On Wed, Apr 12, 2017 at 7:54 AM, Wolf Ihlenfeldt <w...@xemistry.com> wrote:
> On Wed, Apr 12, 2017 at 1:44 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> > (and I wish they had thought of seqR and seqS)
> >
> > In case anyone is interested, here is my pseudocode. The actual methods
> > aren't much longer than this.
> > John, do you agree this is the appropriate approach?
> >
> > Bob
> >
> > https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/
> Jmol/src/org/jmol/symmetry/CIPChirality.java
> >
> > //
> > // getChirality(atom) {
> > // if (atom.getCovalentBondCount() != 4) exit NO_CHIRALITY
>
> Insufficient. Chiral atoms where a FEP is substituting for a ligand
> are certainly important, in real-life chemistry. But of course that
> heavily depends on the atom type - not every FEP stays locked in
> place. Also geometry matters - you want to treat square planar
> different from tetrahedral, so there needs to be at least some kind of
> VSEPR analysis of prospective chiral centers.
>
"Insufficient" is a relative term. I'm just showing what my algorithm does
in Jmol.
I don't know what "FEP" means.
>
> Also I do not see any iteration here.
This is only for Rules 1-3 right now. One thing at a time...
> Cases where the chirality or
> non-chirality of an atom can only be determined after this has been
> done in its substituent sphere (say, identical substituents but one
> with a stereogenic cis-DB and one with a stereogenic trans-DB, or with
> a R and a S center in the substituents) are important - and can of
> course be nested to any depth, and they can appear in any atom or bond
> order, so there needs to be iteration as long as anything can be
> resolved, which then can lead to a possibility to resolve more
> centers. Furthermode, you need to interweave CIP atomic and bond
> stereodescriptor determination, they cannot be handled independently.
>
I don't doubt that. Next up is Rules 4 and 5, where this will surely
become an issue.
Revisions to the pseudocode are welcome.
Bob
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