Replacing PDB atom names with Biopython

Question

I have a pdb containing a protein and one single ligand. I do not like how the ligand's hydrogens are named (1H2, 2H2, 1H3, 2H3, ...) and I would like something like H1, H2, H3, H4, ...

I wrote the following script, the problem is that it seems it's not possible to assign new atom ids. The change is reflected by Atom.id, but this change is not present in the output pdb structure, which retains the old names.

from Bio.PDB import PDBParser, PDBIO

io = PDBIO()
target_pdb_path = 'mypdb.pdb'
pdb = PDBParser(QUIET=True).get_structure('target', target_pdb_path)[0]

hydrogens = []
for atom in pdb.get_atoms():
    if atom.parent.id[0].startswith('H_'):
        # The atom is an hydrogen and is an HETATM record
        if 'H' in atom.name:
            hydrogens.append(atom)

# Rename hydrogens of the ligand
for h_num, h in enumerate(hydrogens, 1):
    # this is working, but the change is not present in the output pdb structure
    h.id = f'H{h_num} '

io.set_structure(pdb)
io.save('test.pdb')

See how assigning h.id did not change the full_id. I tried also replacing the whole full_id tuple, but also this does not work. Unfortunately it seems there's no method to change the id just like other features as Atom.set_bfactor(), Atom.set_coord() etc.

In [233]: h.full_id  # still the old id 3H18
Out[233]: ('target', 0, 'X', ('H_EOD', 401, ' '), ('3H18', ' '))

In [234]: h.id  # my new id
Out[234]: 'H29 '

Does anyone have a solution? Many thanks!

Answer 1

Given @nannarito concerns, I tried to find a way that doesn't need creating new Atom objects, I wasn't able to get a grasp of what goes behind the wheels of Biopython PDB module (I tried but it eludes me). After various attempts I ended up with the following code:

from Bio.PDB import PDBParser, PDBIO



target_pdb_path = 'small_pdb_h_gtp_no-connect_numb.pdb'


pdb = PDBParser(QUIET=True).get_structure('target', target_pdb_path)

hydrogens = []
for atom in pdb[0].get_atoms():
    
    if atom.parent.get_resname() == 'GTP' :
    
        if atom.parent.id[0].startswith('H_'):
            
            print(atom.parent.id ,  atom.name)
            
            # The atom is an hydrogen and is an HETATM record
            if 'H' in atom.name:
                
                print('ok')
                
                hydrogens.append(atom)
            
print('\n\nhydrogens : \n ', hydrogens,'\n\n')            

for h_num, h in enumerate(hydrogens, 1):
    
    
    setattr( h , 'fullname' , f'W{h_num}'  )  ## or  h.fullname = f'W{h_num}'  
    
    print(h.serial_number, h.name , h.id , h.full_id , h.level , h.parent)



atoms = pdb.get_atoms()

for h in atoms :
    
    print(h.serial_number, h.name , h.id , h.full_id , h.level , h.parent)

io = PDBIO()
io.set_structure(pdb)
io.save('test_new_approach.pdb', preserve_atom_numbering = False)

Using same input of answer above I get as output file test_new_approach.pdb:

......
.....
....
...
HETATM  147  C5  GTP A 180      20.554  34.737 -11.307  1.00  0.00           C  
HETATM  148  C6  GTP A 180      19.183  34.712 -11.659  1.00  0.00           C  
HETATM  149  O6  GTP A 180      18.205  34.448 -10.957  1.00  0.00           O  
HETATM  150  N7  GTP A 180      21.168  34.483 -10.079  1.00  0.00           N  
HETATM  151  C8  GTP A 180      22.443  34.655 -10.325  1.00  0.00           C  
HETATM  152  N9  GTP A 180      22.724  35.005 -11.630  1.00  0.00           N  
HETATM  153  W1  GTP A 180      27.642  33.664 -10.448  1.00  0.00           H  
HETATM  154  W2  GTP A 180      26.472  32.436 -10.894  1.00  0.00           H  
HETATM  155  W3  GTP A 180      26.872  34.003 -12.692  1.00  0.00           H  
HETATM  156  W4  GTP A 180      27.038  36.109 -10.945  1.00  0.00           H  
HETATM  157  W5  GTP A 180      26.303  36.091 -13.672  1.00  0.00           H  
HETATM  158  W6  GTP A 180      24.683  36.247 -10.440  1.00  0.00           H  
HETATM  159  W7  GTP A 180      24.926  37.660 -12.845  1.00  0.00           H  
HETATM  160  W8  GTP A 180      23.874  35.594 -13.231  1.00  0.00           H  
HETATM  161  W9  GTP A 180      18.670  35.593 -15.377  1.00  0.00           H  
HETATM  162  W10 GTP A 180      20.293  35.851 -15.834  1.00  0.00           H  
HETATM  163  W11 GTP A 180      27.124  35.555  -7.891  1.00  0.00           H  
HETATM  164  W12 GTP A 180      26.059  32.241  -5.339  1.00  0.00           H  
HETATM  165  W13 GTP A 180      22.030  35.588 -14.193  1.00  0.00           H  
HETATM  166  W14 GTP A 180      30.718  31.035  -4.497  1.00  0.00           H  
HETATM  167  W15 GTP A 180      23.174  34.539  -9.606  1.00  0.00           H  
TER     168      GTP A 180                                                       
END   

