Add heteroatom to pdb file - bioinformatics

Question

I am using Biopython to perform various operations on a pdb file. Subsequently I would like to add some new atoms to the Biopython structure object generated by Biopython. Is there a good/recommended way to do this in Python. It seems Biopython only provides options to write out existing elements of a pdb file and not to create new ones.

Answer 1

You could have a look at the Python package Biotite (https://www.biotite-python.org/), a package I am developing.
In the following example code, a PDB structure is downloaded, read and then an atom is added:
import biotite.database.rcsb as rcsb
import biotite.structure as struc
import biotite.structure.io as strucio
# Download lysozyme structure for example
file_name = rcsb.fetch("1aki", "pdb", target_path=".")
# Read the file into Biotite's structure object (atom array)
atom_array = strucio.load_structure(file_name)
# Add an HETATM
atom = struc.Atom(
coord = [1.0, 2.0, 3.0],
chain_id = "A",
# The residue ID is the last ID in the file +1
res_id = atom_array.res_id[-1] + 1,
res_name = "ABC",
hetero = True,
atom_name = "CA",
element = "C"
)
atom_array += struc.array([atom])
# Save edited structure
strucio.save_structure("1aki_edited.pdb", atom_array)
The last lines of 1aki_edited.pdb:
...
HETATM 1075 O HOH A 203 12.580 21.214 5.006 1.00 0.000 O
HETATM 1076 O HOH A 204 19.687 23.750 -4.851 1.00 0.000 O
HETATM 1077 O HOH A 205 27.098 35.956 -12.358 1.00 0.000 O
HETATM 1078 O HOH A 206 37.255 9.634 10.002 1.00 0.000 O
HETATM 1079 O HOH A 207 43.755 23.843 8.038 1.00 0.000 O
HETATM 1080 CA ABC A 208 1.000 2.000 3.000 1.00 0.000 C

Answer 2

I have used RDKit to add and edit atoms in PDB-files succesfully. Below I've shown a small example of how to add a carbon atom to a PDB-file and creating a new .pdb-file
from rdkit import Chem
from rdkit.Chem import rdGeometry
prot = Chem.MolFromPDBFile("./3etr.pdb") #Read in the .pdb-file
protconf = prot.GetConformer() #create a conformer of the molecule
#create an editable mol-object
mw = Chem.RWMol(mol)
#create an editable conformer. This dictates the atoms coordinates and other attributes
mw_conf = mw.GetConformer()
#add a carbon atom to the editable mol. Returns the index of the new atom, which is the same as prot.GetNumAtoms() + 1
c_idx = mw.AddAtom(Chem.Atom(6))
#cartesian coordinates of the new atom. I think the Point3D object is not strictly necessary. but can be easier to handle in RDKit
coord = rdGeometry.Point3D(1.0, 2.0, 3.0)
#set the new coordinates
mw_conf.SetAtomPosition(c_idx, coord)
#save the edited PDB-file
pdb_out = Chem.MolToPDBFile(mw_conf, "_out.pdb")