Python script that retrieves molecular structure data from online databases (if possible).
Script check following databases:
Type the following in command line:
git clone https://github.com/JureCerar/getpdb.git
cd ./getpdb
pip install .usage: getpdb [-h] [-V] [-v] [-o TYPE] [-d DIR] [--no-ssl-verify] code [code ...]
Retrieves molecular structure data from online databases (if possible)
positional arguments:
code unique structure identifiers (PDB, CID, UniProt, ...)
options:
-h, --help show this help message and exit
-V, --version show version information and exit
-v, --verbose provide verbose output
-o TYPE output file type (supported file types depend on host)
-d DIR, --dir DIR path to a directory that will store the files
--no-ssl-verify disable SSL verification when making requests
examples:
getpdb 1lyz
getpdb P00698 -o cif
getpdb 1lyz 2lyz 3lyz -d ./output
IMPORTANT: This script is not meant for large batch queries (downloads) and should be limited to less than 5 requests per second (otherwise you will be temporarily blocked by server - Error 429). If you have a large data set that you need to compute with, see documentation for that particular database, as there are likely more efficient ways to approach such bulk queries.
Also take a look at other similar github projects:
This program is licensed under the GNU General Public License v3.0
Copyright (C) 2023-2024 Jure Cerar
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.