So setattr( h , 'fullname' , f'W{h_num}' ) seems to do the trick, but for some reasons inexplicable to me, this:

atoms = pdb.get_atoms()

for h in atoms :
    
    print(h.serial_number, h.name , h.id , h.full_id , h.level , h.parent)

bit, used after the setattr( h , 'fullname' , f'W{h_num}' ) before or after the:

io = PDBIO()
io.set_structure(pdb)

still produces:

......
.....
....
...
295 H10 H10 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H10', ' ')) A <Residue GTP het=H_GTP resseq=180 icode= >
296 H11 H11 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H11', ' ')) A <Residue GTP het=H_GTP resseq=180 icode= >
297 H12 H12 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H12', ' ')) A <Residue GTP het=H_GTP resseq=180 icode= >
298 H13 H13 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H13', ' ')) A <Residue GTP het=H_GTP resseq=180 icode= >
299 H14 H14 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H14', ' ')) A <Residue GTP het=H_GTP resseq=180 icode= >
300 H15 H15 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H15', ' ')) A <Residue GTP het=H_GTP resseq=180 icode= >

... the original question gets more intriguing.

I think I got something more:

needed to add h.name = f'W{h_num}' too, like:

h.fullname = f'W{h_num}'  # or setattr( h , 'fullname' , f'W{h_num}'  ) 
    
h.name = f'W{h_num}'  # or setattr( h , 'name' , f'W{h_num}')

to have:

......
.....
....
...
299 W14 H14 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H14', ' ')) A <Residue GTP het=H_GTP resseq=180 icode= >
('target', 0, 'A', ('H_GTP', 180, ' '), ('W14', ' '))
300 W15 H15 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H15', ' ')) A <Residue GTP het=H_GTP resseq=180 icode= >
('target', 0, 'A', ('H_GTP', 180, ' '), ('W15', ' '))

when using:

print(h.serial_number, h.name , h.id , h.full_id , h.level , h.parent)
    
print(h.get_full_id())

so h.get_full_id() returns the updated atom name

but still get old h.id when using:

atoms = pdb.get_atoms()

for h in atoms :
    
    print(h.serial_number, h.name , h.id , h.full_id , h.level , h.parent)

.. so to me it's like something is going on on the Structure object and its parent/child relationships, since it can be corrected by using:

par = h.parent
    
par.detach_child(h.id)

h.fullname = f'W{h_num}'  # or setattr( h , 'fullname' , f'W{h_num}'  ) 

h.name = f'W{h_num}'  # or setattr( h , 'name' , f'W{h_num}')

par.add(h)

but still atom.id doesn't get reinitialized, see:

atoms = pdb.get_atoms()

for h in atoms :
    
    print(h.serial_number, h.name , h.id , h.full_id , h.level , h.parent)

Output:

299 W14 H14 ('target', 0, 'A', ('H_GTP', 180, ' '), ('W14', ' ')) A <Residue GTP het=H_GTP resseq=180 icode= >
300 W15 H15 ('target', 0, 'A', ('H_GTP', 180, ' '), ('W15', ' ')) A <Residue GTP het=H_GTP resseq=180 icode= >

In the end, try using:

par = h.parent
    
par.detach_child(h.id)
    
h.fullname = f'W{h_num}'  

h.name = f'W{h_num}' 
    
h.id = f'W{h_num}' 
    
par.add(h)

... but cannot guarantee that something somewhere isn't wrong.

Answer 2

ok my attempt , needed to create my input and changed output: change atom names H1 ... H15 to X1 .. X15, here input

small_pdb_h_gtp_no-connect_numb.pdb file :

