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dd_distance.py
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dd_distance.py
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import Bio.PDB
from Bio.PDB import *
from openbabel import pybel
import math
parser = PDBParser()
structure = parser.get_structure("1YCR", "1YCR.pdb")
print("Residue,ResidueId,Atom.pdb,Atom.sdf,AtomId.sdf,Distance")
for model in structure:
for chain in model:
for residue in chain:
for atom1 in residue:
min_dist = 10000
closest_lig_atom_type = ''
closest_lig_atom_id = 0
coord1 = atom1.get_coord()
for mol in pybel.readfile('sdf', 'rank1.sdf'):
for atom2 in mol:
coord2 = atom2.coords
P = coord1
Q = coord2
moldistance = math.dist(P,Q)
if moldistance < min_dist:
min_dist = moldistance
closest_lig_atom_id = atom2.idx
closest_lig_atom_type = atom2.type
pdb_atom_type = atom1.get_id ()
residue_name = residue.get_resname()
residue_id = residue.full_id[3][1]
print (f"{residue_name},{residue_id},{pdb_atom_type},{closest_lig_atom_type},{closest_lig_atom_id},{min_dist}")