Hi Markus, On Tue, Jul 8, 2008 at 9:33 AM, markus <[email protected]> wrote: > I want to align two molecules based on just the tips of some feature > direction arrows (a.k.a Projected Pharmacophor Points) > As to my understanding this problem should be solved in the same way, as > already coded in > $RDBASE/Python/Chem/Pharm3D/EmbedLib.py by the function EmbedPharmacophore() > > However I don't know how to use the tips of the feature directions > (a.k.a Projected Points) > instead of the feature centers. > Can I use this in a way? Could anyone give a small example?
The code in EmbedPharmacophore is set up to solve a problem different from what it sounds like you're trying to do: it takes a molecule and a pharmacophore and tries to generate conformations of the molecule that match the pharmacophore. It does this via distance geometry using a process called Embedding (thus the name of the function). It sounds like you are interesting in aligning molecules based on the location of feature points (or feature direction points). This is a much simpler procedure. 1) use Numerics.Alignment.GetAlignmentTransform to get the transformation matrix that converts one set of points into the other 2) use AllChem.TransformMol to transform your probe molecule based on the transformation If what I'm describing sounds like what you want to do and the description above is still too vague, let me know and I'll give more details. -greg
