[Open Babel] InChI undefined stereo bug for symmetric chiral center

[Peter S. <sp...@re...>]

Hello,

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I think inchi output mode may be having trouble with chiral centers that
have symmetric layouts.  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:

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  -XXXX-  08290615282D

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  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

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Babel converts this to an inchi string lacking stereochemical
information, and produces the warning:

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*** Open Babel Warning  in WriteMolecule

  #1 Omitted undefined stereo; Ambiguous stereo: center(s)

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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:

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  -XXXX-  08290615282D

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  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

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The respective inchi's are:

InChI=3D1/CHBrClF/c2-1(3)4/h1H

InChI=3D1/CHBrClF/c2-1(3)4/h1H/t1-/m1/s1

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Smiles output is the same for both:

F[C@@H](Br)Cl

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I'm using:

Open Babel 2.0.2 -- Aug 16 2006 -- 17:22:44

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Would you agree this is a bug?  I think the problem may be that symmetry
detection, which is appropriate for identifying undefined double bond
stereocenters, is being misapplied to chiral centers.

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Thanks for your help,

Peter Spiro

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