COMPND    UNNAMED
AUTHOR    GENERATED BY OPEN BABEL 3.1.1
ATOM      1  N   VAL A   6      20.799  29.221   8.701  1.00  0.00           N  
ATOM      2  CA  VAL A   6      20.474  28.731   7.364  1.00  0.00           C  
ATOM      3  C   VAL A   6      21.733  28.489   6.533  1.00  0.00           C  
ATOM      4  O   VAL A   6      22.566  29.380   6.440  1.00  0.00           O  
ATOM      5  CB  VAL A   6      19.553  29.779   6.711  1.00  0.00           C  
ATOM      6  CG1 VAL A   6      19.327  29.527   5.222  1.00  0.00           C  
ATOM      7  CG2 VAL A   6      18.217  29.772   7.421  1.00  0.00           C  
ATOM      8  N   VAL A   7      21.974  27.342   5.919  1.00  0.00           N  
ATOM      9  CA  VAL A   7      23.122  27.169   5.031  1.00  0.00           C  
ATOM     10  C   VAL A   7      22.555  27.122   3.620  1.00  0.00           C  
ATOM     11  O   VAL A   7      21.609  26.378   3.344  1.00  0.00           O  
ATOM     12  CB  VAL A   7      23.896  25.869   5.351  1.00  0.00           C  
ATOM     13  CG1 VAL A   7      25.132  25.702   4.504  1.00  0.00           C  
ATOM     14  CG2 VAL A   7      24.334  25.857   6.792  1.00  0.00           C  
ATOM     15  N   VAL A   8      23.076  27.936   2.718  1.00  0.00           N  
ATOM     16  CA  VAL A   8      22.670  27.904   1.328  1.00  0.00           C  
ATOM     17  C   VAL A   8      23.672  27.034   0.554  1.00  0.00           C  
ATOM     18  O   VAL A   8      24.852  27.397   0.465  1.00  0.00           O  
ATOM     19  CB  VAL A   8      22.621  29.343   0.825  1.00  0.00           C  
ATOM     20  CG1 VAL A   8      22.080  29.353  -0.590  1.00  0.00           C  
ATOM     21  CG2 VAL A   8      21.725  30.215   1.697  1.00  0.00           C  
ATOM     22  N   LEU A   9      23.250  25.888   0.004  1.00  0.00           N  
ATOM     23  CA  LEU A   9      24.132  24.905  -0.620  1.00  0.00           C  
ATOM     24  C   LEU A   9      23.960  24.767  -2.131  1.00  0.00           C  
ATOM     25  O   LEU A   9      22.841  24.930  -2.621  1.00  0.00           O  
ATOM     26  CB  LEU A   9      23.843  23.559  -0.010  1.00  0.00           C  
ATOM     27  CG  LEU A   9      24.288  23.347   1.414  1.00  0.00           C  
ATOM     28  CD1 LEU A   9      23.675  22.070   1.962  1.00  0.00           C  
ATOM     29  CD2 LEU A   9      25.809  23.357   1.478  1.00  0.00           C  
ATOM     30  N   GLY A  10      24.997  24.458  -2.908  1.00  0.00           N  
ATOM     31  CA  GLY A  10      24.827  24.183  -4.325  1.00  0.00           C  
ATOM     32  C   GLY A  10      26.134  24.261  -5.102  1.00  0.00           C  
ATOM     33  O   GLY A  10      27.188  24.556  -4.534  1.00  0.00           O  
ATOM     34  N   SER A  11      26.094  24.027  -6.416  1.00  0.00           N  
ATOM     35  CA  SER A  11      27.280  24.074  -7.267  1.00  0.00           C  
ATOM     36  C   SER A  11      27.618  25.490  -7.674  1.00  0.00           C  
ATOM     37  O   SER A  11      26.824  26.425  -7.519  1.00  0.00           O  
ATOM     38  CB  SER A  11      27.073  23.274  -8.536  1.00  0.00           C  
ATOM     39  OG  SER A  11      26.744  21.934  -8.227  1.00  0.00           O  
ATOM     40  N   GLY A  12      28.805  25.674  -8.235  1.00  0.00           N  
ATOM     41  CA  GLY A  12      29.215  26.993  -8.714  1.00  0.00           C  
ATOM     42  C   GLY A  12      28.280  27.618  -9.752  1.00  0.00           C  
ATOM     43  O   GLY A  12      27.692  26.945 -10.605  1.00  0.00           O  
ATOM     44  N   GLY A  13      28.091  28.929  -9.645  1.00  0.00           N  
ATOM     45  CA  GLY A  13      27.363  29.714 -10.618  1.00  0.00           C  
ATOM     46  C   GLY A  13      25.862  29.638 -10.485  1.00  0.00           C  
ATOM     47  O   GLY A  13      25.218  30.556 -10.943  1.00  0.00           O  
ATOM     48  N   VAL A  14      25.245  28.666  -9.827  1.00  0.00           N  
ATOM     49  CA  VAL A  14      23.798  28.557  -9.709  1.00  0.00           C  
ATOM     50  C   VAL A  14      23.042  29.783  -9.203  1.00  0.00           C  
ATOM     51  O   VAL A  14      21.827  29.901  -9.354  1.00  0.00           O  
ATOM     52  CB  VAL A  14      23.452  27.347  -8.833  1.00  0.00           C  
ATOM     53  CG1 VAL A  14      24.080  26.099  -9.412  1.00  0.00           C  
ATOM     54  CG2 VAL A  14      23.860  27.539  -7.373  1.00  0.00           C  
ATOM     55  N   GLY A  15      23.716  30.722  -8.558  1.00  0.00           N  
