#biology #bioinformatics

bin+lib GetPDB

Download Protein files from rcsb.org

3 releases (stable)

1.0.1 Sep 26, 2019
1.0.0 Sep 23, 2019
0.1.0 Sep 18, 2019

#205 in Biology

45 downloads per month

Apache-2.0

21KB
208 lines

PDBget

Crates.io license

CLI program to download files from rcsb.org or PDBe

Installation

Using Cargo

cargo install GetPDB
pdbget -v

From sources

git clone https://gitlab.com/philippe_noel/pdbget.git
cd pdbget
cargo install --path
pdbget --help

Usage

Get Protein files 1.0.1
Philippe Noel
Download Protein files on rcsb.org or pdbe

USAGE:
    pdbget [OPTIONS] <PDBs>...

FLAGS:
    -h, --help       Prints help information
    -V, --version    Prints version information

OPTIONS:
    -o <Output>         Output folder where to store files [default: ./]
    -s <Server>         Server name where to download pdb files. 'rcsb', 'pdbe'.
                        Format for rcsb: 'fasta', 'pdb', 'pdbgz', 'cif', 'cifgz', 'xmlgz'.
                        Format for pdbe: 'fasta', 'pdb', 'pdbgz', 'cif', 'xml'.
                         [default: rcsb]
    -t <UriType>        File type to download. 'pdb', 'pdbgz', 'cif', 'cifgz', 'fasta', 'xml', 'xmlgz' [default: PDB]

ARGS:
    <PDBs>...    PDB identifiers

With the -s option, you can specify the server where download files. Possible server are:

  • rcsb : RCSB.org
  • pdbe : PDBe Note that all formats are not available for all server. Check the table.
Format RCSB PDBe
FASTA ✔️ ✔️
PDB ✔️ ✔️
PDBGZ ✔️ ✔️
CIF ✔️ ✔️
CIFGZ ✔️
XML ✔️
XMLGZ ✔️

With the -t option, you can specify the output file format. Possible format are:

  • pdb : PDB format
  • pdbgz : GZ compression of a PDB file
  • cif : CIF format
  • cifgz : GZ compression of a CIF file
  • fasta : FASTA sequence(s) of the protein
  • xml : GZ compression of an XML file (uncompress XML are not provide on rcsb.org)

Dependencies

~20MB
~437K SLoC