Suppose, I want to find the neighboring Hydrogen atoms of a specific C-alpha atom.
from typing import List
from Bio.PDB import Chain, Atom, NeighborSearch, PDBParser
def get_hydrogen_atoms(c_alpha_atom: Atom.Atom):
ns = NeighborSearch(c_alpha_atom)
return ns.search_all(10.0, "H")
p = PDBParser()
structure = p.get_structure('16pk', '16pk.pdb')
c_alpha_list = [atom for atom in structure.get_atoms() if atom.name == 'CA']
hydrogen_list = get_hydrogen_atoms(c_alpha_list[0])
print(hydrogen_list)
Error Output
C:\ProgramData\Miniconda3\python.exe C:/Users/pc/source/repos/_3_extended_features/_dataset_generation.py
Traceback (most recent call last):
File "C:\Users\pc\source\repos\_3_extended_features\_dataset_generation.py", line 35, in <module>
hydrogen_list = get_hydrogen_atoms(c_alpha_list[0])
File "C:\Users\pc\source\repos\_3_extended_features\_dataset_generation.py", line 28, in get_hydrogen_atoms
ns = NeighborSearch(c_alpha_atom)
File "C:\ProgramData\Miniconda3\lib\site-packages\Bio\PDB\NeighborSearch.py", line 45, in __init__
coord_list = [a.get_coord() for a in atom_list]
TypeError: 'Atom' object is not iterable
Process finished with exit code 1
How can I correct this?
Edit:
Passing a list to NeighborSearch() gives out a different error:
def get_hydrogen_atoms(c_alpha_atom: Atom.Atom):
ns = NeighborSearch([c_alpha_atom])
return ns.search_all(10.0, "H")
Error Output
C:\ProgramData\Miniconda3\python.exe C:/Users/pc/source/repos/_3_extended_features/_dataset_generation.py
Traceback (most recent call last):
File "C:\Users\pc\source\repos\_3_extended_features\_dataset_generation.py", line 35, in <module>
hydrogen_list = get_hydrogen_atoms(c_alpha_list[0])
File "C:\Users\pc\source\repos\_3_extended_features\_dataset_generation.py", line 29, in get_hydrogen_atoms
return ns.search_all(10.0, "H")
File "C:\ProgramData\Miniconda3\lib\site-packages\Bio\PDB\NeighborSearch.py", line 113, in search_all
raise PDBException("%s: Unknown level" % level)
Bio.PDB.PDBExceptions.PDBException: H: Unknown level
Process finished with exit code 1
ok got some code :
from Bio.PDB import Chain, Atom, NeighborSearch, PDBParser, Selection
def get_hydrogen_atoms(c_alpha_atom: Atom.Atom, po):
ns = NeighborSearch(po)
return [h for h in ns.search( c_alpha_atom.get_coord(), 10.0, 'A') if h.element == 'H']
p = PDBParser()
# structure = p.get_structure('16pk', '16pk.pdb')
structure = p.get_structure('16pk', 'pH8_5_1bq9_short.pdb')
c_alpha_list = [atom for atom in structure.get_atoms() if atom.name == "CA"]
print('c_alpha_list[0] : ', c_alpha_list[0], c_alpha_list[0].id , c_alpha_list[0].get_serial_number(),'\n')
