Rknots (version 1.3.2)

findGaps: Find gaps in proteins based on euclidean distance between residues of the backbone

Description

Find gaps in proteins based on euclidean distance between residues of the backbone. Return gap positions and accordingly split a chain in subchains.

Usage

findGaps(points3D, cutoff = 7)

Arguments

points3D

an $N$ x 3 matrix of the $x$, $y$, $z$ coordinates of a polygonal link

cutoff

numeric (in Angstrom), distances between consecutive alpha-Carbon atoms greater than cutoff are considered as gaps.

Value

a list of matrices containing the $x$, $y$, $z$ coordinates of the split chains.

Details

Default cutoff is set to 7, approximately twice the average distance between two consecutive alpha-Carbon atoms.

See Also

loadProtein

Examples

## Import a PDB file from the file system
if(require(bio3d)) {
	fn <- system.file("extdata", "1AJC_chainA.pdb", package="Rknots")
	protein <- loadProtein(fn, join.gaps = TRUE)
	str(protein)
	protein.g <- findGaps(protein$A, cutoff = 7)
	str(protein.g)
}