Parsing Pdb file using Biopython parser: How to get all atoms instead of duplicates?
Hello everyone,
I am new in bioinformatics and when tried to parse pdb file using Biopython library came across this error: some atoms which defined twice in residue could not get their coordinates, id, name, etc.
How could I get all atoms instead of duplicates?
Here is my code:
from Bio.PDB.PDBParser import PDBParser
parser = PDBParser(PERMISSIVE=1)
structure = parser.get_structure("test", "/home/chinar/Downloads/Serinthreonine_ protein kinase, PIM 2/1_doc.pdb")
for model in structure:
for chain in model:
for residue in chain:
for atom in residue:
print(atom)
Output:
Warning: PDBConstructionException: Atom C defined twice in residue <Residue UNK het=H_UNK resseq=0 icode= > at line 31.
Exception ignored.
Some atoms or residues may be missing in the data structure.
% message, PDBConstructionWarning)
/usr/local/lib/python3.6/dist-packages/Bio/PDB/PDBParser.py:291:
PDBConstructionWarning:
PDBConstructionException: Atom C defined twice in residue <Residue UNK het=H_UNK resseq=0 icode= > at line 32.
Exception ignored.
Some atoms or residues may be missing in the data structure.
% message, PDBConstructionWarning)
<Atom C>
<Atom N>
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IkramInf •
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movchinar •
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1 answer
from Bio.PDB.PDBParser import PDBParser
parser = PDBParser(PERMISSIVE=1)
structure = parser.get_structure("test", "/home/chinar/Downloads/Serinthreonine_ protein kinase, PIM 2/1_doc.pdb")
atoms = set()
for model in structure:
for chain in model:
for residue in chain:
for atom in residue:
atoms.add(atom)
print(atoms)
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IkramInf •
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Is this a PDB file you have created?
Is the file definitely correctly formed?
After auto docking process the result was a file which format was pdbqt. I have changed the format pdbqt to PDB using UNIX command (cut -c-66 my_docking.pdbqt > my_docking.pdb).
Here is my PDB file: