| pdbaln {bio3d} | R Documentation |
Create multiple sequences alignments from a list of PDB files returning aligned sequence and structure records.
pdbaln(files, pqr = FALSE, ...)
files |
a character vector of PDB file names. |
pqr |
logical, if TRUE the input structures are assumed to be in PQR format. |
... |
extra arguments passed to seqaln function. |
This wrapper function calls the underlying functions read.pdb,
seq.pdb, seqaln and read.fasta.pdb returning a
list of class "3dalign" similar to that returned by
read.fasta.pdb.
As these steps are often error prone it is recomended for most cases that the individual underlying functions are called in sequence with checks made on the valadity of their respective outputs to ensure sensible results.
Returns a list of class "3dalign" with the following five
components:
xyz |
numeric matrix of aligned C-alpha coordinates. |
resno |
character matrix of aligned residue numbers. |
b |
numeric matrix of aligned B-factor values. |
chain |
character matrix of aligned chain identifiers. |
id |
character vector of PDB sequence/structure names. |
ali |
character matrix of aligned sequences. |
See recommendation in details section above.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
read.pdb, seq.pdb, seqaln,
read.fasta,read.fasta.pdb,
core.find, fit.xyz, read.all
## Not run:
files <- get.pdb(c("4q21","5p21"), URLonly=TRUE)
pdbaln(files)
## End(Not run)