powered by
Determine backbone C=O to N-H hydrogen bonding in secondary structure elements.
sse.bridges(sse, type="helix", hbond=TRUE, energy.cut=-1.0)
Returns a numeric matrix of two columns containing the residue ids of the paired residues.
an sse object as obtained with dssp.
dssp
character string specifying ‘helix’ or ‘sheet’.
use hbond records in the dssp output.
cutoff for the dssp hbond energy.
Lars Skjaerven
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.
resno=FALSE
full=TRUE
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
read.pdb, dssp
read.pdb
if (FALSE) { # 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") }
Run the code above in your browser using DataLab