(Reposted from my blog following Greg's suggestion )

Hello all,

Right now, I'm adding stereo (i.e. double bond stereochemistry, and
chirality) to the MDL Mol format in OpenBabel. There are three places
where stereochemical information can be stored in these files: the
coordinates, the atom parity (in the atom block), the bond stereo (in
the bond block).

My current understanding is that where 3D coordinates are present,
there's no need to store stereochemical information in either the atom
parity or the bond block. I think I'll probably set the atom parity
anyway (since I've already written the code, and it helps when you
look at the file to be able to easily identify the chiral centers).

For 2D coordinates, there's no need to store the bond stereochemistry
(as this can be worked out from the coordinates), but chirality needs
to be stored explicitly. The normal way to store this is not using
atom parity (but I'll set this anyway for the same reasons as above),
but by setting one of the bonds on the tetrahedral center to up or

For 0D coordinates, there are no guidelines. I propose to store
cis/trans stereo using the bond stereo (you know, UP [or DOWN] at both
ends of a double bond means cis), and chirality using the atom parity.
The MDL spec states that atom parity should be ignored when read, but
the alternative is to just forget the stereochemistry, or else to
store both cis/trans stereo *and* chirality in the bond block, which
may just about be possible but is likely to be a real mess.

Any thoughts?

- Noel

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