pdbs2sse {bio3d} | R Documentation |
SSE annotation for a PDBs Object
Description
Returns secondary structure element (SSE) annotation ("sse"
object) for a structure in the provided "pdbs"
object.
Usage
pdbs2sse(pdbs, ind = NULL, rm.gaps = TRUE, resno = TRUE, pdb = FALSE, ...)
Arguments
pdbs |
a list of class |
ind |
numeric index pointing to the PDB in which the SSE should
be provided. If |
rm.gaps |
logical, if TRUE SSEs spanning gap containing columns are
omitted from the output in the resulting |
resno |
logical, if TRUE output is in terms of residue numbers rather than residue index (position in sequence). |
pdb |
logical, if TRUE function |
... |
arguments passed to function |
Details
This function provides a "sse"
list object containing
secondary structure elements (SSE) annotation data for a particular
structure in the provided "pdbs"
object. Residue numbers are
provided relative to the alignment in the "pdbs"
object.
When ind=NULL
the function will attemt to return the consensus
SSE annotation, i.e. where there are SSEs across all structures. This
will only work SSE data is found in the "pdbs"
object.
See examples for more details.
Value
Returns a list object of class sse
.
Author(s)
Lars Skjaerven
References
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
See Also
Examples
## Not run:
attach(transducin)
## calculate RMSF
rf <- rmsf(pdbs$xyz)
## Fetch SSE annotation, output in terms of alignment index
sse <- pdbs2sse(pdbs, ind=1, rm.gaps=FALSE, resno=FALSE)
## Add SSE annotation to plot
plotb3(rf, sse=sse)
## Calculate RMSF only for non-gap columns
gaps.pos <- gap.inspect(pdbs$xyz)
rf <- rmsf(pdbs$xyz[, gaps.pos$f.inds])
## With gap columns removed, output in terms of residue number
sse <- pdbs2sse(pdbs, ind=1, rm.gaps=TRUE, resno=TRUE)
gaps.res <- gap.inspect(pdbs$ali)
plotb3(rf, sse=sse, resno=pdbs$resno[1, gaps.res$f.inds])
detach(transducin)
## End(Not run)