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and scoring functions - Added cost, weight and scoring functions using atom-based Crippen logP contributions - Added relevant tests for the new functionality - Fixed a bug in the O3A::trans() method (it returned the weighted RMSD and not the unweighted one as O3A::align()) Also the API of the method has been changed (now it takes a reference to a Transform3D object rather than returning a pointer to a newly created one) Important points: ----------------- - The constructors now accept optional pointers to MolHistogram objects instead of pointers to arrays of double. I think it is better for performance, since rebuilding the histogram involves running through two nested loops over all atoms, even though the 3DDistanceMat is provided to the O3A constructor. This change breaks binary compatibility with previous C++ programs linking to RDKit MolAlign library; I do not think this is big issue, and while I was there I made other changes which cause binary incompatibility. If needed, we may preserve binary compatibility reverting the MolHistogram change and the other ones. - From Python, nothing changed in the interface to previous MMFFO3A functionality. It MIGHT be more appropriate to change the "GetO3A()" function into "GetMMFFO3A()", but I have not done that to avoid breaking existing scripts; the choice is yours - As of now, the code contains a number of conditional compilation directives checking for the USE_O3A_CONSTRUCTOR macro; if USE_O3A_CONSTRUCTOR is defined, then the code is built with an alternative O3A constructor which allows choosing whether one wishes to use MMFF or Crippen descriptors. Otherwise, no alternative constructor is built, but rather two functions which return a pointer to an O3A object. I prefer by far the first solution (namely, with USE_O3A_CONSTRUCTOR defined), but again, the choice is yours. The code is tested and works in both cases. - Custom cost, weight and scoring functions can easily be defined in external programs without need to rebuild the RDKit, allowing flexibility. The new custom functionality can be accessed by calling the "bigger" O3A constructor.