How can I programmatically add a Hydrogen 'Atom' to a 'Residue' object?

Question

I know the algorithm for creating a Hydrogen atom and adding to a residue:

Point3d  create_hydrogen(Point3d C, Point3d N, Point3d CA, Point3d H) 
{
  H.set(N);
  H -= C;
  H.norm();

  Point3d tmp2(N);
  tmp2 -= CA;
  tmp2.norm();

  H += tmp2;
  H.norm(N_H_BOND_LENGTH);
  H += N;

  return H;
}

Point3d  create_hydrogen(Residue prev_residue, Residue residue, Point3d H) 
{
  return create_hydrogen(prev_residue.find_atom(" C  "), 
                              residue.find_atom(" N  "),
                              residue.find_atom(" CA "), 
                                   H);
}

Atom create_hydrogen(Residue prev_residue, Residue residue) 
{
  Atom H = make_shared_atom(0, " H  ", 1);
  create_hydrogen(prev_residue, residue, H);
  residue.add(H);
  return H;
}

I didn't find this implementation in BioPython.

Is this already implemented in BioPython? If YES, in which module?

If NO, what would be the implementation like in BioPython?

Added image of peptide bond too try to depict the problem at hand, I believe the hydrogen in cause is the one on the peptide bond plane(pale yellow) indentifiedin purple

Answer 1

The other answer is correct. But I thought I'd give a few pointers in how one can understand how to do something with a given Python module —teach a man to fish kind of thing...

In a Jupyter Notebook or IPython shell (don't), you can do:

• help(function) print out the docstring
• dir(object) shows all the public and magic attributes and methods —note a class will not show the instance methods
• type(object) or object.__class__ gives you what the class is, but object.__class__.__mro__ tells you what it inherits.
• in the standard library module inspect is the function inspect.getsource(function), which for a notebook is messy due to newlines so needs to be print_code = lambda fun: print(inspect.getsource(fun)) and print_code(fun).

In your case you read a file...

from Bio import PDB
parser = PDB.PDBParser()
structure : PDB.Structure.Structure = parser.get_structure("tryp-cage", "1L2Y.first.pdb")

So parser.get_structure "magically" makes a structure, eh? This means it can add stuff! As mentioned print_code(parser.get_structure) will reveal its secrets, or within it call some self._private_fun(), which can be inspected (self = parser) all the way down the rabbit hole. Until you find a nice constructor that declares nicely an atom instance or whatever you ever fancy searching for —that is the great thing of open source code.

In the specific case of PDB module, everything inherits Entity, which has the attribute child_list, which is what the iterators (__iter__ is the topmost) read without making a copy. The end of the above rabbit hole may just add a child Entity-inheriting class instance to this list, but it also do other things that is worth keeping an eye out.

In the case of residue.add(atom), creating the Bio.PDB.Atom.Atom instance is slightly problematic as there's no typehinting or :type xxx: declarations in the docstring. But doing type(atom.bfactor) etc. on the attributes of an existing atom will reveal how to do it. One the serial number is a PDB thing, which is sequential for the model.

last_serial = list(structure.get_residues())[-1].child_list[-1].serial_number + 1
residue.add(PDB.Atom.Atom(name=' H  ', coord=np.array([1,1,1]), bfactor=0., occupancy=1., altloc=' ', fullname=' H  ', serial_number=last_serial+1,element='H'))

The coordinates will not be [1,1,1], but the point that you have calculate. Say for H, this would be coplanar with C, CA and N, that is 1 and smidge Å away from N at an angle not quite in the middle as found in amide bonds.

Answer 2

Not sure but here https://biopython.org/docs/1.75/api/Bio.PDB.Residue.html Bio.PDB.Residue module Your can find :

add(self, atom) :

      Add an Atom object.

Checks for adding duplicate atoms, and raises a PDBConstructionException if so.

