We have ~3200 structures in ChEMBL which need a solution... that's
what I started with. It's a challenge... seriously, I'm happy with the
fact that the CDK does stereo at all nowadays :)

So Open Babel should be able to handle this already - https://github.com/openbabel/openbabel/blob/master/src/stereo/squareplanar.cpp. Would be good to see if having the API to represent it actually solves the problems.

Yes, they like such input. Mind you, please try it with the latest
version, because ChemSpider is giving a lot of feedback like this too.

Will do.

J

On 17 Sep 2013, at 07:58, Egon Willighagen <egon.willighagen@gmail.com> wrote:

On Mon, Sep 16, 2013 at 10:42 PM, John May <john.wilkinsonmay@gmail.com> wrote:
How should we represent the planar stereochemistry of this compound?

Difficult to say as the structure diagrams aren't there any more…. but I
guess you're refer to square planar. This is one of the molecules right and
you're referring to the Pt atom?

http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=144206182

Yes, following the links to PubChem is what I did too.

What should the API be?

You need three conformations to represented the U, 4 and Z shapes…
unsurprisingly as it with SMILES (@SP1, @SP2, @SP3). In that example though
I'm not sure why you need square planar - is there another way I can arrange
the neighbours?

Sterically, no. But that means that a computer will have to start
making the same assumptions we do too: the two rings in which the Pt
participates are that small that you cannot do it otherwise. But
without a square planar data holder, you cannot make that info
explicit. What ring would be large enough?

I would leave this out for now - would be good if we could get conversion
between tetrahedral, double bond working correctly first before adding the
more exotic. Even then I would say cumulated double bond stereo would be
more useful as chiral examples are easy to find (e.g. lamenallenic acid). I
actually have a patch for handling trigonal pyramidal stereo centres (for
the hash code) but I scanned through PubChem and could not find a single
chiral example.

Blog a challenge :)

Really, I would guess Rich Apodaca will know an example or two...

There's always "the" example for SMILES specs
"S[As@@](F)(Cl)(Br)N" but I couldn't justify it for a single case (link to
any chiral examples in a databases much appreciated).

We have ~3200 structures in ChEMBL which need a solution... that's
what I started with. It's a challenge... seriously, I'm happy with the
fact that the CDK does stereo at all nowadays :)

And, secondly, what format could handle this stereochemistry and could
we suggest to ChEMBL?

SMILES :-) - no coordination bonds though.

Actually reminds me that ChEMBL
has about 50 SMILES with valence errors due to the coordination bonds being
converted to sigma bonds - I should get round to reporting those. Would be
interesting to see if these have been removed now in this update.

Yes, they like such input. Mind you, please try it with the latest
version, because ChemSpider is giving a lot of feedback like this too.

Egon

PS. I you have seen I found a bit more time for CDK hacking again...
last week I was ill, and workload is still insane... (in that sense, I
don't understand why I haven't left academia yet... with ~60 hours I
could easily bootstrap a spin off... if only I had a strong product...
CDK is not commercially strong enough yet)

--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: 0000-0001-7542-0286

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