A couple of simple helper functions for running TM-align with tmtools

tm_tools_helper_functions.py

from tmtools import tm_align
from tmtools.io import get_structure, get_residue_data

### Helper function to load data from PDB file
# Input is the filename of a PDB file
# Output is an object with the sequence and coordinates of the structure
##### Note: This works well for PDB files from AlphaFold, but you may have to modify for PDBs from the Protein Data Bank because I believe they can have multiple "chains"
def get_pdb_data_from_file(file):
  s1 = get_structure(file)
  chain1 = next(s1.get_chains())
  coords1, seq1 = get_residue_data(chain1)
  return((coords1, seq1))

### Helper function to run TM-align for a given pair of kinases
# Inputs are two objects created using the "get_pdb_data_from_file" function above
# Outputs are a translation vector "t", rotation matrix "u", and two TM-scores: one normalized by the length of the first protein and the other normalized by the length of the second protein.
def tm_align_objects(obj1, obj2):
    coords1, seq1 = obj1
    coords2, seq2 = obj2
    res = tm_align(coords1, coords2, seq1, seq2)
    return(res.t, res.u, res.tm_norm_chain1, res.tm_norm_chain2)

Hi, how to get PDB of Aligned Structures?