Download PDB Coordinate Files

Downloads PDB coordinate files from the RCSB Protein Data Bank.

get.pdb(ids, path = ".", URLonly=FALSE, overwrite = FALSE, gzip = FALSE, 
     split = FALSE, format = "pdb", verbose = TRUE, ncore = 1, ...)

Arguments

ids	A character vector of one or more 4-letter PDB codes/identifiers or 6-letter PDB-ID_Chain-ID of the files to be downloaded, or a ‘blast’ object containing ‘pdb.id’.
path	The destination path/directory where files are to be written.
URLonly	logical, if TRUE a character vector containing the URL path to the online file is returned and files are not downloaded. If FALSE the files are downloaded.
overwrite	logical, if FALSE the file will not be downloaded if it alread exist.
gzip	logical, if TRUE the gzipped PDB will be downloaded and extracted locally.
split	logical, if TRUE pdbsplit funciton will be called to split pdb files into separated chains.
format	format of the data file: ‘pdb’ or ‘cif’ for PDB and mmCIF file formats, respectively.
verbose	print details of the reading process.
ncore	number of CPU cores used to do the calculation. ncore>1 requires package ‘parallel’ installed.
...	extra arguments passed to pdbsplit function.

Details

This is a basic function to automate file download from the PDB.

Value

Returns a list of successfully downloaded files. Or optionally if URLonly is TRUE a list of URLs for said files.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

For a description of PDB format (version3.3) see:
http://www.wwpdb.org/documentation/format33/v3.3.html.

Author

Barry Grant

See also

read.pdb, write.pdb, atom.select, read.fasta.pdb, read.fasta, pdbsplit

Examples

# \donttest{
# PDB server connection required - testing excluded

## PDB file paths
get.pdb( c("1poo", "1moo"), URLonly=TRUE )
#> [1] "https://files.rcsb.org/download/1poo.pdb"
#> [2] "https://files.rcsb.org/download/1moo.pdb"

## These URLs can be used by 'read.pdb'
pdb <- read.pdb( get.pdb("5p21", URL=TRUE) )
summary(pdb)
#> 
#>  Call:  read.pdb(file = get.pdb("5p21", URL = TRUE))
#> 
#>    Total Models#: 1
#>      Total Atoms#: 1567,  XYZs#: 4701  Chains#: 1  (values: A)
#> 
#>      Protein Atoms#: 1323  (residues/Calpha atoms#: 166)
#>      Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)
#> 
#>      Non-protein/nucleic Atoms#: 244  (residues: 213)
#>      Non-protein/nucleic resid values: [ GNP (1), HOH (211), MG (1) ]
#> 
#> + attr: atom, xyz, seqres, helix, sheet,
#>         calpha, remark, call

## Download PDB file
## get.pdb("5p21")
# }