[chimera-dev] Numpy multiarray import problem

[Mateusz Dobrychłop]

Dear Chimera Team,

I am working on my own Chimera Extension. After succesful installation of
BioPython using Chimera's Python copy, I've encountered another BioPython -
related problem, that is also related to the numpy library.

I'm trying to import something from the BioPython library, and BioPython is
trying to import from numpy. I recieve a following error:

RuntimeError: module compiled against API version 8 but this version of
numpy is 7

...

  File "/home/mateusz/pyry4.4/Modules/Trans/ComponentRepresentation.py",
line 6, in <module>
    from Bio.PDB                            import PDBParser, PDBIO,
NeighborSearch
  File
"/home/mateusz/.local/UCSF-Chimera64-1.8.1/lib/python2.7/site-packages/Bio/PDB/NeighborSearch.py",
line 10, in <module>
    from Bio.KDTree import KDTree
  File
"/home/mateusz/.local/UCSF-Chimera64-1.8.1/lib/python2.7/site-packages/Bio/KDTree/__init__.py",
line 10, in <module>
    from KDTree import KDTree
  File
"/home/mateusz/.local/UCSF-Chimera64-1.8.1/lib/python2.7/site-packages/Bio/KDTree/KDTree.py",
line 20, in <module>
    from Bio.KDTree import _CKDTree
<type 'exceptions.ImportError'>: numpy.core.multiarray failed to import

I tried to install numpy the same way I installed BioPython (using
Chimera's Python copy), but this does not solve the problem. I also tried
to import numpy.core.multiarray directly in Chimera's IDLE and it did
import.

I'm using Chimera 1.8.1 on Ubuntu 12.10 (64 - bit).

Is there anything I can do to make it work?

Best wishes,
Mateusz
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