On 9 December 2012 23:31, John May <johnmay@ebi.ac.uk> wrote:
Hi All,

I noticed that what I term auxiliary atom type properties, such as PI_BONDCOUNT, LONEPAIR_COUNT, SINGLE_COUNT… etc. are never configured. Some algorithms try to use this information (e.g. this line in  CDKHueckelAromaticityDetector) but there is no obvious way to get at this information. It would be natural to add this to AtomTypeManipulator.configure() but as these are stored in a map it mean creating a HashMap on every single atom :/.

It would be good to have these properties accessible but I can't see a useful way of doing it

Perhaps a different flavour of AtomTypeManipulator.configure(), to set only these properties and to be used only when required?


Any thoughts are most welcome.

Many thanks,
me John May | Predoctoral Student – Chemoinformatics and Metabolism
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
johnmay@ebi.ac.uk | +44–(0) 1223 49 2603

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