Pattern for adding values to b-factors with biotite

add_bfactor.py

from biotite.structure.io.pdb import get_structure, PDBFile

#################################################
# residue id, atom name : value in [0..1] domain
# input data
values = {
    (1, 'CA'): 0.5,
    (2, 'C'): 0.8,
}

pdb_fname = "test.pdb"
pdb_fname_output = "test_bfactor.pdb"

##############################
# read PDB structure
structure = PDBFile.read(pdb_fname).get_structure(model=1)

##############################
# assign bfactors
structure.set_annotation(
    "b_factor", np.zeros(structure.array_length(), float)
)
for (resi, name), value in values.items():
    mask = (structure.atom_name == name) & (structure.res_id == resi)
    structure.b_factor[mask] = value * 100.0  # scale to make b-factor in range [0..100]

##############################
# save PDB file with bfactors
pdb_file = PDBFile()
pdb_file.set_structure(structure)
pdb_file.write(pdb_fname_output)