[chemfp] chemfp-1.0 on Windows

[Chris Morley]

I'm having some difficulties with chemfp-1.0 on Windows 7, Python 2.7.1, 
some of which are due to my unfamiliarity with python, and so probably 
not specific to chemfp.

The installation is fine by:
setup.py install
with only a few warnings from the Visual Studio compiler, including an 
unrecognized compiler option -O3.

Scripts like sdf2fps are obviously not aimed at Windows and do not work 
directly in a command window, but they do if prefaced by "python". I 
have not found how to do this from an arbitrary data folder - setting 
PYTHONPATH to various likely folders was unsuccessful. The installation 
provides sdf2fps.py, etc. in 
C:\Python27\Lib\site-packages\chemfp\commandline. Should I be using these?

A "k-nearest neighbor search" with simsearch worked ok, as did ob2fps. 
But anything involving arena.py crashes:

  > python ..\simsearch --threshold 0.738 -q pubchem_queries.fps 
pubchem_targets.fps
Traceback (most recent call last):
   File "..\simsearch", line 5, in <module>
     main()
   File 
"C:\Users\Christopher\Documents\CHEM\chemfp-1.0\chemfp\commandline\simsea
rch.py", line 217, in main
     targets = chemfp.load_fingerprints(targets)
   File 
"C:\Users\Christopher\Documents\CHEM\chemfp-1.0\chemfp\__init__.py", line
  192, in load_fingerprints
     return arena.fps_to_arena(reader, metadata=metadata, reorder=reorder)
   File 
"C:\Users\Christopher\Documents\CHEM\chemfp-1.0\chemfp\arena.py", line 57
0, in fps_to_arena
     return reorder_fingerprints(fingerprints)
   File 
"C:\Users\Christopher\Documents\CHEM\chemfp-1.0\chemfp\arena.py", line 54
2, in reorder_fingerprints
     new_ids = [fingerprints.ids[item.index] for item in ordering]
MemoryError

It crashes similarly with the python API:

>>> arena = chemfp.load_fingerprints("pubchem_targets.fps")


I admire your patience in working round all the quirks in the OpenBabel 
code!

Chris