findGaps: Find gaps in proteins based on euclidean distance between...

Description Usage Arguments Details Value Note Author(s) See Also Examples

View source: R/findGaps.R

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

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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.

Details

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

Value

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

Note

Gap finding is highly recommended. Notice that it is performed by default by loadProtein and that in the following example this option has been disabled by purpose. This is a low-level function.

Author(s)

Federico Comoglio, [email protected]

See Also

loadProtein

Examples

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## 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)
}

Rknots documentation built on May 29, 2017, 1:38 p.m.