Rknots (version 1.3.0)

closeAndProject: Close the protein backbone and perform a Principal Component Analysis (requires an object of class 'Knot')

Description

Close the protein backbone and perform a Principal Component Analysis, This function formally prepares a protein for the computation of an invariant. It requires the protein structure as an object of class 'Knot'.

Usage

closeAndProject(protein, ...)

Arguments

protein

an object of class 'Knot'

...

additional parameters to be passed to lower level functions (e.g. w for controlling the extension of the endpoints in centroidClosure

Value

• an object of class 'Knot' containing the processed structure.

References

Lua RC, Grosberg AY (2006) Statistics of Knots, Geometry of Conformations, and Evolution of Proteins. PLoS Comput Biol 2(5): e45. doi:10.1371/journal.pcbi.0020045

See Also

Knot-class, centroidClosure

Examples

## Loading from the file system
fn <- system.file("extdata", "1AJC_chainA.pdb", package="Rknots")
protein <- loadProtein(fn)
protein <- newKnot(protein$A)
protein.cp <- closeAndProject(protein)

# Plot the results
par(mfrow = c(1,2))        
plot(protein, lwd = 2)    
plot(protein.cp, lwd = 2)