Find details about a given ligand in a PDB structure using biopython

gistfile1.py

from Bio.PDB import *
import sys
p = PDBParser(PERMISSIVE=1)
ligand_id = "ADE"
radius = 5.4
pdbl = PDBList()
structure_id = "1Y26"
pdbl.retrieve_pdb_file(structure_id, pdir="/tmp")
filename = "1y26.pdb"
#see for more details: http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc153
structure = p.get_structure(structure_id, filename)
models = structure.get_list()

#iterate over the models 
for aModel in models:
	#get all the chains in this model
	chains = aModel.get_list()
	#compute the surface of this model
	#surface = get_surface()
	#rd = ResidueDepth(aModel, filename)

	#get all the atoms in this model
	model_atoms = Selection.unfold_entities(aModel,'A')
	#create a NeighborSearch
	ns = NeighborSearch(model_atoms)

	#search the chains in for the ligand_id
	for aChain in chains:
		residues = aChain.get_list()
		for aResidue in residues:
			if aResidue.get_resname() == ligand_id:
				atom_list = Selection.unfold_entities(aResidue, 'A')
				#pick a center
				center = atom_list[0].get_coord()
				neighbors = ns.search(center, radius)
				residue_list = Selection.unfold_entities(neighbors, 'R')
				for aResidue in residue_list:
					print aResidue.get_full_id()
				break