I've been working on another system where oxygen frequently exceeds a
standard valency of two (organometallics). So far, I've been getting
around the automatic bond deletion in an older version of Open Babel by
modifying the element.txt file. By changing the MaxBnd column for oxygen
to a higher value (e.g. 6), the oxygen atom retains the extra bonds. But
that approach obviously causes other problems, including representation of
hydrogens.
Would it be helpful to have an option in ConnectTheDots to manually disable
the max valence cleanup step? For example, rdkit
<http://www.rdkit.org/docs/RDKit_Book.html#molecular-sanitization> has
flags to selectively disable certain aspects of molecular sanitation.
Another question: if you manually build a hydronium ion bond-by-bond,
what's the proper way to set the charge for SMILES export?
OBAtom::SetFormalCharge? Something with SetTotalCharge? Is there a way to
do this automatically on the molecule?
Thanks!
Ben
On Wed, Oct 25, 2017 at 9:51 AM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> > atom by atom, and then call `ConnectTheDots()` to add bonds
>
> Not surprisingly, for a general-purpose library, Open Babel has a
> general-purpose bond perception algorithm. As you note, it will ensure
> oxygen atoms have a maximum of two bonds. This ensures PDB and other
> crystallography files with disordered atoms still retain “normal” valency.
>
> > How should I then approach this SMARTS matching problem? My system has
> regular
> > water molecules and I have only coordinates and atomic numbers, so a
> priori I
> > don't know which oxygen atoms belong to H3O+ and which hydrogen atoms are
> > bridging hydrogen in H5O2+.
>
> I would say *that* is your key problem, not SMARTS. You can certainly
> adapt the ConnectTheDots code - it simply loops through all atoms and
> checks where the distance between atoms is smaller than the sum of the
> covalent radii. Those are “bonds.” (OB’s code will sort along the Z axis
> and adds a few additional checks for performance reasons, but that’s the
> basics of the algorithm.)
>
> You’ll need a special-purpose bond detection algorithm for your needs. You
> might find larger hydrogen-bonded clusters beyond H5O2, for example. I’ve
> found systems with unusual bond distances. That’s part of chemistry.
>
> -Geoff
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