A script that automatically downloads a batch of PDB files from the Protein Databank at http://www.rcsb.org.
Run ./pdb_download.py --help --help for usage information:
usage: pdb_download.py [-h] [-i INPUT] [-o OUTPUT]
The RMSD measures the average distance between atoms
of 2 protein or ligand structures.
By default, all atoms but hydrogen atoms of the protein are included in the RMSD calculation.
NOTE: Both structures must contain the same number of atoms in similar order.
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Path to a text file with PDB codes.
-o OUTPUT, --output OUTPUT
Path of an output directory
The input file should contain 1 4-letter PDB code per line. E.g.,
3EIY
1HTG
1RX1
[...]
Input File:
A simple text file where each line contains one PDB code.
1A28 1AI5 1AZM 1B9V 1BR6 1C1B 1CTR 1CVU 1CX2 1D3H 1DD7 1DDS 1EOC 1EXA 1EZQ 1F0S [...]
Command:
./pdb_download.py -i ~/Desktop/codes.txt -o ~/Desktop/pdbs
Screen Output:
0% 100%
[########### ] | ETA[sec]: 21.753
Screenshot of File Output:
