SSE Backbone Hydrogen Bonding
Determine backbone C=O to N-H hydrogen bonding in secondary structure elements.
sse.bridges(sse, type="helix", hbond=TRUE, energy.cut=-1.0)
sse |
an sse object as obtained with |
type |
character string specifying ‘helix’ or ‘sheet’. |
hbond |
use hbond records in the dssp output. |
energy.cut |
cutoff for the dssp hbond energy. |
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.
Returns a numeric matrix of two columns containing the residue ids of the paired residues.
Lars Skjaerven
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
## 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")
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