bio3d (version 2.1-3)

get.pdb: 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, 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.

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.

Value

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

Details

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

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 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")