Can’t try it just now but who knows it may work

Googling around I found out that if you plan to add Hydrogens to PDB files [I believe nowadays PDBx is the repository grade standard] you could do thar following PDB format rules. I am copying them from UCSF Chimera website (https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#hydrogens):

Hydrogen Atoms

In brief, conventions for hydrogen atoms in version 3.0 PDB format are as follows:

Hydrogen atom records follow the records of all other atoms of a particular residue.
A hydrogen atom name starts with H. The next part of the name is based on the name of the connected nonhydrogen atom. For example, in amino acid residues, H is followed by the remoteness indicator (if any) of the connected atom, followed by the branch indicator (if any) of the connected atom; if more than one hydrogen is connected to the same atom, an additional digit is appended so that each hydrogen atom will have a unique name. Hydrogen atoms in standard nucleotides and amino acids (other than the rarely seen HXT) are named according to the IUPAC recommendations (Markley et al., Pure Appl Chem 70:117 (1998)). Names of hydrogen atoms in HETATM residues are determined in a similar fashion.
If the name of a hydrogen has four characters, it is left-justified starting in column 13; if it has fewer than four characters, it is left-justified starting in column 14. 

In the following excerpt from entry 1vm3, atom H is attached to atom N. Atom HA is attached to atom CA; the remoteness indicator A is the same for these atoms. Two hydrogen atoms are connected to CB, one is connected to CG, three are connected to CD1, and three are connected to CD2.

