sse.bridges {bio3d}

SSE Backbone Hydrogen Bonding

Description

Determine backbone C=O to N-H hydrogen bonding in secondary structure elements.

Usage

sse.bridges(sse, type="helix", hbond=TRUE, energy.cut=-1.0)

Arguments

sse

an sse object as obtained with dssp.

type

character string specifying ‘helix’ or ‘sheet’.

hbond

use hbond records in the dssp output.

energy.cut

cutoff for the dssp hbond energy.

Details

Simple functionality to parse the ‘BP’ and ‘hbond’ records of the DSSP output.

Requires input from function dssp with arguments resno=FALSE and full=TRUE.

Value

Returns a numeric matrix of two columns containing the residue ids of the paired residues.

Author(s)

Lars Skjaerven

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

See Also

read.pdb, dssp

Examples

## Not run: 
# Read a PDB file
pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )
sse <- dssp(pdb, resno=FALSE, full=TRUE)

sse.bridges(sse, type="helix")

## End(Not run)