There has been a bit of discussion about this anyway, I find the tutorial in the RDKit book is pretty good, but perhaps we can fill in the gaps here as well.
In addition, I have a PR that makes the constrained depictions from distance matrices work with both the N**2 and diagonal (N*N-1)/2 matrices, this has been an area of confusion as well. This probably won't be ready this week though. On Wed, Nov 23, 2016 at 12:34 AM, Greg Landrum <greg.land...@gmail.com> wrote: > 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 > > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > Rdkit-devel mailing list > Rdkit-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-devel > >
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