seq.pdb {bio3d}R Documentation

Extract The Aminoacid Sequence From A PDB Object

Description

Return a vector of the one-letter IUPAC or three-letter PDB style aminoacid codes from a given PDB object.

Usage

seq.pdb(pdb, inds = NULL, aa1 = TRUE)

Arguments

pdb a PDB structure object obtained from read.pdb.
inds a list object of ATOM and XYZ indices as obtained from atom.select.
aa1 logical, if TRUE then the one-letter IUPAC sequence is returned. IF FALSE then the three-letter PDB style sequence is returned.

Details

See the functions atom.select and aa321 for further details.

Value

A character vector of aminoacid codes.

Author(s)

Barry Grant

References

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

For a description of IUPAC one-letter codes see:
http://www.chem.qmul.ac.uk/iupac/AminoAcid/

For a description of PDB residue codes see Appendix 4:
http://msdlocal.ebi.ac.uk/docs/pdb_format/appendix.html

See Also

read.pdb, atom.select, aa321, read.fasta

Examples

##pdb <- read.pdb( get.pdb("5p21", URLonly=TRUE) )
##seq.pdb(pdb)

[Package bio3d version 1.0-6 Index]