PDBget

CLI program to download files from rcsb.org

Installation

From sources

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

Usage

```bash Get Protein files 1.0.0 Philippe Noel Download Protein files on rcsb.org or pdbe

USAGE: pdbget [OPTIONS] ...

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

OPTIONS: -o

Output folder where to store files [default: ./] -s 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 File type to download. 'pdb', 'pdbgz', 'cif', 'cifgz', 'fasta', 'xml', 'xmlgz' [default: PDB]

ARGS: ... 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 | :heavycheckmark: | :heavycheckmark: | | PDB | :heavycheckmark: | :heavycheckmark: | | PDBGZ | :heavycheckmark: | :heavycheckmark: | | CIF | :heavycheckmark: | :heavycheckmark: | | CIFGZ | :heavycheckmark: | :x: | | XML | :x: | :heavycheckmark: | | XMLGZ | :heavycheckmark: | :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)