bio3d (version 2.3-4)

pdbseq: 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

pdbseq(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.

Value

A character vector of aminoacid codes.

Details

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

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 more information on PDB residue codes see: http://ligand-expo.rcsb.org/ld-search.html

See Also

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

Examples

# NOT RUN {
pdb <- read.pdb( "5p21" )
pdbseq(pdb)

#pdbseq(pdb, inds=atom.select(pdb, resno=5:15, elety="CA"), aa1=FALSE)
# }