[Joelib-devel] Re: [Open Babel] Re: Atom types and protonation models

[Peter Murray-R. <pm...@ca...>]

This is an extremely important area and one which the OpenChemistry 
movement should encourage.

[I have crossposted to the three lists mentioned above, but suggest that 
the listowners should comment if they don't like this. Crossposting often 
becomes undirected in later stages.]

IMO it is essential that the community all uses the same approach to atom 
type definition. (This doesn't necessarily mean a single monolithic 
approach, but an agreement on how to make sure that all systems behave in 
the same way. There should be operational definitions of atoms types where 
possible based on chemical and/or geometrical environment whose 
interpretation should be reproducible on all of the systems that adopt this 
approach. To ensure uniformity I believe that all algorithms should - as 
far as possible - come from external files and be independently of 
programming language.  SMARTS is a useful approach here, and I would also 
suggest XML and a representational language. (If readers are keen, I'd be 
happy to see how CML can be extended to support this).

There are many fuzzy concepts such as "trigonal N" and "aromatic". These 
can be determined by different criteria (neighbouring atoms, geometry, MO 
calculation, etc.). Where possible the name should suggest the method, e.g. 
"planar three-coordinate nitrogen", "nitrogen with aromatic ligand", etc. 
Unless there is clear nomenclature and algorithmic definition of concepts, 
the program systems won't be implemented in the same way and we are limited 
to "CDKaromatic", "BabelHydrogen", etc.

The first step could be to coordinate the current approaches independently 
of program system. This is a sizeable task, but it's the sort of thing that 
IUPAC is doing for graphic representation of chemical structures, See 
http://www.angelfire.com/sc3/iupacstructure for very impressive discussion 
coordinated by Jonathan Brecher. I think that atom types is outwith the 
scope of this particular activity (I am sure there is cross-readership) but 
ultimately it would be valuable for IUPAC to have a view on atom types.

P.