InChI generation code not recognizing stereo

[greglandrum]

reported by Jan Holst Jensen

> For example: InChI strings generated for spiro.mol (spiro.mol - attached):
>
> IUPAC:
> InChI=1S/2C9H14Cl2/c2*1-7(10)3-9(4-7)5-8(2,11)6-9/h2*3-6H2,1-2H3/t2*7-,8-,9-/m10/s1
> RDKit: InChI=1S/2C9H14Cl2/c2*1-7(10)3-9(4-7)5-8(2,11)6-9/h2*3-6H2,1-2H3

This one still doesn't recognize the stereo. I'll file a bug for it:
In [2]: Chem.MolToInchi(Chem.MolFromMolFile('spiro.mol'))
[09:53:16] WARNING: Omitted undefined stereo
Out[2]: 'InChI=1S/2C9H14Cl2/c2*1-7(10)3-9(4-7)5-8(2,11)6-9/h2*3-6H2,1-2H3'

Here's the file:

spiro.mol
  ACD/Labs0709041010  

 22 24  0  0  0  0  0  0  0  0  1 V2000
    9.2912   -9.4308    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8009   -6.9967    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    7.7063   -7.9840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8986   -9.1405    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1531   -6.3991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5689   -7.8459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7408   -6.2812    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8789   -9.3129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3257   -7.7280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1335   -6.5716    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   15.2311   -8.7153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6519  -14.7621    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1616  -12.3280    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    8.0670  -13.3153    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2593  -14.4717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5138  -11.7304    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9296  -13.1772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1015  -11.6125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2396  -14.6442    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6864  -13.0593    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.4941  -11.9029    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5918  -14.0466    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  3  4  1  1  0  0  0
  1  3  1  0  0  0  0
  5  3  1  0  0  0  0
  6  1  1  0  0  0  0
  5  6  1  0  0  0  0
  7  6  1  0  0  0  0
  6  8  1  1  0  0  0
  9  7  1  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  0  0  0  0
  9 11  1  1  0  0  0
 14 13  1  0  0  0  0
 14 15  1  1  0  0  0
 12 14  1  0  0  0  0
 16 14  1  0  0  0  0
 17 12  1  0  0  0  0
 16 17  1  0  0  0  0
 18 17  1  0  0  0  0
 17 19  1  1  0  0  0
 20 18  1  0  0  0  0
 19 20  1  0  0  0  0
 21 20  1  0  0  0  0
 20 22  1  1  0  0  0
M  END
>  <NAME>
spiro 

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