I agree - the 2D and 3D cases should behave similarly, and I think modifying the 2D case to be true if all atoms have 2D coords is sensible
On Wed, Jul 18, 2012 at 5:47 PM, John May <[email protected]> wrote: > Hi all, > > I got stung for not fully reading some doc today and thought I would share > to get some opinions on whether the method behaviour should/could change. > I'll explain more in a bit but here's what I was doing. > > The following snippet (https://gist.github.com/3139004) checks if the the > container has coordinates for it's atoms and will invoke the renderer if it > does. If we don't have coordinates we handle appropriately. > > if (GeometryTools.has2DCoordinates(container)) { > renderer.paint(container, new AWTDrawVisitor(g2), bounds, true); > } else { > // can log or invoke g2.drawString() to display "no coordinates" > } > > > This will work for the majority of cases however if can cause the paint > method to throw an exception. In my mind the 'has2DCoordinates' tells me > whether we have coordinates for all atoms in our container/molecule. However > what it will actually tell you is whether any of your atoms have 2D > coordinates. As I said this was my fault for not fully reading the doc and > assuming 'Determines if this AtomContainer contains 2D coordinates' means > all atoms. There is the method 'has2DCoordinatesNew' which we can use to get > an integer and determine full (2) or partial coordinates (1). In my mind a > method like 'has2DCoordinates' would be mainly used to check an input is > valid (as above) and not fail. > > It should be noted that equivalent 'has3DCoordinates' will return true only > if all atoms have 3D coordinates as I had presumed with the 2D method. > > It would be good to unify the 'has2DCoordinates' and 'has3DCoordinates' to > behave the same way. Personally I would opt to change 'has2DCoordinates' as > I can see the use cases for such a method being used more for preventing > errors then checking molecules with partial atoms. > > Please let me know your opinions. > > Many thanks, > John > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Cdk-devel mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-devel > -- Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
