PDBget

CLI program to download files from rcsb.org

Installation

From sources

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

Usage

Get Protein files 1.0.0
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 | :heavy_check_mark: | :heavy_check_mark: | | PDB | :heavy_check_mark: | :heavy_check_mark: | | PDBGZ | :heavy_check_mark: | :heavy_check_mark: | | CIF | :heavy_check_mark: | :heavy_check_mark: | | CIFGZ | :heavy_check_mark: | :x: | | XML | :x: | :heavy_check_mark: | | XMLGZ | :heavy_check_mark: | :x: |

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)