bio3d (version 2.4-4)

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)

Value

A character vector of aminoacid codes.

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.

Author

Barry Grant

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:
https://www.insdc.org/documents/feature_table.html#7.4.3

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

if (FALSE) {
pdb <- read.pdb( "5p21" )
pdbseq(pdb)

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