.5)
# 
# print(core, vol=0.7)
# print(core, vol=1.0)
# 
# ## End(Not run)