seq.pdb {bio3d} | R Documentation |
Return a vector of the one-letter IUPAC or three-letter PDB style aminoacid codes from a given PDB object.
seq.pdb(pdb, inds = NULL, aa1 = TRUE)
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. |
See the functions atom.select
and aa321
for further details.
A character vector of aminoacid codes.
Barry Grant
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
read.pdb
, atom.select
,
aa321
, read.fasta
##pdb <- read.pdb( get.pdb("5p21", URLonly=TRUE) ) ##seq.pdb(pdb)