[BioPython] using NeighborSearch

[Minami Mo]

Hi,

I am a new user to Biopython. I have to use the NeighborSearch
function to find out the contacting atoms within certain distance.
However, it returns error immediately when i instantiates the class
NeighborSearch. below is a fragment of the code:

s=p.get_structure('1i4f','1I4F.pdb')
atom_list=Selection.unfold_entities(s,'A')
ns=NeighborSearch(atom_list)  // error returns here
center=atom.get_coord()
R=5.0
neighbor_l=ns.search(center,R)
residue_list=Selection.unfold_entities(neighbor_l,'R')

/// ------------ error message

Traceback (most recent call last):
  File "run.py", line 21, in ?
    ns=NeighborSearch(atom_list)
  File "/ZB/IMPRS/siu/Linux/lib/python2.3/site-packages/Bio/PDB/NeighborSearch.py",
line 40, in __init__
    self.kdt.set_coords(self.coords)
  File "/ZB/IMPRS/siu/Linux/lib/python2.3/site-packages/Bio/KDTree/KDTree.py",
line 141, in set_coords
    self.kdt.set_data(coords, coords.shape[0])
  File "/ZB/IMPRS/siu/Linux/lib/python2.3/site-packages/Bio/KDTree/CKDTree.py",
line 42, in set_data
    def set_data(*args): return apply(_CKDTree.KDTree_set_data,args)
SystemError: NULL result without error in PyObject_Call

Does anyone have any idea about this?
Thanks!

Minami