您可以查看我正在开发的Python软件包 Biotite （https://www.biotite-python.org/）。 在以下示例代码中，下载，读取PDB结构，然后添加原子：

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)

1aki_edited.pdb的最后几行：

...
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 

我已经使用RDKit成功地添加和编辑了PDB文件中的原子。下面我展示了一个小例子，说明如何向PDB文件中添加碳原子并创建新的.pdb文件

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(1.0,3.0)

#set the new coordinates
mw_conf.SetAtomPosition(c_idx,coord) 

#save the edited PDB-file
pdb_out = Chem.MolToPDBFile(mw_conf,"_out.pdb")