ATOM     56  CA  GLY A  15      23.016  31.867  -8.019  1.00  0.00           C  
ATOM     57  C   GLY A  15      22.880  31.944  -6.498  1.00  0.00           C  
ATOM     58  O   GLY A  15      22.118  32.782  -6.042  1.00  0.00           O  
ATOM     59  N   LYS A  16      23.638  31.182  -5.686  1.00  0.00           N  
ATOM     60  CA  LYS A  16      23.597  31.199  -4.210  1.00  0.00           C  
ATOM     61  C   LYS A  16      23.834  32.561  -3.602  1.00  0.00           C  
ATOM     62  O   LYS A  16      23.068  33.033  -2.760  1.00  0.00           O  
ATOM     63  CB  LYS A  16      24.593  30.232  -3.570  1.00  0.00           C  
ATOM     64  CG  LYS A  16      24.311  28.785  -3.934  1.00  0.00           C  
ATOM     65  CD  LYS A  16      25.192  27.838  -3.179  1.00  0.00           C  
ATOM     66  CE  LYS A  16      26.652  28.055  -3.425  1.00  0.00           C  
ATOM     67  NZ  LYS A  16      26.949  27.601  -4.751  1.00  0.00           N1+
ATOM     68  N   SER A  17      24.877  33.238  -4.071  1.00  0.00           N  
ATOM     69  CA  SER A  17      25.190  34.560  -3.573  1.00  0.00           C  
ATOM     70  C   SER A  17      24.268  35.615  -4.118  1.00  0.00           C  
ATOM     71  O   SER A  17      24.071  36.602  -3.432  1.00  0.00           O  
ATOM     72  CB  SER A  17      26.604  34.908  -3.927  1.00  0.00           C  
ATOM     73  OG  SER A  17      27.409  33.729  -3.728  1.00  0.00           O  
ATOM     74  N   ALA A  18      23.680  35.451  -5.313  1.00  0.00           N  
ATOM     75  CA  ALA A  18      22.810  36.455  -5.871  1.00  0.00           C  
ATOM     76  C   ALA A  18      21.496  36.379  -5.125  1.00  0.00           C  
ATOM     77  O   ALA A  18      20.955  37.417  -4.776  1.00  0.00           O  
ATOM     78  CB  ALA A  18      22.613  36.235  -7.354  1.00  0.00           C  
ATOM     79  N   LEU A  19      20.989  35.191  -4.814  1.00  0.00           N  
ATOM     80  CA  LEU A  19      19.844  35.014  -3.938  1.00  0.00           C  
ATOM     81  C   LEU A  19      20.085  35.556  -2.524  1.00  0.00           C  
ATOM     82  O   LEU A  19      19.305  36.384  -2.066  1.00  0.00           O  
ATOM     83  CB  LEU A  19      19.470  33.531  -3.907  1.00  0.00           C  
ATOM     84  CG  LEU A  19      18.824  32.928  -5.141  1.00  0.00           C  
ATOM     85  CD1 LEU A  19      18.781  31.438  -5.031  1.00  0.00           C  
ATOM     86  CD2 LEU A  19      17.401  33.437  -5.328  1.00  0.00           C  
ATOM     87  N   THR A  20      21.156  35.175  -1.820  1.00  0.00           N  
ATOM     88  CA  THR A  20      21.471  35.686  -0.501  1.00  0.00           C  
ATOM     89  C   THR A  20      21.646  37.203  -0.512  1.00  0.00           C  
ATOM     90  O   THR A  20      20.988  37.911   0.261  1.00  0.00           O  
ATOM     91  CB  THR A  20      22.726  34.996   0.064  1.00  0.00           C  
ATOM     92  CG2 THR A  20      23.091  35.495   1.437  1.00  0.00           C  
ATOM     93  OG1 THR A  20      22.462  33.599   0.110  1.00  0.00           O  
ATOM     94  N   VAL A  21      22.471  37.750  -1.410  1.00  0.00           N  
ATOM     95  CA  VAL A  21      22.686  39.189  -1.491  1.00  0.00           C  
ATOM     96  C   VAL A  21      21.419  39.954  -1.866  1.00  0.00           C  
ATOM     97  O   VAL A  21      21.240  41.085  -1.417  1.00  0.00           O  
ATOM     98  CB  VAL A  21      23.871  39.505  -2.398  1.00  0.00           C  
ATOM     99  CG1 VAL A  21      24.142  40.980  -2.468  1.00  0.00           C  
ATOM    100  CG2 VAL A  21      25.140  38.840  -1.868  1.00  0.00           C  
ATOM    101  N   GLN A  22      20.472  39.394  -2.613  1.00  0.00           N  
ATOM    102  CA  GLN A  22      19.197  40.059  -2.841  1.00  0.00           C  
ATOM    103  C   GLN A  22      18.364  40.109  -1.555  1.00  0.00           C  
ATOM    104  O   GLN A  22      17.817  41.169  -1.258  1.00  0.00           O  
ATOM    105  CB  GLN A  22      18.451  39.349  -3.987  1.00  0.00           C  
ATOM    106  CG  GLN A  22      17.112  39.921  -4.504  1.00  0.00           C  
ATOM    107  CD  GLN A  22      17.229  41.246  -5.220  1.00  0.00           C  
ATOM    108  NE2 GLN A  22      18.028  41.314  -6.268  1.00  0.00           N  
ATOM    109  OE1 GLN A  22      16.583  42.229  -4.878  1.00  0.00           O  
ATOM    110  N   PHE A  23      18.259  39.026  -0.754  1.00  0.00           N  
ATOM    111  CA  PHE A  23      17.568  39.052   0.531  1.00  0.00           C  