ATOM     10  N   LEU A   2       4.595   6.365   3.756  1.00  0.00           N
ATOM     11  CA  LEU A   2       4.471   5.443   2.633  1.00  0.00           C
ATOM     12  C   LEU A   2       5.841   5.176   2.015  1.00  0.00           C
ATOM     13  O   LEU A   2       6.205   4.029   1.755  1.00  0.00           O
ATOM     14  CB  LEU A   2       3.526   6.037   1.578  1.00  0.00           C
ATOM     15  CG  LEU A   2       2.790   4.919   0.823  1.00  0.00           C
ATOM     16  CD1 LEU A   2       3.803   3.916   0.262  1.00  0.00           C
ATOM     17  CD2 LEU A   2       1.817   4.196   1.769  1.00  0.00           C
ATOM     18  H   LEU A   2       4.169   7.246   3.704  1.00  0.00           H
ATOM     19  HA  LEU A   2       4.063   4.514   2.992  1.00  0.00           H
ATOM     20  HB2 LEU A   2       2.804   6.675   2.065  1.00  0.00           H
ATOM     21  HB3 LEU A   2       4.099   6.623   0.873  1.00  0.00           H
ATOM     22  HG  LEU A   2       2.234   5.353   0.004  1.00  0.00           H
ATOM     23 HD11 LEU A   2       4.648   4.447  -0.148  1.00  0.00           H
ATOM     24 HD12 LEU A   2       3.334   3.331  -0.516  1.00  0.00           H
ATOM     25 HD13 LEU A   2       4.137   3.260   1.052  1.00  0.00           H
ATOM     26 HD21 LEU A   2       0.941   3.892   1.216  1.00  0.00           H
ATOM     27 HD22 LEU A   2       1.522   4.860   2.568  1.00  0.00           H
ATOM     28 HD23 LEU A   2       2.296   3.323   2.188  1.00  0.00           H


```

Answer 3

OK my attempt, input pdb created in pymol with fab AVGLWPT , AVGLWPT , hydro=0 and saved as avgwpt.pdb :

ATOM      1  N   ALA     1      67.846  51.727  15.161  1.00  0.00           N  
ATOM      2  CA  ALA     1      68.522  53.021  15.161  1.00  0.00           C  
ATOM      3  C   ALA     1      70.022  52.847  15.161  1.00  0.00           C  
ATOM      4  O   ALA     1      70.553  51.730  15.150  1.00  0.00           O  
ATOM      5  CB  ALA     1      68.014  53.813  16.378  1.00  0.00           C  
ATOM      6  N   VAL     2      70.773  53.896  15.173  1.00  0.00           N  
ATOM      7  CA  VAL     2      72.223  53.728  15.173  1.00  0.00           C  
ATOM      8  C   VAL     2      72.922  55.066  15.188  1.00  0.00           C  
ATOM      9  O   VAL     2      72.296  56.134  15.198  1.00  0.00           O  
ATOM     10  CB  VAL     2      72.665  52.877  13.916  1.00  0.00           C  
ATOM     11  CG1 VAL     2      74.193  52.762  13.664  1.00  0.00           C  
ATOM     12  CG2 VAL     2      72.143  51.420  13.932  1.00  0.00           C  
ATOM     13  N   GLY     3      74.212  55.098  15.190  1.00  0.00           N  
ATOM     14  CA  GLY     3      74.888  56.392  15.204  1.00  0.00           C  
ATOM     15  C   GLY     3      76.388  56.218  15.203  1.00  0.00           C  
ATOM     16  O   GLY     3      76.917  55.104  15.192  1.00  0.00           O  
ATOM     17  N   LEU     4      77.138  57.267  15.215  1.00  0.00           N  
ATOM     18  CA  LEU     4      78.589  57.099  15.215  1.00  0.00           C  
ATOM     19  C   LEU     4      79.288  58.437  15.230  1.00  0.00           C  
ATOM     20  O   LEU     4      78.660  59.507  15.241  1.00  0.00           O  
ATOM     21  CB  LEU     4      79.040  56.251  13.992  1.00  0.00           C  
ATOM     22  CG  LEU     4      78.445  54.825  13.832  1.00  0.00           C  
ATOM     23  CD1 LEU     4      79.094  54.113  12.637  1.00  0.00           C  
ATOM     24  CD2 LEU     4      78.610  53.968  15.098  1.00  0.00           C  
ATOM     25  N   TRP     5      80.577  58.469  15.232  1.00  0.00           N  
ATOM     26  CA  TRP     5      81.254  59.763  15.246  1.00  0.00           C  
ATOM     27  C   TRP     5      82.754  59.589  15.245  1.00  0.00           C  
ATOM     28  O   TRP     5      83.281  58.478  15.233  1.00  0.00           O  
ATOM     29  CB  TRP     5      80.817  60.551  16.512  1.00  0.00           C  
ATOM     30  CG  TRP     5      79.341  60.958  16.536  1.00  0.00           C  
ATOM     31  CD1 TRP     5      78.304  60.258  17.187  1.00  0.00           C  
ATOM     32  CD2 TRP     5      78.731  62.003  15.872  1.00  0.00           C  
ATOM     33  CE2 TRP     5      77.340  61.929  16.130  1.00  0.00           C  
ATOM     34  CE3 TRP     5      79.257  63.017  15.031  1.00  0.00           C  
ATOM     35  NE1 TRP     5      77.049  60.848  16.950  1.00  0.00           N  
ATOM     36  CZ2 TRP     5      76.464  62.876  15.556  1.00  0.00           C  
ATOM     37  CZ3 TRP     5      78.372  63.946  14.482  1.00  0.00           C  
ATOM     38  CH2 TRP     5      76.996  63.879  14.742  1.00  0.00           C  
ATOM     39  N   PRO     6      83.505  60.638  15.257  1.00  0.00           N  
ATOM     40  CA  PRO     6      84.959  60.560  15.257  1.00  0.00           C  
ATOM     41  C   PRO     6      85.498  60.036  16.599  1.00  0.00           C  
ATOM     42  O   PRO     6      84.724  59.735  17.507  1.00  0.00           O  
ATOM     43  CB  PRO     6      85.354  62.018  14.978  1.00  0.00           C  
