Re: [Open Babel] calculate chemical descriptors from published paper

2019-05-14 Thread Noel O'Boyle
Ah right. No - we don't do R and S assignment. But I don't see how a sensible QSAR model could possibly relate the count of R and S centers to a physical property. What does that even mean? OBAtom.IsChiral() does not do what you think it's doing. In fact, in the development version it has been rem

Re: [Open Babel] calculate chemical descriptors from published paper

2019-05-14 Thread Stefano Forli
Hi Noel, that is an interesting issue and I believe would be good to clarify for future references. I've tried to deal with it in the past, and I believe I resorted in using OBAtom.IsChiral() I've tried playing with the OBStereoFacade multiple times, but I never understood it, and the document

Re: [Open Babel] calculate chemical descriptors from published paper

2019-05-14 Thread Andrew Dalke
Hi Spencer, Here's a solution which indirectly builds on the Open Babel functionality to find rings and identify components. A direct algorithm would do as Noel suggest: use something like a depth-first search to find all ring atoms and from that figure out the number of connected ring syste

Re: [Open Babel] calculate chemical descriptors from published paper

2019-05-14 Thread Spencer Trinh
Great, thanks Andrew! I'll look into your code. Appreciate you taking the time to write that. Vào Th 3, 14 thg 5, 2019 vào lúc 12:56 Andrew Dalke < da...@dalkescientific.com> đã viết: > Hi Spencer, > > Here's a solution which indirectly builds on the Open Babel > functionality to find rings a