ATOM    112  C   PHE A  23      18.183  40.098   1.444  1.00  0.00           C  
ATOM    113  O   PHE A  23      17.500  40.989   1.922  1.00  0.00           O  
ATOM    114  CB  PHE A  23      17.614  37.706   1.233  1.00  0.00           C  
ATOM    115  CG  PHE A  23      16.806  37.646   2.525  1.00  0.00           C  
ATOM    116  CD1 PHE A  23      15.460  37.952   2.534  1.00  0.00           C  
ATOM    117  CD2 PHE A  23      17.420  37.237   3.694  1.00  0.00           C  
ATOM    118  CE1 PHE A  23      14.729  37.821   3.695  1.00  0.00           C  
ATOM    119  CE2 PHE A  23      16.685  37.107   4.854  1.00  0.00           C  
ATOM    120  CZ  PHE A  23      15.341  37.392   4.850  1.00  0.00           C  
HETATM  121  PA  GTP A 180      26.277  33.726  -8.045  1.00  0.00           P  
HETATM  122  PB  GTP A 180      27.017  31.171  -6.766  1.00  0.00           P  
HETATM  123  PG  GTP A 180      29.710  30.132  -5.989  1.00  0.00           P  
HETATM  124  C5' GTP A 180      26.615  33.475 -10.679  1.00  0.00           C  
HETATM  125  O5' GTP A 180      25.804  33.834  -9.555  1.00  0.00           O  
HETATM  126  C4' GTP A 180      26.219  34.288 -11.894  1.00  0.00           C  
HETATM  127  O4' GTP A 180      24.826  34.017 -12.143  1.00  0.00           O  
HETATM  128  C3' GTP A 180      26.372  35.802 -11.724  1.00  0.00           C  
HETATM  129  O3' GTP A 180      26.880  36.347 -12.936  1.00  0.00           O  
HETATM  130  C2' GTP A 180      24.932  36.243 -11.481  1.00  0.00           C  
HETATM  131  O2' GTP A 180      24.719  37.581 -11.901  1.00  0.00           O  
HETATM  132  C1' GTP A 180      24.069  35.240 -12.240  1.00  0.00           C  
HETATM  133  N1  GTP A 180      19.000  35.036 -13.013  1.00  0.00           N  
HETATM  134  O1A GTP A 180      25.089  33.867  -7.187  1.00  0.00           O1-
HETATM  135  O1B GTP A 180      26.072  30.050  -6.958  1.00  0.00           O1-
HETATM  136  O1G GTP A 180      29.197  28.937  -5.265  1.00  0.00           O  
HETATM  137  C2  GTP A 180      20.022  35.339 -13.903  1.00  0.00           C  
HETATM  138  N2  GTP A 180      19.627  35.619 -15.147  1.00  0.00           N  
HETATM  139  O2A GTP A 180      27.427  34.635  -7.843  1.00  0.00           O  
HETATM  140  O2B GTP A 180      26.960  31.913  -5.483  1.00  0.00           O  
HETATM  141  O2G GTP A 180      30.881  29.816  -6.827  1.00  0.00           O1-
HETATM  142  N3  GTP A 180      21.301  35.367 -13.569  1.00  0.00           N  
HETATM  143  O3A GTP A 180      26.807  32.212  -7.961  1.00  0.00           O  
HETATM  144  O3B GTP A 180      28.517  30.631  -6.995  1.00  0.00           O  
HETATM  145  O3G GTP A 180      30.013  31.278  -5.117  1.00  0.00           O  
HETATM  146  C4  GTP A 180      21.489  35.054 -12.257  1.00  0.00           C  
HETATM  147  C5  GTP A 180      20.554  34.737 -11.307  1.00  0.00           C  
HETATM  148  C6  GTP A 180      19.183  34.712 -11.659  1.00  0.00           C  
HETATM  149  O6  GTP A 180      18.205  34.448 -10.957  1.00  0.00           O  
HETATM  150  N7  GTP A 180      21.168  34.483 -10.079  1.00  0.00           N  
HETATM  151  C8  GTP A 180      22.443  34.655 -10.325  1.00  0.00           C  
HETATM  152  N9  GTP A 180      22.724  35.005 -11.630  1.00  0.00           N  
HETATM  286  H1  GTP A 180      27.642  33.664 -10.448  1.00  0.00           H  
HETATM  287  H2  GTP A 180      26.472  32.436 -10.894  1.00  0.00           H  
HETATM  288  H3  GTP A 180      26.872  34.003 -12.692  1.00  0.00           H  
HETATM  289  H4  GTP A 180      27.038  36.109 -10.945  1.00  0.00           H  
HETATM  290  H5  GTP A 180      26.303  36.091 -13.672  1.00  0.00           H  
HETATM  291  H6  GTP A 180      24.683  36.247 -10.440  1.00  0.00           H  
HETATM  292  H7  GTP A 180      24.926  37.660 -12.845  1.00  0.00           H  
HETATM  293  H8  GTP A 180      23.874  35.594 -13.231  1.00  0.00           H  
HETATM  294  H9  GTP A 180      18.670  35.593 -15.377  1.00  0.00           H  
HETATM  295  H10 GTP A 180      20.293  35.851 -15.834  1.00  0.00           H  
HETATM  296  H11 GTP A 180      27.124  35.555  -7.891  1.00  0.00           H  
HETATM  297  H12 GTP A 180      26.059  32.241  -5.339  1.00  0.00           H  
HETATM  298  H13 GTP A 180      22.030  35.588 -14.193  1.00  0.00           H  
HETATM  299  H14 GTP A 180      30.718  31.035  -4.497  1.00  0.00           H  
HETATM  300  H15 GTP A 180      23.174  34.539  -9.606  1.00  0.00           H  