po = Selection.unfold_entities(structure, 'A')
hydrogen_list = get_hydrogen_atoms(c_alpha_list[0], po)
print('hydrogen_list : \n',hydrogen_list)
print('\nSelection (po) : \n', po)
had to use a different PDB file because I needed the H atoms,
pH8_5_1bq9_short.pdb :
HETATM 1 N FME A 1 23.447 -5.765 5.119 1.00 19.07 N
HETATM 2 CN FME A 1 23.308 -6.776 4.291 1.00 20.46 C
HETATM 3 O1 FME A 1 22.504 -6.713 3.357 1.00 24.75 O
HETATM 4 CA FME A 1 22.488 -4.745 5.410 1.00 18.15 C
HETATM 5 CB FME A 1 22.433 -4.342 6.827 1.00 21.15 C
HETATM 6 CG FME A 1 22.198 -5.618 7.751 1.00 22.84 C
HETATM 7 SD FME A 1 20.445 -6.032 7.772 1.00 23.40 S
HETATM 8 CE FME A 1 20.476 -7.587 8.656 1.00 28.76 C
HETATM 9 C FME A 1 22.699 -3.530 4.487 1.00 17.12 C
HETATM 10 O FME A 1 23.804 -3.248 4.077 1.00 20.25 O
HETATM 0 3HE FME A 1 19.574 -7.938 8.726 1.00 28.76 H new
HETATM 0 2HG FME A 1 22.713 -6.369 7.418 1.00 22.84 H new
HETATM 0 2HE FME A 1 21.032 -8.221 8.177 1.00 28.76 H new
HETATM 0 2HB FME A 1 23.260 -3.901 7.077 1.00 21.15 H new
HETATM 0 1HG FME A 1 22.508 -5.438 8.652 1.00 22.84 H new
HETATM 0 1HE FME A 1 20.838 -7.447 9.545 1.00 28.76 H new
HETATM 0 1HB FME A 1 21.717 -3.701 6.961 1.00 21.15 H new
HETATM 0 HN FME A 1 24.199 -5.711 5.532 1.00 19.07 H new
HETATM 0 HCN FME A 1 23.841 -7.577 4.415 1.00 20.46 H new
HETATM 0 HA FME A 1 21.619 -5.138 5.231 1.00 18.15 H new
ATOM 11 N ALA A 2 21.633 -2.939 4.043 1.00 15.50 N
ATOM 12 CA ALA A 2 21.644 -1.884 3.062 1.00 15.08 C
ATOM 13 C ALA A 2 20.899 -0.661 3.519 1.00 13.72 C
ATOM 14 O ALA A 2 20.278 -0.702 4.584 1.00 13.49 O
ATOM 15 CB ALA A 2 21.083 -2.339 1.710 1.00 17.86 C
ATOM 0 H ALA A 2 20.842 -3.144 4.312 1.00 15.50 H new
ATOM 0 HA ALA A 2 22.579 -1.652 2.951 1.00 15.08 H new
ATOM 0 HB1 ALA A 2 21.110 -1.599 1.083 1.00 17.86 H new
ATOM 0 HB2 ALA A 2 21.618 -3.072 1.368 1.00 17.86 H new
ATOM 0 HB3 ALA A 2 20.166 -2.634 1.823 1.00 17.86 H new
ATOM 16 N LYS A 3 21.005 0.412 2.774 1.00 12.48 N
ATOM 17 CA LYS A 3 20.341 1.658 3.029 1.00 12.61 C
ATOM 18 C LYS A 3 19.415 1.991 1.879 1.00 11.53 C
ATOM 19 O LYS A 3 19.784 1.753 0.701 1.00 11.66 O
ATOM 20 CB LYS A 3 21.338 2.806 3.273 1.00 13.38 C
ATOM 21 CG LYS A 3 22.062 2.721 4.593 1.00 16.70 C
ATOM 22 CD LYS A 3 23.062 3.847 4.814 1.00 18.05 C
ATOM 23 CE LYS A 3 23.806 3.576 6.136 1.00 20.42 C
ATOM 24 NZ LYS A 3 24.878 4.503 6.403 1.00 22.91 N
ATOM 0 H LYS A 3 21.494 0.433 2.067 1.00 12.48 H new
ATOM 0 HA LYS A 3 19.821 1.557 3.842 1.00 12.61 H new
ATOM 0 HB2 LYS A 3 21.992 2.812 2.556 1.00 13.38 H new
ATOM 0 HB3 LYS A 3 20.862 3.650 3.230 1.00 13.38 H new
ATOM 0 HG2 LYS A 3 21.411 2.732 5.312 1.00 16.70 H new
