gemmi_pdb_structure_hierarchy_iteration_atom_coordinates.py

1import gemmi
2
3# Read a structure from a PDB or mmCIF file
4st = gemmi.read_structure('path/to/file.pdb')
5
6# Iterate through the hierarchy
7for model in st:
8    for chain in model:
9        for residue in chain:
10            for atom in residue:
11                # Print chain, residue name, atom name, and coordinates
12                print(f'{chain.name} {residue.name} {atom.name} {atom.pos.x:.3f} {atom.pos.y:.3f} {atom.pos.z:.3f}')
13
14# Accessing specific data
15# Get the first model, first chain, and first residue
16res = st[0][0][0]
17print(f'First residue: {res.name}')