Hi Dave, On Tue, Nov 22, 2016 at 11:08 AM, David Cosgrove <davidacosgrov...@gmail.com > wrote:
> > I really couldn't decide whether this should just be for you, or to the > whole list, so I decided to defer the decision to you! > Seems like it's appropriate for the -devel list, so I'm including it on the reply. > I'm looking at GenerateDepictionMatching3DStructure in > $RDBASE/rdkit/Chem/AllChem.py. There seems to be a discrepancy between > what it says it does and what it actually does. As far as I can see, the > reference molecule needs to be the same as the target molecule in terms of > atom order up to the number of atoms in the target molecule, it generates a > distance matrix from the given conformation of the reference and that is > used to make the 2D coordinates for the target. I can't see the need for a > depiction for the reference, as the docstring suggests, and the 'piece of > the molecule is constrained', whilst technically correct (anything in the > reference after the number of atoms in the target is ignored) isn't doing > what I thought it would. > Yes, the documentation for that function is pretty badly wrong. > So, as I move it into the core C++ code, I propose: > a) Correcting the documentation so that it describes what is happening > b) Putting some extra checks in, to ensure that, for example, the > reference molecule has at least as many atoms as the target molecule. > c) Adding an optional 4th parameter that is a query molecule that will > allow a mapping of a subset of atoms on the reference onto the target, and > generating a distance matrix just for those atoms. That way, you would be > able to take a set of molecules with a common core that are aligned in 3D > space and generate a similarly arranged set of 2D depictions. This would > not be a breaking change. > These changes all make sense to me. -greg
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