#181 InChI undefined stereo bug for symmetric chiral center

[Peter Spiro]

Inchi output mode incorrectly considers chiral centers
with symmetric layouts to be undefined. Here are the
contents of a mol file containing a chiral center which
I believe is properly defined, and which has a
perfectly equilateral layout:

-XXXX- 08290615282D

4 3 0 0 0 0 0 0 0 0999 V2000
-1.7320 -1.0000 0.0000 F 0 0 0 0 0 0 0
0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 1 0 0 0 0
0 0 0 0 0
0.0000 2.0000 0.0000 Br 0 0 0 0 0 0 0
0 0 0 0 0
1.7320 -1.0000 0.0000 Cl 0 0 0 0 0 0 0
0 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
2 1 1 1 0 0 0
M END

Command line babel converts this to an inchi string
lacking stereochemical information, and produces the
warning:

*** Open Babel Warning in WriteMolecule
#1 Omitted undefined stereo; Ambiguous stereo: center(s)

But it produces a different inchi string containing
stereochemical information, and doesn’t give a warning,
if I perturb all the angles slightly from 120 degrees:

-XXXX- 08290615282D
4 3 0 0 0 0 0 0 0 0999 V2000
-1.7320 -0.9000 0.0000 F 0 0 0 0 0 0 0
0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 1 0 0 0 0
0 0 0 0 0
0.0000 2.0000 0.0000 Br 0 0 0 0 0 0 0
0 0 0 0 0
1.7320 -0.9000 0.0000 Cl 0 0 0 0 0 0 0
0 0 0 0 0
2 3 1 0 0 0 0
2 4 1 0 0 0 0
2 1 1 1 0 0 0
M END

The respective inchi’s are:
InChI=1/CHBrClF/c2-1(3)4/h1H
InChI=1/CHBrClF/c2-1(3)4/h1H/t1-/m1/s1

Smiles output is the same for both:
FC@@HCl

I’m using:
Open Babel 2.0.2 -- Aug 16 2006 -- 17:22:44

I think the problem may be that symmetry detection,
which is appropriate for identifying undefined double
bond stereocenters, is being misapplied to chiral centers.

[Geoff Hutchison]

Logged In: YES
user_id=21420

This is fixed with an update to the InChI library, now contained in 2.1.0b1 and
the 2.0 SVN branch.

Peter noted this fix to me via e-mail. Marking this closed.

Cheers,
-Geoff