ATOM 0 HG3 LYS A 3 22.527 1.871 4.644 1.00 16.70 H new
ATOM 0 HD2 LYS A 3 23.689 3.892 4.076 1.00 18.05 H new
ATOM 0 HD3 LYS A 3 22.606 4.702 4.851 1.00 18.05 H new
ATOM 0 HE2 LYS A 3 23.170 3.611 6.868 1.00 20.42 H new
ATOM 0 HE3 LYS A 3 24.166 2.676 6.116 1.00 20.42 H new
ATOM 0 HZ1 LYS A 3 25.266 4.294 7.176 1.00 22.91 H new
ATOM 0 HZ2 LYS A 3 25.479 4.458 5.748 1.00 22.91 H new
ATOM 0 HZ3 LYS A 3 24.551 5.330 6.449 1.00 22.91 H new
ATOM 25 N TRP A 4 18.274 2.598 2.165 1.00 10.75 N
ATOM 26 CA TRP A 4 17.283 3.019 1.181 1.00 10.69 C
ATOM 27 C TRP A 4 16.875 4.472 1.502 1.00 11.37 C
ATOM 28 O TRP A 4 16.812 4.872 2.651 1.00 17.19 O
ATOM 29 CB TRP A 4 16.012 2.143 1.352 1.00 11.20 C
ATOM 30 CG TRP A 4 16.164 0.734 0.997 1.00 11.80 C
ATOM 31 CD1 TRP A 4 16.913 -0.218 1.669 1.00 12.50 C
ATOM 32 CD2 TRP A 4 15.535 0.036 -0.079 1.00 11.53 C
ATOM 33 NE1 TRP A 4 16.806 -1.435 1.050 1.00 12.76 N
ATOM 34 CE2 TRP A 4 15.959 -1.302 -0.013 1.00 12.61 C
ATOM 35 CE3 TRP A 4 14.642 0.421 -1.079 1.00 11.88 C
ATOM 36 CZ2 TRP A 4 15.531 -2.258 -0.929 1.00 13.18 C
ATOM 37 CZ3 TRP A 4 14.217 -0.527 -1.989 1.00 12.54 C
ATOM 38 CH2 TRP A 4 14.668 -1.858 -1.894 1.00 14.26 C
output :
c_alpha_list[0] : <Atom CA> CA 4
hydrogen_list :
[<Atom HB1>, <Atom HB3>, <Atom H>, <Atom 2HE>, <Atom 3HE>, <Atom 1HE>, <Atom HB3>, <Atom HA>, <Atom HG2>, <Atom HB2>, <Atom HCN>, <Atom HA>, <Atom HN>, <Atom 1HB>, <Atom 2HB>, <Atom 2HG>, <Atom 1HG>, <Atom H>, <Atom HB2>, <Atom HA>, <Atom HD2>, <Atom HG3>, <Atom HD3>, <Atom HZ2>, <Atom HE3>, <Atom HE2>, <Atom HZ1>]
Selection (po) :
[<Atom N>, <Atom CN>, <Atom O1>, <Atom CA>, <Atom CB>, <Atom CG>, <Atom SD>, <Atom CE>, <Atom C>, <Atom O>, <Atom 3HE>, <Atom 2HG>, <Atom 2HE>, <Atom 2HB>, <Atom 1HG>, <Atom 1HE>, <Atom 1HB>, <Atom HN>, <Atom HCN>, <Atom HA>, <Atom N>, <Atom CA>, <Atom C>, <Atom O>, <Atom CB>, <Atom H>, <Atom HA>, <Atom HB1>, <Atom HB2>, <Atom HB3>, <Atom N>, <Atom CA>, <Atom C>, <Atom O>, <Atom CB>, <Atom CG>, <Atom CD>, <Atom CE>, <Atom NZ>, <Atom H>, <Atom HA>, <Atom HB2>, <Atom HB3>, <Atom HG2>, <Atom HG3>, <Atom HD2>, <Atom HD3>, <Atom HE2>, <Atom HE3>, <Atom HZ1>, <Atom HZ2>, <Atom HZ3>, <Atom N>, <Atom CA>, <Atom C>, <Atom O>, <Atom CB>, <Atom CG>, <Atom CD1>, <Atom CD2>, <Atom NE1>, <Atom CE2>, <Atom CE3>, <Atom CZ2>, <Atom CZ3>, <Atom CH2>]
the selection list contains both ATOM and HETATM
have a look at : https://www.biostars.org/p/269579/ How to use biopython neighborsearch?
and Bio.PDB.NeighborSearch module :https://biopython.org/docs/1.75/api/Bio.PDB.NeighborSearch.html ;
Bio.PDB.Atom module :https://biopython.org/docs/1.75/api/Bio.PDB.Atom.html