ATOM     44  CG  PRO     6      84.201  62.829  15.588  1.00  0.00           C  
ATOM     45  CD  PRO     6      82.967  61.980  15.271  1.00  0.00           C  
ATOM     46  N   THR     7      86.770  59.913  16.774  1.00  0.00           N  
ATOM     47  CA  THR     7      87.263  59.414  18.054  1.00  0.00           C  
ATOM     48  C   THR     7      88.771  59.342  18.062  1.00  0.00           C  
ATOM     49  O   THR     7      89.436  59.668  17.100  1.00  0.00           O  
ATOM     50  CB  THR     7      86.639  58.014  18.376  1.00  0.00           C  
ATOM     51  CG2 THR     7      87.080  57.358  19.702  1.00  0.00           C  
ATOM     52  OG1 THR     7      85.224  58.110  18.479  1.00  0.00           O  
TER   
END

pic :

code :

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
molecule create in pymol with fab AVGLWPT , AVGLWPT , hydro=0

"""

import Bio
print('########## Biopython  VERSION ##########################################')
print('\n\n BIOPYTHON_VERSION : ', Bio.__version__)
print('###################################################################')

from Bio.PDB import (
                    PDBParser,
                    Atom,
                    PDBIO
                    )


structure_code = 'avgwpt'

structure_name = structure_code

parser_pdb= PDBParser(QUIET=False)    ### shows warnings

structure_whole = parser_pdb.get_structure(structure_name, structure_name+".pdb")  


last_serial = list(structure_whole.get_atoms())[-1].serial_number

print(" last_serial : ",last_serial)

for model in structure_whole:
    
    for chain in model:
        
        for resi in chain:
        
            print('1 : ', resi)
            
            print('2 : ',resi.id)
            
            try :
            
                print('3 : ',chain[resi.id[1]-1])
                
                doable = True
                
            except :
                
                print('3 : ','residue -1 missing !!!!!!!!!!!!!!!!!!!!!!1')
                
                doable = False
                
            
            print('4 : ',[i for i in resi.get_atoms()])
            
            if doable:
                
                print('5 : ','ok')
            
            else:
                
                print('5 : ','NO')
                
            
            if doable:
                
                
                print(chain[resi.id[1]-1]['C'])
                
                print(chain[resi.id[1]-1]['C'].get_vector(), type(chain[resi.id[1]-1]['C'].get_vector()))
                
                print(chain[resi.id[1]]['N'].get_vector())
                
                c = chain[resi.id[1]-1]['C'].get_vector()
                
                n = chain[resi.id[1]]['N'].get_vector()
                
                ca = chain[resi.id[1]]['CA'].get_vector()
                
                nc = n-c
                
                nca = n-ca
                
                print('vector BN : ', nc)
                
                nc.normalize()
                
                print('vector BN normalize : ', nc)
                
                print('vector B2B : ', nca)
                
                nca.normalize()
                
                print('vector B2B normalize : ', nca)
                
                print('sum of nc + nca : ' , nsum := nc + nca)
                
                nsum.normalize()
                
                nsum**1.023
                
                nsum += n
                
                print(nsum)
                
                print(nsum.get_array(), type(nsum.get_array()))
                
                resi.add(Atom.Atom(name=' H  ', coord = nsum.get_array(), bfactor=0., occupancy=1., altloc=' ', fullname=' H  ', serial_number = last_serial ,element='H'))
            
                last_serial += 1

io=PDBIO() 

io.set_structure(structure_whole ) 

io.save(structure_name+"_H_added.pdb" , preserve_atom_numbering = True) 

output , saved as avgwpt_H_added.pdb:

ATOM      1  N   ALA     1      67.846  51.727  15.161  1.00  0.00           N  
ATOM      2  CA  ALA     1      68.522  53.021  15.161  1.00  0.00           C  
ATOM      3  C   ALA     1      70.022  52.847  15.161  1.00  0.00           C  
ATOM      4  O   ALA     1      70.553  51.730  15.150  1.00  0.00           O  
ATOM      5  CB  ALA     1      68.014  53.813  16.378  1.00  0.00           C  
ATOM      6  N   VAL     2      70.773  53.896  15.173  1.00  0.00           N  
ATOM      7  CA  VAL     2      72.223  53.728  15.173  1.00  0.00           C  
ATOM      8  C   VAL     2      72.922  55.066  15.188  1.00  0.00           C  
ATOM      9  O   VAL     2      72.296  56.134  15.198  1.00  0.00           O  
ATOM     10  CB  VAL     2      72.665  52.877  13.916  1.00  0.00           C  
ATOM     11  CG1 VAL     2      74.193  52.762  13.664  1.00  0.00           C  
ATOM     12  CG2 VAL     2      72.143  51.420  13.932  1.00  0.00           C  
ATOM     52  H   VAL     2      70.368  54.810  15.182  1.00  0.00           H  