using code :

from Bio.PDB import PDBParser, PDBIO

from Bio.PDB.Atom import Atom

io = PDBIO()

target_pdb_path = 'small_pdb_h_gtp_no-connect_numb.pdb'


pdb = PDBParser(QUIET=True).get_structure('target', target_pdb_path)[0]

hydrogens = []
for atom in pdb.get_atoms():
    
    if atom.parent.id[0].startswith('H_'):
        
        print(atom.parent.id ,  atom.name)
        
        # The atom is an hydrogen and is an HETATM record
        if 'H' in atom.name:
            
            print('ok')
            
            hydrogens.append(atom)
            
print('\n\nhydrogens : \n ', hydrogens)            

# Rename hydrogens of the ligand
for h_num, h in enumerate(hydrogens, 1):
    
    # this is working, but the change is not present in the output pdb structure
    
    print(h.id, h.full_id , type(h))
    
    par = h.parent
    
    par.detach_child(h.id)
    
    print(par ,'  ...  ', h.parent)
    
    
    
    """
    https://biopython.org/docs/latest/api/Bio.PDB.Atom.html?highlight=atom#module-Bio.PDB.Atom
    
    Bio.PDB.Atom module

    Atom class, used in Structure objects
    
    
    class Bio.PDB.Atom.Atom(name, coord, bfactor, occupancy, altloc, fullname, serial_number, element=None, pqr_charge=None, radius=None)
    
    __init__(name, coord, bfactor, occupancy, altloc, fullname, serial_number, element=None, pqr_charge=None, radius=None)
    """
    
    h_new = Atom(f'X{h_num}' , h.get_coord() , h.get_bfactor() , h.get_occupancy() , h.get_altloc() , f'X{h_num}' , 
                 
                 h.get_serial_number() ,  'H'  , h.get_charge() , h.get_radius())
    
    par.add(h_new)
    
    
    print(h_new.id ,h_new.name , h_new.full_id)
    
    print(h_new.id ,h_new.name , h_new.full_id[4][0])
    
    print(par , h_new.parent , '\n\n')
    
    

io.set_structure(pdb)
io.save('test.pdb', preserve_atom_numbering = False)

I get as output :

