aa123 {bio3d}R Documentation

Convert Between 1-letter and 3-letter Aminoacid Codes

Description

Convert between one-letter IUPAC aminoacid codes and three-letter PDB style aminoacid codes.

Usage

aa123(aa)
aa321(aa)

Arguments

aa a character vector of individual aminoacid codes.

Details

Standard conversions will map ‘A’ to ‘ALA’, ‘G’ to ‘GLY’, etc. Non-standard codes in aa will generate a warning and return ‘UNK’ or ‘X’.

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, read.fasta

Examples

# Simple conversion
aa123(c("D","L","A","G","S","H"))
aa321(c("ASP", "LEU", "ALA", "GLY", "SER", "HIS"))

## Not run: 
# Extract sequence from PDB file's ATOM and SEQRES cards
pdb <- read.pdb(system.file("examples/1bg2.pdb", package="bio3d"))
s <- aa321(pdb$seqres)                   # SEQRES
a <- aa321(pdb$atom[pdb$calpha,"resid"]) # ATOM

# Write both sequences to fasta file
write.fasta(id=c("seqres","atom"), seqs=seqbind(s,a), file="eg2.fa")
## End(Not run)

[Package bio3d version 1.0-6 Index]