ATOM     13  N   GLY     3      74.212  55.098  15.190  1.00  0.00           N  
ATOM     14  CA  GLY     3      74.888  56.392  15.204  1.00  0.00           C  
ATOM     15  C   GLY     3      76.388  56.218  15.203  1.00  0.00           C  
ATOM     16  O   GLY     3      76.917  55.104  15.192  1.00  0.00           O  
ATOM     53  H   GLY     3      74.741  54.249  15.182  1.00  0.00           H  
ATOM     17  N   LEU     4      77.138  57.267  15.215  1.00  0.00           N  
ATOM     18  CA  LEU     4      78.589  57.099  15.215  1.00  0.00           C  
ATOM     19  C   LEU     4      79.288  58.437  15.230  1.00  0.00           C  
ATOM     20  O   LEU     4      78.660  59.507  15.241  1.00  0.00           O  
ATOM     21  CB  LEU     4      79.040  56.251  13.992  1.00  0.00           C  
ATOM     22  CG  LEU     4      78.445  54.825  13.832  1.00  0.00           C  
ATOM     23  CD1 LEU     4      79.094  54.113  12.637  1.00  0.00           C  
ATOM     24  CD2 LEU     4      78.610  53.968  15.098  1.00  0.00           C  
ATOM     54  H   LEU     4      76.733  58.181  15.224  1.00  0.00           H  
ATOM     25  N   TRP     5      80.577  58.469  15.232  1.00  0.00           N  
ATOM     26  CA  TRP     5      81.254  59.763  15.246  1.00  0.00           C  
ATOM     27  C   TRP     5      82.754  59.589  15.245  1.00  0.00           C  
ATOM     28  O   TRP     5      83.281  58.478  15.233  1.00  0.00           O  
ATOM     29  CB  TRP     5      80.817  60.551  16.512  1.00  0.00           C  
ATOM     30  CG  TRP     5      79.341  60.958  16.536  1.00  0.00           C  
ATOM     31  CD1 TRP     5      78.304  60.258  17.187  1.00  0.00           C  
ATOM     32  CD2 TRP     5      78.731  62.003  15.872  1.00  0.00           C  
ATOM     33  CE2 TRP     5      77.340  61.929  16.130  1.00  0.00           C  
ATOM     34  CE3 TRP     5      79.257  63.017  15.031  1.00  0.00           C  
ATOM     35  NE1 TRP     5      77.049  60.848  16.950  1.00  0.00           N  
ATOM     36  CZ2 TRP     5      76.464  62.876  15.556  1.00  0.00           C  
ATOM     37  CZ3 TRP     5      78.372  63.946  14.482  1.00  0.00           C  
ATOM     38  CH2 TRP     5      76.996  63.879  14.742  1.00  0.00           C  
ATOM     55  H   TRP     5      81.105  57.620  15.224  1.00  0.00           H  
ATOM     39  N   PRO     6      83.505  60.638  15.257  1.00  0.00           N  
ATOM     40  CA  PRO     6      84.959  60.560  15.257  1.00  0.00           C  
ATOM     41  C   PRO     6      85.498  60.036  16.599  1.00  0.00           C  
ATOM     42  O   PRO     6      84.724  59.735  17.507  1.00  0.00           O  
ATOM     43  CB  PRO     6      85.354  62.018  14.978  1.00  0.00           C  
ATOM     44  CG  PRO     6      84.201  62.829  15.588  1.00  0.00           C  
ATOM     45  CD  PRO     6      82.967  61.980  15.271  1.00  0.00           C  
ATOM     56  H   PRO     6      83.072  61.539  15.267  1.00  0.00           H  
ATOM     46  N   THR     7      86.770  59.913  16.774  1.00  0.00           N  
ATOM     47  CA  THR     7      87.263  59.414  18.054  1.00  0.00           C  
ATOM     48  C   THR     7      88.771  59.342  18.062  1.00  0.00           C  
ATOM     49  O   THR     7      89.436  59.668  17.100  1.00  0.00           O  
ATOM     50  CB  THR     7      86.639  58.014  18.376  1.00  0.00           C  
ATOM     51  CG2 THR     7      87.080  57.358  19.702  1.00  0.00           C  
ATOM     52  OG1 THR     7      85.224  58.110  18.479  1.00  0.00           O  
ATOM     57  H   THR     7      87.409  60.156  16.044  1.00  0.00           H  
TER      58      THR     7                                                       
END   

pic :

Not sure I got the code above (in question) right, can't read it , had to use comments as trace.

Spent a while banging my head with : HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures

and trying to figure out their alghoritm, [code (https://seq2fun.dcmb.med.umich.edu//HAAD/haad.f90) is in FORTRAN90] from the paper , but no luck, if anybody wants to help eplaining this bit:

For constructing the sp2H2 and sp2H1 H-atoms, we first decide on the orientation of the conjugated plane or the aromatic ring with respect to the neighboring heavy atoms; the normal vector of the conjugated plane is determined by taking the cross product of two vectors between the heavy atoms. For the sp2H2 H-atoms (illustrated in Fig. 1b), the normal vector of the conjugated plane is the cross product of the unit vectors B→N and B2→B; then the two H-atoms are placed at positions A1 and H, which are within the conjugated plane respected to the B→N vector with the exact bond angle from CHARMM22 force field. For sp2H1 H-atoms, two conformations are possible. The first is to place the H-atom in the peptide plane as illustrated in Fig. 1b, where A1 and B1 represent the alpha carbon atoms. The position of H in this case is decided by using the same method as the one used to determine the position of the sp2H2 H-atoms while holding the trans-conformation.

it refers to Fig.1 of linked freely available article