Python Script to Modify Text File -- 2

Write a script that will execute the modifications to a pdb file (a specific text file format) in order to execute the molecular docking program lightdock

1. Download and install Lightdock (https://github.com/lightdock/lightdock)
2. Test Lightdock for Protein-DNA binding using tutorial (https://lightdock.org/tutorials/0.9.2/dna_docking)
3. Write python script that will:
a. Execute the reduce function for “trim” and “build” of the hydrogen in the protein and DNA molecule pdb file (https://github.com/rlabduke/reduce)
b. Execute the pdb_atom_renumber on the protein pdb (https://github.com/haddocking/pdb-tools/)
c. Execute the reduce to amber script on the DNA pdb (https://lightdock.org/tutorials/0.9.2/dna_docking under 3.2 DNA Section)
d. Ensure DNA pdb atoms are compliant with amber.py (https://github.com/lightdock/lightdock/blob/master/lightdock/scoring/dna/data/amber.py)
e. Ensure the column spacing of the DNA pdb atoms are compliant (https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM)
4. Test script on protein and DNA pdb provided when job is accepted and run in lightdock for ensure functionality