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, ...)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 |
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.
|
... |
extra arguments passed to |
This is a basic function to automate file download from the PDB.
Returns a list of successfully downloaded files. Or optionally if URLonly is TRUE a list of URLs for said files.
Barry Grant
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.
# PDB server connection required - testing excluded
## PDB file paths
get.pdb( c("1poo", "1moo"), URLonly=TRUE )
## These URLs can be used by 'read.pdb'
pdb <- read.pdb( get.pdb("5p21", URL=TRUE) )
summary(pdb)
## Download PDB file
## get.pdb("5p21")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.