R: SSE annotation for a PDBs Object

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 `"pdbs"` containing PDB file data, as obtained from `read.fasta.pdb` or `pdbaln`.
`ind` | numeric index pointing to the PDB in which the SSE should be provided. If `ind=NULL`, then the consensus SSE is returned.
`rm.gaps` | logical, if TRUE SSEs spanning gap containing columns are omitted from the output in the resulting `sse` object.
`resno` | logical, if TRUE output is in terms of residue numbers rather than residue index (position in sequence).
`pdb` | logical, if TRUE function `dssp` will be called on the corresponding `pdb` object rather than to use `pdbs$sse` to obtain the SSE object.
`...` | arguments passed to function `dssp`.

### 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

`dssp`, `pdbaln`, `read.fasta.pdb`.

### 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)

[Package bio3d version 2.3-3 Index]