Hi All, thanks for the suggestions. Greg, that's part of what's needed but there's also some more complex logic needed. For instance, if the atom the H is attached to is rotatable e.g. an OH group) then it is more complex than if it is fixed (e.g a N in a ring). I was wondering whether anyone had already encoded these types of rules.
BTW I also found https://oddt.readthedocs.io/en/latest/ which seems to handle a whole range of interaction types nicely, and can use RDKit as its underlying toolkit (as well as OBabel). Tim On Tue, Sep 8, 2020 at 1:24 PM Greg Landrum <greg.land...@gmail.com> wrote: > Hi Tim, > > Assuming that you already have the indices of the atoms that you're > interested in looking at, it's pretty easy to calculate the angle between > three arbitrary atoms. Here's an example: > > In [3]: m = Chem.AddHs(Chem.MolFromSmiles('COCCCCCO')) > > In [4]: AllChem.EmbedMolecule(m) > Out[4]: 0 > > In [5]: conf = m.GetConformer() > > In [6]: ps = [conf.GetAtomPosition(x) for x in range(conf.GetNumAtoms())] > > The atom0 - atom1 - atom2 angle: > In [7]: (ps[1]-ps[0]).AngleTo(ps[1]-ps[2]) > Out[7]: 1.8295300825582068 > > > Those happened to be bonded, but that's not necessary, here's the atom1 - > atom6 - atom3 angle: > In [15]: (ps[6]-ps[1]).AngleTo(ps[6]-ps[3]) > Out[15]: 0.4862648980647286 > > Is that what you're looking for? > > -greg > > > > On Mon, Sep 7, 2020 at 3:06 PM Tim Dudgeon <tdudgeon...@gmail.com> wrote: > >> Hi RDKitters, >> I was wondering whether anyone has any RDKit code that checks on the >> geometry of a H-bond. >> e.g. once a donor and acceptor are located within a reasonable >> distance of each other to check on the angles involved to establish if that >> is a reasonable H-bond. >> Tim >> >> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
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