('H_GTP', 180, ' ') PA
('H_GTP', 180, ' ') PB
('H_GTP', 180, ' ') PG
('H_GTP', 180, ' ') C5'
('H_GTP', 180, ' ') O5'
('H_GTP', 180, ' ') C4'
('H_GTP', 180, ' ') O4'
('H_GTP', 180, ' ') C3'
('H_GTP', 180, ' ') O3'
('H_GTP', 180, ' ') C2'
('H_GTP', 180, ' ') O2'
('H_GTP', 180, ' ') C1'
('H_GTP', 180, ' ') N1
('H_GTP', 180, ' ') O1A
('H_GTP', 180, ' ') O1B
('H_GTP', 180, ' ') O1G
('H_GTP', 180, ' ') C2
('H_GTP', 180, ' ') N2
('H_GTP', 180, ' ') O2A
('H_GTP', 180, ' ') O2B
('H_GTP', 180, ' ') O2G
('H_GTP', 180, ' ') N3
('H_GTP', 180, ' ') O3A
('H_GTP', 180, ' ') O3B
('H_GTP', 180, ' ') O3G
('H_GTP', 180, ' ') C4
('H_GTP', 180, ' ') C5
('H_GTP', 180, ' ') C6
('H_GTP', 180, ' ') O6
('H_GTP', 180, ' ') N7
('H_GTP', 180, ' ') C8
('H_GTP', 180, ' ') N9
('H_GTP', 180, ' ') H1
ok
('H_GTP', 180, ' ') H2
ok
('H_GTP', 180, ' ') H3
ok
('H_GTP', 180, ' ') H4
ok
('H_GTP', 180, ' ') H5
ok
('H_GTP', 180, ' ') H6
ok
('H_GTP', 180, ' ') H7
ok
('H_GTP', 180, ' ') H8
ok
('H_GTP', 180, ' ') H9
ok
('H_GTP', 180, ' ') H10
ok
('H_GTP', 180, ' ') H11
ok
('H_GTP', 180, ' ') H12
ok
('H_GTP', 180, ' ') H13
ok
('H_GTP', 180, ' ') H14
ok
('H_GTP', 180, ' ') H15
ok


hydrogens : 
  [<Atom H1>, <Atom H2>, <Atom H3>, <Atom H4>, <Atom H5>, <Atom H6>, <Atom H7>, <Atom H8>, <Atom H9>, <Atom H10>, <Atom H11>, <Atom H12>, <Atom H13>, <Atom H14>, <Atom H15>]


H1 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H1', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= >   ...   None
X1 X1 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X1', ' '))
X1 X1 X1
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= > 


H2 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H2', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= >   ...   None
X2 X2 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X2', ' '))
X2 X2 X2
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= > 


H3 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H3', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= >   ...   None
X3 X3 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X3', ' '))
X3 X3 X3
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= > 


H4 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H4', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= >   ...   None
X4 X4 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X4', ' '))
X4 X4 X4
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= > 


H5 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H5', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= >   ...   None
X5 X5 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X5', ' '))
X5 X5 X5
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= > 


H6 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H6', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= >   ...   None
X6 X6 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X6', ' '))
X6 X6 X6
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= > 


H7 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H7', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= >   ...   None
X7 X7 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X7', ' '))
X7 X7 X7
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= > 


H8 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H8', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= >   ...   None
X8 X8 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X8', ' '))
X8 X8 X8
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= > 


H9 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H9', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= >   ...   None
X9 X9 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X9', ' '))
X9 X9 X9
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= > 


H10 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H10', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= >   ...   None
X10 X10 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X10', ' '))
X10 X10 X10
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= > 


H11 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H11', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= >   ...   None
X11 X11 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X11', ' '))
X11 X11 X11
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= > 


H12 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H12', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= >   ...   None
X12 X12 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X12', ' '))
X12 X12 X12
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= > 


H13 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H13', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= >   ...   None
X13 X13 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X13', ' '))
X13 X13 X13
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= > 


H14 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H14', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= >   ...   None
X14 X14 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X14', ' '))
X14 X14 X14
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= > 


H15 ('target', 0, 'A', ('H_GTP', 180, ' '), ('H15', ' ')) <class 'Bio.PDB.Atom.Atom'>
<Residue GTP het=H_GTP resseq=180 icode= >   ...   None
X15 X15 ('target', 0, 'A', ('H_GTP', 180, ' '), ('X15', ' '))
X15 X15 X15
<Residue GTP het=H_GTP resseq=180 icode= > <Residue GTP het=H_GTP resseq=180 icode= > 

with file test.pdb :

