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

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?

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. 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).

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.

J

On 16 Sep 2013, at 18:59, Egon Willighagen <egon.willighagen@gmail.com> wrote:

Hi all,

ChEMBL 17 removed about 3200 compounds with metal ions. One is
https://www.ebi.ac.uk/chembldb/compound/inspect/CHEMBL414804

They wrote:

"Structures for around 3200 metal-containing compounds have been
removed from the database (though the bioactivity and other
information for these compounds is retained). The decision was taken
to remove these compounds because they are often difficult to
represent appropriately in mol file format or generate InChIs from,
and may cause problems for subsequent processing in various chemistry
toolkits. Some exceptions have been made for metals that are part of
pharmaceutical salts e.g., Ranitidine Bismuth Citrate, Silver
Sulfadiazine and Bacitracin Zinc. For compounds where the structure
has been removed (e.g.,
https://www.ebi.ac.uk/chembldb/compound/inspect/CHEMBL414804), the
molecular formula has been retained, but the compound image has been
replaced by a 'metal containing' icon. For more information, please
see the ChEMBL-og:
http://chembl.blogspot.co.uk/2013/03/to-remove-or-not-to-remove-that-is.html
and http://chembl.blogspot.co.uk/2013/08/removal-of-metal-containing-compounds.html"

The problem indicated is that the MDL molfile format does not handle
all these compounds well, though I think the problem with this example
is the stereochemistry...

How should we represent the planar stereochemistry of this compound?
What should the API be?

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

Egon


--
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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