[Cdk-devel] Meaning of Bond stereo field, AtomParity

[rich a. <che...@ya...>]

I have some newbie-type questions about how CDK
perceives stereochemistry. These questions arose
during efforts to update the CDK-Octet compatability
layer (CDKTools - http://octet.sourceforge.net).

(1) I'm uncertain about the meaning of the Bond
"stereo" field. I've looked at the javadocs for
Molecule, Bond, and CDKConstants - and browsed around
other documentation but I found no clarification. For
example, when I go:

Molecule molecule = ...; // some molecule
int someStereoField = 234;

... // building the molecule

molecule.addBond(0, 1, 2.0d, someStereoField);

... // finish building

how is the someStereoField interpreted? Are clients
free to use any integer they choose or are the values
limited to a certain range? Is this field intended to
represent solely E/Z stereochemistry or are other uses
such as wedge/hash allowed?

(2) Similarly, I'm confused about AtomParity. In a
recent thread:

http://sourceforge.net/mailarchive/message.php?msg_id=8651094

I found some information. Let's say I have an
AtomPairity defined by:

central Atom = atom #0
first Atom = atom #1
second Atom = atom #2
third Atom = atom #3
fourth Atom = atom #4
parity = +1

Then how can I use this information to mentally
re-create the configuration around atom #0? The MDL
molfile spec shows one way to do this, as does the
SMILES spec - are either of these procedures used in
CDK?

Also, what can be said about the rules clients must
follow to specify an AtomParity? If, for example,
"third Atom" is null, but "fourth Atom" is not, is
this a legal construct? What if "central Atom" is not
specified?

many thanks,
r


		
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