ATOM      1  N   VAL A   6      20.799  29.221   8.701  1.00  0.00           N  
ATOM      2  CA  VAL A   6      20.474  28.731   7.364  1.00  0.00           C  
....
....
ATOM    119  CE2 PHE A  23      16.685  37.107   4.854  1.00  0.00           C  
ATOM    120  CZ  PHE A  23      15.341  37.392   4.850  1.00  0.00           C  
HETATM  121  PA  GTP A 180      26.277  33.726  -8.045  1.00  0.00           P  
HETATM  122  PB  GTP A 180      27.017  31.171  -6.766  1.00  0.00           P  
HETATM  123  PG  GTP A 180      29.710  30.132  -5.989  1.00  0.00           P  
HETATM  124  C5' GTP A 180      26.615  33.475 -10.679  1.00  0.00           C  
HETATM  125  O5' GTP A 180      25.804  33.834  -9.555  1.00  0.00           O  
HETATM  126  C4' GTP A 180      26.219  34.288 -11.894  1.00  0.00           C  
HETATM  127  O4' GTP A 180      24.826  34.017 -12.143  1.00  0.00           O  
HETATM  128  C3' GTP A 180      26.372  35.802 -11.724  1.00  0.00           C  
HETATM  129  O3' GTP A 180      26.880  36.347 -12.936  1.00  0.00           O  
HETATM  130  C2' GTP A 180      24.932  36.243 -11.481  1.00  0.00           C  
HETATM  131  O2' GTP A 180      24.719  37.581 -11.901  1.00  0.00           O  
HETATM  132  C1' GTP A 180      24.069  35.240 -12.240  1.00  0.00           C  
HETATM  133  N1  GTP A 180      19.000  35.036 -13.013  1.00  0.00           N  
HETATM  134  O1A GTP A 180      25.089  33.867  -7.187  1.00  0.00           O  
HETATM  135  O1B GTP A 180      26.072  30.050  -6.958  1.00  0.00           O  
HETATM  136  O1G GTP A 180      29.197  28.937  -5.265  1.00  0.00           O  
HETATM  137  C2  GTP A 180      20.022  35.339 -13.903  1.00  0.00           C  
HETATM  138  N2  GTP A 180      19.627  35.619 -15.147  1.00  0.00           N  
HETATM  139  O2A GTP A 180      27.427  34.635  -7.843  1.00  0.00           O  
HETATM  140  O2B GTP A 180      26.960  31.913  -5.483  1.00  0.00           O  
HETATM  141  O2G GTP A 180      30.881  29.816  -6.827  1.00  0.00           O  
HETATM  142  N3  GTP A 180      21.301  35.367 -13.569  1.00  0.00           N  
HETATM  143  O3A GTP A 180      26.807  32.212  -7.961  1.00  0.00           O  
HETATM  144  O3B GTP A 180      28.517  30.631  -6.995  1.00  0.00           O  
HETATM  145  O3G GTP A 180      30.013  31.278  -5.117  1.00  0.00           O  
HETATM  146  C4  GTP A 180      21.489  35.054 -12.257  1.00  0.00           C  
HETATM  147  C5  GTP A 180      20.554  34.737 -11.307  1.00  0.00           C  
HETATM  148  C6  GTP A 180      19.183  34.712 -11.659  1.00  0.00           C  
HETATM  149  O6  GTP A 180      18.205  34.448 -10.957  1.00  0.00           O  
HETATM  150  N7  GTP A 180      21.168  34.483 -10.079  1.00  0.00           N  
HETATM  151  C8  GTP A 180      22.443  34.655 -10.325  1.00  0.00           C  
HETATM  152  N9  GTP A 180      22.724  35.005 -11.630  1.00  0.00           N  
HETATM  153  X1  GTP A 180      27.642  33.664 -10.448  1.00  0.00           H  
HETATM  154  X2  GTP A 180      26.472  32.436 -10.894  1.00  0.00           H  
HETATM  155  X3  GTP A 180      26.872  34.003 -12.692  1.00  0.00           H  
HETATM  156  X4  GTP A 180      27.038  36.109 -10.945  1.00  0.00           H  
HETATM  157  X5  GTP A 180      26.303  36.091 -13.672  1.00  0.00           H  
HETATM  158  X6  GTP A 180      24.683  36.247 -10.440  1.00  0.00           H  
HETATM  159  X7  GTP A 180      24.926  37.660 -12.845  1.00  0.00           H  
HETATM  160  X8  GTP A 180      23.874  35.594 -13.231  1.00  0.00           H  
HETATM  161  X9  GTP A 180      18.670  35.593 -15.377  1.00  0.00           H  
HETATM  162  X10 GTP A 180      20.293  35.851 -15.834  1.00  0.00           H  
HETATM  163  X11 GTP A 180      27.124  35.555  -7.891  1.00  0.00           H  
HETATM  164  X12 GTP A 180      26.059  32.241  -5.339  1.00  0.00           H  
HETATM  165  X13 GTP A 180      22.030  35.588 -14.193  1.00  0.00           H  
HETATM  166  X14 GTP A 180      30.718  31.035  -4.497  1.00  0.00           H  
HETATM  167  X15 GTP A 180      23.174  34.539  -9.606  1.00  0.00           H  
TER     168      GTP A 180                                                       
END