print.core: Printing Core Positions and Returning Indices

In bio3d: Biological Structure Analysis

Printing Core Positions and Returning Indices

Description

Print method for core.find objects.

Usage

## S3 method for class 'core'
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

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: 
##-- 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)

bio3d documentation built on Oct. 30, 2024, 1:08 a.m.