get.pdb {bio3d}R Documentation

Download PDB Coordinate Files

Description

Downloads PDB coordinate files from the RCSB Protein Data Bank.

Usage

get.pdb(ids, path = "./", URLonly=FALSE)

Arguments

ids A character vector of one or more 4-letter PDB codes/identifiers of the files to be downloaded.
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.

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 (version2.2) see:
http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/guide2.2_frame.html .

See Also

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

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) )
pdb.summary(pdb)

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

[Package bio3d version 1.0-6 Index]