get.pdb {bio3d}

Download PDB Coordinate Files

Description

Downloads PDB coordinate files from the RCSB Protein Data Bank.

Usage

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.

Author(s)

Barry Grant

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.

See Also

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

Examples

# 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")