aa123 {bio3d} | R Documentation |
Convert between one-letter IUPAC aminoacid codes and three-letter PDB style aminoacid codes.
aa123(aa) aa321(aa)
aa |
a character vector of individual aminoacid codes. |
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’.
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
# 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)