get.pdb {bio3d} | R Documentation |
Downloads PDB coordinate files from the RCSB Protein Data Bank.
get.pdb(ids, path = "./", URLonly=FALSE)
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. |
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 (version2.2) see:
http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/guide2.2_frame.html
.
read.pdb
, write.pdb
,
atom.select
, read.fasta.pdb
,
read.fasta
## 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")