On 09/09/2020 01:33, Tim Dudgeon wrote:
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).
More precisely:
https://oddt.readthedocs.io/en/latest/rst/oddt.html?module-oddt.interactions#module-oddt.interactions
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
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
