From: Nina J. <ni...@ac...> - 2006-07-06 14:43:39
|
Egon Willighagen <ewi...@un...> wrote: > On Thursday 06 July 2006 15:57, Nina Jeliazkova wrote: > > The method process(IAtomContainer molecule) throws an exception when some > > descriptor can not be calculated, which is quite logical. > > In the future (not-so-far-future I hope...) it will write a patch that takes > advantage of the DataFeatures technology being incorporated into SVN (it's > now being used in SaveAs in Bioclipse). This techology allows querying which > data features (eg. has_3d_coordinates) is present in some IChemObject. The > IChemFileFormat's support this too, so that one can determine of a > IChemObject can be saved into a certain file format. See [1]. > > Similarly, it's my intention to do this for descriptors too, though in this > case not hard coded in the source code, but extracted from the QSAR > descriptor ontology. See [2]. This will be very useful, although I guess exception may be thrown for a different reason not captured by DataFeatures analysis. > > > However, if an exception is thrown for a descriptor in the middle of the > > list (in my example MomentsOfInertia can't be calculated because of missing > > 3D coordinates), this prevents from calculation the rest of descriptors, > > which may not need 3D coordinates and can otherwise be safely calculated. > > > > Is this an intentional behaviour? > > Dunno. > > > The next question is more about design - is there a reason for classNames, > > descriptors, specList and instantiate* functions to be private rather than > > protected? Private means these can't be accessed in a descendant class, so > > this essentially forbids creation of a descendant class. > > If you have the need to subclass it, it likely means that the code can be > improved, in which I would welcome any patch. Whatfor do you need to subclass > it? As I've just replied to Rajarshi, to add descriptors from a different package. You are right, there will be no need for subclassing if the condition verifies for IMolecularDescriptor implementation rather then for "org.openscience.cdk.qsar.descriptors.molecular" package. I'll try to make a patch. egards, nina > > Egon > > 1.http://qsar.sourceforge.net/ontologies/data-features/index.xhtml > 2.http://qsar.sourceforge.net/dicts/qsar-descriptors/index.xhtml |