[BioPython] protein-ligand interactions

[mitlox]

Thank you very much for your code, it works and the output is exactly 
for what I was looking for.

I try to get a structureCA object to write out the results in a PDB file 
(outCA.pdb) like this:
ATOM   5275  CA  ILE A 881      17.242  57.141  22.062  1.00 
38.49           C
ATOM   5283  CA  VAL A 882      16.292  57.880  25.678  1.00 
38.90           C 
....

And the second reason for a structureCA object is that I do not want use:
structureCA = Bio.PDB.PDBParser().get_structure(outCA.pdb, outCA.pdb)

Unfortunately I get this error with the extension:
ILE 881 3.64203
VAL 882 3.58559
ALA 885 4.62673
THR 886 4.95211
ILE 963 4.64252
ASP 964 3.08788
Traceback (most recent call last):
  File "interaction.py", line 31, in ?
    io.save('out.pdb')
  File 
"/usr/lib/python2.4/site-packages/biopython-1.49-py2.4-linux-i686.egg/Bio/PDB/PDBIO.py", 
line 121, in save
    for model in self.structure.get_list():
AttributeError: 'list' object has no attribute 'get_list'

Here is the code:
import Bio.PDB
import numpy

pdb_code = "1E8W"
pdb_filename = "1E8W.pdb"

structure = Bio.PDB.PDBParser().get_structure(pdb_code, pdb_filename)
model = structure[0]
chainA = model["A"]
structureCA = []

def residue_dist_to_ligand(protein_residue, ligand_residue) :
    """Returns distance from the protein C-alpha to the closest ligand 
atom."""
    distances = []
    for atom in ligand_residue :
        diff_vector  = protein_residue["CA"].coord - atom.coord
        distances.append(numpy.sqrt(numpy.sum(diff_vector * diff_vector)))
    return min(distances)

#From looking at the PDB file, ligand is last residue in chain A, named QUE
ligand_res = chainA.child_list[-1]
assert ligand_res.resname == "QUE"
for protein_res in chainA.child_list[:-1] :
    dist = residue_dist_to_ligand(protein_res, ligand_res)
    if dist < 5.0 :
        print protein_res.resname, protein_res.id[1], dist
    structureCA.append(protein_res)

io=Bio.PDB.PDBIO()
io.set_structure(structureCA)
io.save('outCA.pdb')

How can I get a structureCA object of the results?

Thank you in advance.

Best regards