findGaps: Find gaps in proteins based on euclidean distance between...
In FedericoComoglio/Rknots: Topological Analysis of Knotted Proteins, Biopolymers and 3D Structures

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

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

1	findGaps(points3D, cutoff = 7)

`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.

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

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

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.

Federico Comoglio, federico.comoglio@bsse.ethz.ch

loadProtein

## 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)
}